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Lin P, Sledziona J, Akkaya-Colak KB, Mihaylova MM, Lane AN. Determination of fatty acid uptake and desaturase activity in mammalian cells by NMR-based stable isotope tracing. Anal Chim Acta 2024; 1303:342511. [PMID: 38609261 PMCID: PMC11016156 DOI: 10.1016/j.aca.2024.342511] [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: 10/20/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Mammalian cells both import exogenous fatty acids and synthesize them de novo. Palmitate, the end product of fatty acid synthase (FASN) is a substrate for stearoyl-CoA desaturases (Δ-9 desaturases) that introduce a single double bond into fatty acyl-CoA substrates such as palmitoyl-CoA and stearoyl-CoA. This process is particularly upregulated in lipogenic tissues and cancer cells. Tracer methodology is needed to determine uptake versus de novo synthesis of lipids and subsequent chain elongation and desaturation. Here we describe an NMR method to determine the uptake of 13C-palmitate from the medium into HCT116 human colorectal cancer cells, and the subsequent desaturation and incorporation into complex lipids. RESULTS Exogenous 13C16-palmitate was absorbed from the medium by HCT116 cells and incorporated primarily into complex glycerol lipids. Desaturase activity was determined from the quantification of double bonds in acyl chains, which was greatly reduced by ablation of the major desaturase SCD1. SIGNIFICANCE The NMR approach requires minimal sample preparation, is non-destructive, and provides direct information about the level of saturation and incorporation of fatty acids into complex lipids.
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Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, Dept. of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - James Sledziona
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd, Columbus, OH, 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Kubra B Akkaya-Colak
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd, Columbus, OH, 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Maria M Mihaylova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd, Columbus, OH, 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Dept. of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
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2
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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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3
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Holling GA, Chavel CA, Sharda AP, Lieberman MM, James CM, Lightman SM, Tong JH, Qiao G, Emmons TR, Giridharan T, Hou S, Intlekofer AM, Higashi RM, Fan TWM, Lane AN, Eng KH, Segal BH, Repasky EA, Lee KP, Olejniczak SH. CD8+ T cell metabolic flexibility elicited by CD28-ARS2 axis-driven alternative splicing of PKM supports antitumor immunity. Cell Mol Immunol 2024; 21:260-274. [PMID: 38233562 PMCID: PMC10902291 DOI: 10.1038/s41423-024-01124-2] [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: 07/14/2023] [Accepted: 12/26/2023] [Indexed: 01/19/2024] Open
Abstract
Metabolic flexibility has emerged as a critical determinant of CD8+ T-cell antitumor activity, yet the mechanisms driving the metabolic flexibility of T cells have not been determined. In this study, we investigated the influence of the nuclear cap-binding complex (CBC) adaptor protein ARS2 on mature T cells. In doing so, we discovered a novel signaling axis that endows activated CD8+ T cells with flexibility of glucose catabolism. ARS2 upregulation driven by CD28 signaling reinforced splicing factor recruitment to pre-mRNAs and affected approximately one-third of T-cell activation-induced alternative splicing events. Among these effects, the CD28-ARS2 axis suppressed the expression of the M1 isoform of pyruvate kinase in favor of PKM2, a key determinant of CD8+ T-cell glucose utilization, interferon gamma production, and antitumor effector function. Importantly, PKM alternative splicing occurred independently of CD28-driven PI3K pathway activation, revealing a novel means by which costimulation reprograms glucose metabolism in CD8+ T cells.
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Affiliation(s)
- G Aaron Holling
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Colin A Chavel
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anand P Sharda
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Mackenzie M Lieberman
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Caitlin M James
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Shivana M Lightman
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jason H Tong
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Guanxi Qiao
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tiffany R Emmons
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Massachusetts Institute of Technology, Boston, MA, 02139, USA
| | - Thejaswini Giridharan
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Shengqi Hou
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Richard M Higashi
- Center for Environmental Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, Lexington, KY, 40536, USA
| | - Teresa W M Fan
- Center for Environmental Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, Lexington, KY, 40536, USA
| | - Andrew N Lane
- Center for Environmental Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, Lexington, KY, 40536, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Brahm H Segal
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Elizabeth A Repasky
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Kelvin P Lee
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Scott H Olejniczak
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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Zhang X, Su Y, Lane AN, Stromberg AJ, Fan TWM, Wang C. Correction: Bayesian kinetic modeling for tracer-based metabolomic data. BMC Bioinformatics 2024; 25:14. [PMID: 38200423 PMCID: PMC10782720 DOI: 10.1186/s12859-024-05635-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Affiliation(s)
- Xu Zhang
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA.
| | - Ya Su
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, 23220, USA
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Arnold J Stromberg
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA
| | - Teresa W M Fan
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Chi Wang
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA.
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.
- Division of Cancer Biostatistics, Department of Internal Medicine, University of Kentucky, Lexington, 40536, USA.
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5
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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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6
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Wu H, Kren BT, Lane AN, Cassel TA, Higashi RM, Fan TWM, Scaria GS, Shekels LL, Klein MA, Albrecht JH. Cyclin D1 extensively reprograms metabolism to support biosynthetic pathways in hepatocytes. J Biol Chem 2023; 299:105407. [PMID: 38152849 PMCID: PMC10687208 DOI: 10.1016/j.jbc.2023.105407] [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: 03/11/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 12/29/2023] Open
Abstract
Cell proliferation requires metabolic reprogramming to accommodate biosynthesis of new cell components, and similar alterations occur in cancer cells. However, the mechanisms linking the cell cycle machinery to metabolism are not well defined. Cyclin D1, along with its main partner cyclin-dependent kinase 4 (Cdk4), is a pivotal cell cycle regulator and driver oncogene that is overexpressed in many cancers. Here, we examine hepatocyte proliferation to define novel effects of cyclin D1 on biosynthetic metabolism. Metabolomic studies reveal that cyclin D1 broadly promotes biosynthetic pathways including glycolysis, the pentose phosphate pathway, and the purine and pyrimidine nucleotide synthesis in hepatocytes. Proteomic analyses demonstrate that overexpressed cyclin D1 binds to numerous metabolic enzymes including those involved in glycolysis and pyrimidine synthesis. In the glycolysis pathway, cyclin D1 activates aldolase and GAPDH, and these proteins are phosphorylated by cyclin D1/Cdk4 in vitro. De novo pyrimidine synthesis is particularly dependent on cyclin D1. Cyclin D1/Cdk4 phosphorylates the initial enzyme of this pathway, carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD), and metabolomic analysis indicates that cyclin D1 depletion markedly reduces the activity of this enzyme. Pharmacologic inhibition of Cdk4 along with the downstream pyrimidine synthesis enzyme dihydroorotate dehydrogenase synergistically inhibits proliferation and survival of hepatocellular carcinoma cells. These studies demonstrate that cyclin D1 promotes a broad network of biosynthetic pathways in hepatocytes, and this model may provide insights into potential metabolic vulnerabilities in cancer cells.
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Affiliation(s)
- Heng Wu
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
| | - Betsy T Kren
- Research Service, Minneapolis VA Health Care System, Minneapolis, Minnesota, 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, USA
| | - Teresa A Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, and Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 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, 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, Kentucky, USA
| | - George S Scaria
- Hematology and Oncology Division, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Laurie L Shekels
- Research Service, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Mark A Klein
- Hematology and Oncology Division, Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - Jeffrey H Albrecht
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, Minnesota, USA.
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7
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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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8
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Fan TWM, Winnike J, Al-Attar A, Belshoff AC, Lorkiewicz PK, Tan JL, Wu M, Higashi RM, Lane AN. Differential Inhibition of Anaplerotic Pyruvate Carboxylation and Glutaminolysis-Fueled Anabolism Underlies Distinct Toxicity of Selenium Agents in Human Lung Cancer. Metabolites 2023; 13:774. [PMID: 37512481 PMCID: PMC10383978 DOI: 10.3390/metabo13070774] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Past chemopreventive human trials on dietary selenium supplements produced controversial outcomes. They largely employed selenomethionine (SeM)-based diets. SeM was less toxic than selenite or methylseleninic acid (MSeA) to lung cancer cells. We thus investigated the toxic action of these Se agents in two non-small cell lung cancer (NSCLC) cell lines and ex vivo organotypic cultures (OTC) of NSCLC patient lung tissues. Stable isotope-resolved metabolomics (SIRM) using 13C6-glucose and 13C5,15N2-glutamine tracers with gene knockdowns were employed to examine metabolic dysregulations associated with cell type- and treatment-dependent phenotypic changes. Inhibition of key anaplerotic processes, pyruvate carboxylation (PyC) and glutaminolysis were elicited by exposure to MSeA and selenite but not by SeM. They were accompanied by distinct anabolic dysregulation and reflected cell type-dependent changes in proliferation/death/cell cycle arrest. NSCLC OTC showed similar responses of PyC and/or glutaminolysis to the three agents, which correlated with tissue damages. Altogether, we found differential perturbations in anaplerosis-fueled anabolic pathways to underlie the distinct anti-cancer actions of the three Se agents, which could also explain the failure of SeM-based chemoprevention trials.
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Affiliation(s)
- Teresa W.-M. Fan
- Center for Environmental and Systems Biochemistry, Department Toxicology & Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA; (A.A.-A.); (R.M.H.); (A.N.L.)
| | - Jason Winnike
- Department of Chemistry, University of Louisville, Louisville, KY 40202, USA; (J.W.); (A.C.B.); (P.K.L.)
| | - Ahmad Al-Attar
- Center for Environmental and Systems Biochemistry, Department Toxicology & Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA; (A.A.-A.); (R.M.H.); (A.N.L.)
| | - Alexander C. Belshoff
- Department of Chemistry, University of Louisville, Louisville, KY 40202, USA; (J.W.); (A.C.B.); (P.K.L.)
| | - Pawel K. Lorkiewicz
- Department of Chemistry, University of Louisville, Louisville, KY 40202, USA; (J.W.); (A.C.B.); (P.K.L.)
| | - Jin Lian Tan
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA;
| | - Min Wu
- Seahorse Bioscience, Billerica, MA 01862, USA
| | - Richard M. Higashi
- Center for Environmental and Systems Biochemistry, Department Toxicology & Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA; (A.A.-A.); (R.M.H.); (A.N.L.)
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry, Department Toxicology & Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA; (A.A.-A.); (R.M.H.); (A.N.L.)
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9
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Tong Y, Qi Y, Xiong G, Li J, Scott TL, Chen J, He D, Li L, Wang C, Lane AN, Xu R. The PLOD2/succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness. Proc Natl Acad Sci U S A 2023; 120:e2214942120. [PMID: 37155842 PMCID: PMC10194013 DOI: 10.1073/pnas.2214942120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/31/2022] [Accepted: 03/08/2023] [Indexed: 05/10/2023] Open
Abstract
Aberrant accumulation of succinate has been detected in many cancers. However, the cellular function and regulation of succinate in cancer progression is not completely understood. Using stable isotope-resolved metabolomics analysis, we showed that the epithelial mesenchymal transition (EMT) was associated with profound changes in metabolites, including elevation of cytoplasmic succinate levels. The treatment with cell-permeable succinate induced mesenchymal phenotypes in mammary epithelial cells and enhanced cancer cell stemness. Chromatin immunoprecipitation and sequence analysis showed that elevated cytoplasmic succinate levels were sufficient to reduce global 5-hydroxymethylcytosinene (5hmC) accumulation and induce transcriptional repression of EMT-related genes. We showed that expression of procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (PLOD2) was associated with elevation of cytoplasmic succinate during the EMT process. Silencing of PLOD2 expression in breast cancer cells reduced succinate levels and inhibited cancer cell mesenchymal phenotypes and stemness, which was accompanied by elevated 5hmC levels in chromatin. Importantly, exogenous succinate rescued cancer cell stemness and 5hmC levels in PLOD2-silenced cells, suggesting that PLOD2 promotes cancer progression at least partially through succinate. These results reveal the previously unidentified function of succinate in enhancing cancer cell plasticity and stemness.
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Affiliation(s)
- Yuxin Tong
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
| | - Yifei Qi
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
| | - Gaofeng Xiong
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
| | - Junyan Li
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
| | - Timothy L. Scott
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY40536
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY40536
| | - Jie Chen
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
| | - Daheng He
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
| | - Linzhang Li
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY40536
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY40536
| | - Ren Xu
- Markey Cancer Center, University of Kentucky, Lexington, KY40536
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40536
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10
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Zhang Q, Li Z, Rao X, Allison DB, Qiao Q, Zhang Z, Kong Y, Wang R, Fan TW, Higashi RM, Lane AN, Liu X. Abstract 4840: Dysregulation of mitochondrial function by PLK1-mediated PDHA1 phosphorylation promotes Cr(VI)-associated lung cancer progression. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4840] [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: 04/07/2023]
Abstract
Abstract
Hexavalent chromium (Cr(VI)), an class I environmental carcinogen, not only induces lung epithelial cell transformation but also promotes lung cancer progression by alterations of the cell cycle and cellular energy metabolism. Using Cr(VI)-transformed (CrT) bronchial epithelial cells (BEAS-2B) and parental BEAS-2B cells, we demonstrate that the level of polo-like kinase 1 (PLK1) is highly upregulated in CrT cells, which blocks mitochondrial function, and further promotes cell proliferation both in vitro and in vivo. Cells expressing a high level of PLK1 exhibited repressed mitochondrial activity due to defective modulation of pyruvate dehydrogenase E1 subunit alpha 1 (PDHA1), which facilitates the carbon influx to TCA cycle via catalyzing pyruvate/Acetyl-CoA conversion. Mechanistically, we show that PDHA1 can be directly phosphorylated by PLK1 at T57, which triggers collapse of E1 and PDHA1 degradation via activation of mitophagy. These defects resulted in the inhibition of oxidative phosphorylation and reduction of mitochondrial reactive oxygen species (ROS) generation, eventually inhibiting mitochondrial-mediated apoptotic response. Defining the role of PLK1 in metabolic reprogramming in Cr(VI)-associated cancer progression may give us a new perspective and a target to inhibit Cr(VI)-induced cancer development. In addition, PLK1 inhibitors may be used to increase the chemo-sensitivity of cancer cells by restoring the normal function of mitochondria, thus alleviating the drug resistance caused by dysfunction and hyperpolarization of mitochondria.
Citation Format: Qiongsi Zhang, Zhiguo Li, Xiongjian Rao, Derek B. Allison, Qi Qiao, Zhuangzhuang Zhang, Yifan Kong, Ruixin Wang, Teresa W. Fan, Richard M. Higashi, Andrew N. Lane, Xiaoqi Liu. Dysregulation of mitochondrial function by PLK1-mediated PDHA1 phosphorylation promotes Cr(VI)-associated lung cancer progression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4840.
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Affiliation(s)
| | - Zhiguo Li
- 1University of Kentucky, Lexington, KY
| | | | | | - Qi Qiao
- 1University of Kentucky, Lexington, KY
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11
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Zhang X, Su Y, Lane AN, Stromberg AJ, Fan TWM, Wang C. Bayesian kinetic modeling for tracer-based metabolomic data. BMC Bioinformatics 2023; 24:108. [PMID: 36949395 PMCID: PMC10035190 DOI: 10.1186/s12859-023-05211-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/23/2022] [Accepted: 02/24/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Stable Isotope Resolved Metabolomics (SIRM) is a new biological approach that uses stable isotope tracers such as uniformly [Formula: see text]-enriched glucose ([Formula: see text]-Glc) to trace metabolic pathways or networks at the atomic level in complex biological systems. Non-steady-state kinetic modeling based on SIRM data uses sets of simultaneous ordinary differential equations (ODEs) to quantitatively characterize the dynamic behavior of metabolic networks. It has been increasingly used to understand the regulation of normal metabolism and dysregulation in the development of diseases. However, fitting a kinetic model is challenging because there are usually multiple sets of parameter values that fit the data equally well, especially for large-scale kinetic models. In addition, there is a lack of statistically rigorous methods to compare kinetic model parameters between different experimental groups. RESULTS We propose a new Bayesian statistical framework to enhance parameter estimation and hypothesis testing for non-steady-state kinetic modeling of SIRM data. For estimating kinetic model parameters, we leverage the prior distribution not only to allow incorporation of experts' knowledge but also to provide robust parameter estimation. We also introduce a shrinkage approach for borrowing information across the ensemble of metabolites to stably estimate the variance of an individual isotopomer. In addition, we use a component-wise adaptive Metropolis algorithm with delayed rejection to perform efficient Monte Carlo sampling of the posterior distribution over high-dimensional parameter space. For comparing kinetic model parameters between experimental groups, we propose a new reparameterization method that converts the complex hypothesis testing problem into a more tractable parameter estimation problem. We also propose an inference procedure based on credible interval and credible value. Our method is freely available for academic use at https://github.com/xuzhang0131/MCMCFlux . CONCLUSIONS Our new Bayesian framework provides robust estimation of kinetic model parameters and enables rigorous comparison of model parameters between experimental groups. Simulation studies and application to a lung cancer study demonstrate that our framework performs well for non-steady-state kinetic modeling of SIRM data.
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Affiliation(s)
- Xu Zhang
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA.
| | - Ya Su
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, 23220, USA
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Arnold J Stromberg
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA
| | - Teresa W M Fan
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Chi Wang
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA.
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.
- Division of Cancer Biostatistics, Department of Internal Medicine, University of Kentucky, Lexington, 40536, USA.
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12
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Brown K, Jenkins LMM, Crooks DR, Surman DR, Mazur SJ, Xu Y, Arimilli BS, Yang Y, Lane AN, Fan TWM, Schrump DS, Linehan WM, Ripley RT, Appella E. Targeting mutant p53-R248W reactivates WT p53 function and alters the onco-metabolic profile. Front Oncol 2023; 12:1094210. [PMID: 36713582 PMCID: PMC9874945 DOI: 10.3389/fonc.2022.1094210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
TP53 is the most commonly mutated gene in cancer, and gain-of-function mutations have wide-ranging effects. Efforts to reactivate wild-type p53 function and inhibit mutant functions have been complicated by the variety of TP53 mutations. Identified from a screen, the NSC59984 compound has been shown to restore activity to mutant p53 in colorectal cancer cells. Here, we investigated its effects on esophageal adenocarcinoma cells with specific p53 hot-spot mutations. NSC59984 treatment of cells reactivated p53 transcriptional regulation, inducing mitochondrial intrinsic apoptosis. Analysis of its effects on cellular metabolism demonstrated increased utilization of the pentose phosphate pathway and inhibition of glycolysis at the fructose-1,6-bisphosphate to fructose 6-phosphate junction. Furthermore, treatment of cells with NSC59984 increased reactive oxygen species production and decreased glutathione levels; these effects were enhanced by the addition of buthionine sulfoximine and inhibited by N-acetyl cysteine. We found that the effects of NSC59984 were substantially greater in cells harboring the p53 R248W mutation. Overall, these findings demonstrate p53-dependent effects of NSC59984 on cellular metabolism, with increased activity in cells harboring the p53 R248W mutation. This research highlights the importance of defining the mutational status of a particular cancer to create a patient-centric strategy for the treatment of p53-driven cancers.
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Affiliation(s)
- Kate Brown
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States,*Correspondence: Kate Brown,
| | - Lisa M. Miller Jenkins
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Daniel R. Crooks
- Urologic Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Deborah R. Surman
- Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Sharlyn J. Mazur
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Yuan Xu
- Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Bhargav S. Arimilli
- Urologic Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ye Yang
- Urologic Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, UK, Lexington, KY, United States
| | - Teresa W-M. Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology, Markey Cancer Center, UK, Lexington, KY, United States
| | - David S. Schrump
- Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - W. Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - R. Taylor Ripley
- Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
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13
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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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14
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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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15
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Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
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Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
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16
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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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Fan TWM, Daneshmandi S, Cassel TA, Uddin MB, Sledziona J, Thompson PT, Lin P, Higashi RM, Lane AN. Abstract 2537: Beta-glucan reprograms immunomodulatory metabolism in human macrophage and ex vivo in lung cancer tissues. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2537] [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
We combined multiplex Stable Isotope-Resolved Metabolomics (mSIRM) with Reverse Phase Protein Array (RPPA) to map the time course changes of IM metabolic network and key protein regulators in four human donors’ MΦ’s in response to differential polarization and whole glucan particulates (WGP) treatments. We found consistent and plastic network responses to polarization durations and WGP treatments compared to those of the mouse counterparts. Consistent responses included enhanced 15N2-tryptophan catabolism to quinolinate, 2H2-glucose oxidation to ribose/ribulose-5-phosphate, and conversion of 13C5-glutamine to itaconate in response to pro-inflammatory (M1) versus anti-inflammatory (M2) stimuli. WGP robustly induced the buildup of 2H2-glucose-derived 6-phosphogluconate, -lactate, and -IMP, 13C5-glutamine-derived fructose-1,6-bisphosphate, and increased enrichment of 2H-labeled UDP-N-acetylglucosamine in M2-MΦ’s. However, the Krebs cycle activity was variably enhanced by M2 stimuli or WGP treatment. The consistent effects were related to increased release of proinflammatory IM effectors IL-1β/CXCL10/IFNγ/TNFα by M1-MΦ’s and enhanced release of IL-1β/TNFα to above M1-MΦ’s levels in WGP-treated M2-MΦ’s while boosting the latter in anti-inflammatory IL-10 release and maintenance of NAD+ synthesis. They were also related to lower phagocytosis in M1-MΦ’s and WGP-treated M2-MΦ’s versus M2-MΦ’s. Together with the expression changes of key protein regulators, we suggest enhanced tryptophan catabolism with blocked NAD+ and UTP synthesis to be key to the consistent changes in immune functions in response to M1 stimuli. Likewise, increased glucose utilization via glycolysis and the oxidative branch of the pentose phosphate pathway, and blockade of glutamine-fueled N-linked glycosylation could be linked to reversion of M2 to M1-type immune functions. Reprogrammed Krebs cycle and glutamine conversion to UTP occurred variably in WGP-treated ex vivo organotypic tissue cultures (OTCs) of human non-small cell lung cancer (NSCLC), which could reflect variable M1 repolarization of tumor associated MΦ’s. This in turn correlated with IL-1β/TNFα releases and compromised tumor status, making patient-derived OTCs a unique model for studying variable immunotherapeutic efficacy in cancer patients. In conclusion, consistent and variable IM metabolic responses were evident in four human donors’ MΦ’s. WGP repolarized some M2 to M1-type responses while boosting other M2-type responses. NSCLC OTCs from six patients showed variable M1 repolarization in response to WGP.
Citation Format: Teresa W. M. Fan, Saeed Daneshmandi, Teresa A. Cassel, Mohammad B. Uddin, James Sledziona, Patrick T. Thompson, Penghui Lin, Richard M. Higashi, Andrew N. Lane. Beta-glucan reprograms immunomodulatory metabolism in human macrophage and ex vivo in lung cancer tissues [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 2537.
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19
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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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20
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Chen X, Sunkel B, Wang M, Kang S, Wang T, Gnanaprakasam JNR, Liu L, Cassel TA, Scott DA, Muñoz-Cabello AM, Lopez-Barneo J, Yang J, Lane AN, Xin G, Stanton B, Fan TWM, Wang R. Succinate dehydrogenase/complex II is critical for metabolic and epigenetic regulation of T cell proliferation and inflammation. Sci Immunol 2022; 7:eabm8161. [PMID: 35486677 PMCID: PMC9332111 DOI: 10.1126/sciimmunol.abm8161] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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] [Indexed: 01/23/2023]
Abstract
Effective T cell-mediated immune responses require the proper allocation of metabolic resources to sustain growth, proliferation, and cytokine production. Epigenetic control of the genome also governs T cell transcriptome and T cell lineage commitment and maintenance. Cellular metabolic programs interact with epigenetic regulation by providing substrates for covalent modifications of chromatin. By using complementary genetic, epigenetic, and metabolic approaches, we revealed that tricarboxylic acid (TCA) cycle flux fueled biosynthetic processes while controlling the ratio of succinate/α-ketoglutarate (α-KG) to modulate the activities of dioxygenases that are critical for driving T cell inflammation. In contrast to cancer cells, where succinate dehydrogenase (SDH)/complex II inactivation drives cell transformation and growth, SDH/complex II deficiency in T cells caused proliferation and survival defects when the TCA cycle was truncated, blocking carbon flux to support nucleoside biosynthesis. Replenishing the intracellular nucleoside pool partially relieved the dependence of T cells on SDH/complex II for proliferation and survival. SDH deficiency induced a proinflammatory gene signature in T cells and promoted T helper 1 and T helper 17 lineage differentiation. An increasing succinate/α-KG ratio in SDH-deficient T cells promoted inflammation by changing the pattern of the transcriptional and chromatin accessibility signatures and consequentially increasing the expression of the transcription factor, PR domain zinc finger protein 1. Collectively, our studies revealed a role of SDH/complex II in allocating carbon resources for anabolic processes and epigenetic regulation in T cell proliferation and inflammation.
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Affiliation(s)
- Xuyong Chen
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Benjamin Sunkel
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Meng Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The 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, 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, The Ohio State University, Columbus, OH, USA
| | - JN Rashida Gnanaprakasam
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, 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, The Ohio State University, Columbus, OH, USA
| | - Teresa A. Cassel
- Center for Environmental and Systems Biochemistry, Dept. 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
| | - Ana M. Muñoz-Cabello
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario "Virgen del Rocío"/CSIC/Universidad de Sevilla, Spain
| | - Jose Lopez-Barneo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario "Virgen del Rocío"/CSIC/Universidad de Sevilla, Spain
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry, Dept. of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Gang Xin
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Benjamin Stanton
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Teresa W.-M. Fan
- Center for Environmental and Systems Biochemistry, Dept. 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, The Ohio State University, Columbus, OH, USA
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21
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Chihanga T, Vicente-Muñoz S, Ruiz-Torres S, Pal B, Sertorio M, Andreassen PR, Khoury R, Mehta P, Davies SM, Lane AN, Romick-Rosendale LE, Wells SI. Head and Neck Cancer Susceptibility and Metabolism in Fanconi Anemia. Cancers (Basel) 2022; 14:cancers14082040. [PMID: 35454946 PMCID: PMC9025423 DOI: 10.3390/cancers14082040] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 02/06/2023] Open
Abstract
Fanconi anemia (FA) is a rare inherited, generally autosomal recessive syndrome, but it displays X-linked or dominant negative inheritance for certain genes. FA is characterized by a deficiency in DNA damage repair that results in bone marrow failure, and in an increased risk for various epithelial tumors, most commonly squamous cell carcinomas of the head and neck (HNSCC) and of the esophagus, anogenital tract and skin. Individuals with FA exhibit increased human papilloma virus (HPV) prevalence. Furthermore, a subset of anogenital squamous cell carcinomas (SCCs) in FA harbor HPV sequences and FA-deficient laboratory models reveal molecular crosstalk between HPV and FA proteins. However, a definitive role for HPV in HNSCC development in the FA patient population is unproven. Cellular metabolism plays an integral role in tissue homeostasis, and metabolic deregulation is a known hallmark of cancer progression that supports uncontrolled proliferation, tumor development and metastatic dissemination. The metabolic consequences of FA deficiency in keratinocytes and associated impact on the development of SCC in the FA population is poorly understood. Herein, we review the current literature on the metabolic consequences of FA deficiency and potential effects of resulting metabolic reprogramming on FA cancer phenotypes.
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Affiliation(s)
- Tafadzwa Chihanga
- Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (T.C.); (S.R.-T.); (B.P.)
| | - Sara Vicente-Muñoz
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (S.V.-M.); (L.E.R.-R.)
| | - Sonya Ruiz-Torres
- Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (T.C.); (S.R.-T.); (B.P.)
| | - Bidisha Pal
- Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (T.C.); (S.R.-T.); (B.P.)
| | - Mathieu Sertorio
- Department of Radiation Oncology, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA;
| | - Paul R. Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Ruby Khoury
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (R.K.); (P.M.); (S.M.D.)
| | - Parinda Mehta
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (R.K.); (P.M.); (S.M.D.)
| | - Stella M. Davies
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (R.K.); (P.M.); (S.M.D.)
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA;
| | - Lindsey E. Romick-Rosendale
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (S.V.-M.); (L.E.R.-R.)
| | - Susanne I. Wells
- Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (T.C.); (S.R.-T.); (B.P.)
- Correspondence: ; Tel.: +1-513-636-5986
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22
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Fan TW, Higashi RM, Song H, Daneshmandi S, Mahan AL, Purdom MS, Bocklage TJ, Pittman TA, He D, Wang C, Lane AN. Innate immune activation by checkpoint inhibition in human patient-derived lung cancer tissues. eLife 2021; 10:69578. [PMID: 34406120 PMCID: PMC8476122 DOI: 10.7554/elife.69578] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 04/20/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Although Pembrolizumab-based immunotherapy has significantly improved lung cancer patient survival, many patients show variable efficacy and resistance development. A better understanding of the drug’s action is needed to improve patient outcomes. Functional heterogeneity of the tumor microenvironment (TME) is crucial to modulating drug resistance; understanding of individual patients’ TME that impacts drug response is hampered by lack of appropriate models. Lung organotypic tissue slice cultures (OTC) with patients’ native TME procured from primary and brain-metastasized (BM) non-small cell lung cancer (NSCLC) patients were treated with Pembrolizumab and/or beta-glucan (WGP, an innate immune activator). Metabolic tracing with 13C6-Glc/13C5,15N2-Gln, multiplex immunofluorescence, and digital spatial profiling (DSP) were employed to interrogate metabolic and functional responses to Pembrolizumab and/or WGP. Primary and BM PD-1+ lung cancer OTC responded to Pembrolizumab and Pembrolizumab + WGP treatments, respectively. Pembrolizumab activated innate immune metabolism and functions in primary OTC, which were accompanied by tissue damage. DSP analysis indicated an overall decrease in immunosuppressive macrophages and T cells but revealed microheterogeneity in immune responses and tissue damage. Two TMEs with altered cancer cell properties showed resistance. Pembrolizumab or WGP alone had negligible effects on BM-lung cancer OTC but Pembrolizumab + WGP blocked central metabolism with increased pro-inflammatory effector release and tissue damage. In-depth metabolic analysis and multiplex TME imaging of lung cancer OTC demonstrated overall innate immune activation by Pembrolizumab but heterogeneous responses in the native TME of a patient with primary NSCLC. Metabolic and functional analysis also revealed synergistic action of Pembrolizumab and WGP in OTC of metastatic NSCLC.
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Affiliation(s)
- Teresa Wm Fan
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, United States.,Markey Cancer Center, University of Kentucky, Lexington, United States
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, United States.,Markey Cancer Center, University of Kentucky, Lexington, United States
| | - Huan Song
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, United States.,Markey Cancer Center, University of Kentucky, Lexington, United States
| | - Saeed Daneshmandi
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, United States.,Markey Cancer Center, University of Kentucky, Lexington, United States
| | - Angela L Mahan
- Markey Cancer Center, University of Kentucky, Lexington, United States.,Departement of Surgery, University of Kentucky, Lexington, United States
| | - Matthew S Purdom
- Markey Cancer Center, University of Kentucky, Lexington, United States.,Departement of Pathology and Laboratory Medicine, University of Kentucky, Lexington, United States
| | - Therese J Bocklage
- Markey Cancer Center, University of Kentucky, Lexington, United States.,Departement of Pathology and Laboratory Medicine, University of Kentucky, Lexington, United States
| | - Thomas A Pittman
- Department of Neurosurgery, University of Kentucky, Lexington, United States
| | - Daheng He
- Markey Cancer Center, University of Kentucky, Lexington, United States.,Department Internal Medicine, University of Kentucky, Lexington, United States
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, United States.,Department Internal Medicine, University of Kentucky, Lexington, United States
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, United States.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, United States.,Markey Cancer Center, University of Kentucky, Lexington, United States
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23
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Jiang H, Hao Y, Ding N, Thapa P, Alshahrani A, Lane AN, Wei Q. Abstract 2018: Understanding the functional significance of Sulfiredoxin in cancer cell metabolism. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2018] [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
Intracellular antioxidant enzymes are critical for the maintenance of redox homeostasis under both physiological and pathological conditions, and their expression levels are frequently upregulated in different types of human cancer. Compared to normal cells, cancer cells accommodate energy needs preferentially through aerobic glycolysis that predisposes advantages in cell growth, proliferation, survival, and chemotherapeutic resistance. Whether and how redox enzymes contribute to cancer cell metabolism has not been fully explored. Sulfiredoxin (Srx) is a unique reducing enzyme that can restore the peroxidase activity of hyperoxidized peroxiredoxins. It also promotes oncogenic signaling to facilitate tumor growth and malignant progression in multiple types of human cancer including non-small cell lung cancer. To investigate the significance and molecular mechanism of Srx in cancer cell metabolism, endogenously expressed Srx in human non-small cell lung cancer cells was depleted by lentivirus mediated ShRNA knockdown technique. Features of cellular metabolism, including the uptake/consumption of glucose, the production of lactate, the rate of extracellular acidification and the generation of energy were measured using series of quantitative assays and the seahorse real-time cell metabolic analysis. In particular, the fate and routes of glucose metabolism in groups of control and Srx-depleted cells were determined and compared with the addition of C13-glucose into the culture medium, and metabolites were qualitatively and quantitatively measured using stable isotope-resolved metabolomic method. To determine the molecular mechanism of metabolic change, genes differentially expressed in control and Srx knockdown cells were identified by DNA microarray. Genes with statistically significant changes on expression levels were further validated by quantitative real-time PCR at the transcript level and immunoblotting at the protein level. We demonstrated that knockdown of Srx in human lung cancer cells leads to a significant change of glucose metabolism, characterized by the metabolic reprogramming from predominantly glycolysis to oxidative phosphorylation. This transition is likely resulted from a profound change of gene expression pattern due to the knockdown of Srx. For example, among those downregulated genes there are transporters for glucose and monocarboxylate. In summary, our data indicate that depletion of Srx in lung cancer cells leads to metabolic reprogramming that favors oxidative phosphorylation, and further investigation of this process may be valuable for the complete understanding of the functional significance of redox enzymes in the development of not only lung but also other types of human cancer.
Citation Format: Hong Jiang, Yanning Hao, Na Ding, Pratik Thapa, Aziza Alshahrani, Andrew N. Lane, Qiou Wei. Understanding the functional significance of Sulfiredoxin in cancer cell metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2018.
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Affiliation(s)
- Hong Jiang
- University of Kentucky College of Medicine, Lexington, KY
| | - Yanning Hao
- University of Kentucky College of Medicine, Lexington, KY
| | - Na Ding
- University of Kentucky College of Medicine, Lexington, KY
| | - Pratik Thapa
- University of Kentucky College of Medicine, Lexington, KY
| | | | - Andrew N. Lane
- University of Kentucky College of Medicine, Lexington, KY
| | - Qiou Wei
- University of Kentucky College of Medicine, Lexington, KY
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24
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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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25
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Lin P, Dai L, Crooks DR, Neckers LM, Higashi RM, Fan TWM, Lane AN. NMR Methods for Determining Lipid Turnover via Stable Isotope Resolved Metabolomics. Metabolites 2021; 11:202. [PMID: 33805301 PMCID: PMC8065598 DOI: 10.3390/metabo11040202] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/28/2022] Open
Abstract
Lipids comprise diverse classes of compounds that are important for the structure and properties of membranes, as high-energy fuel sources and as signaling molecules. Therefore, the turnover rates of these varied classes of lipids are fundamental to cellular function. However, their enormous chemical diversity and dynamic range in cells makes detailed analysis very complex. Furthermore, although stable isotope tracers enable the determination of synthesis and degradation of complex lipids, the numbers of distinguishable molecules increase enormously, which exacerbates the problem. Although LC-MS-MS (Liquid Chromatography-Tandem Mass Spectrometry) is the standard for lipidomics, NMR can add value in global lipid analysis and isotopomer distributions of intact lipids. Here, we describe new developments in NMR analysis for assessing global lipid content and isotopic enrichment of mixtures of complex lipids for two cell lines (PC3 and UMUC3) using both 13C6 glucose and 13C5 glutamine tracers.
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Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA; (P.L.); (R.M.H.); (T.W-M.F.)
| | - Li Dai
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (L.D.); (D.R.C.); (L.M.N.)
| | - Daniel R. Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (L.D.); (D.R.C.); (L.M.N.)
| | - Leonard M. Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (L.D.); (D.R.C.); (L.M.N.)
| | - Richard M. Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA; (P.L.); (R.M.H.); (T.W-M.F.)
- Department Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA
| | - Teresa W-M. Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA; (P.L.); (R.M.H.); (T.W-M.F.)
- Department Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA; (P.L.); (R.M.H.); (T.W-M.F.)
- Department Toxicology & Cancer Biology, University of Kentucky, 789 S. Limestone St, Lexington, KY 40536, USA
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Yanckello LM, Hoffman JD, Chang YH, Lin P, Nehra G, Chlipala G, McCulloch SD, Hammond TC, Yackzan AT, Lane AN, Green SJ, Hartz AMS, Lin AL. Apolipoprotein E genotype-dependent nutrigenetic effects to prebiotic inulin for modulating systemic metabolism and neuroprotection in mice via gut-brain axis. Nutr Neurosci 2021; 25:1669-1679. [PMID: 33666538 PMCID: PMC8799401 DOI: 10.1080/1028415x.2021.1889452] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE The goal of the study was to identify the potential nutrigenetic effects to inulin, a prebiotic fiber, in mice with different human apolipoprotein E (APOE) genetic variants. Specifically, we compared responses to inulin for the potential modulation of the systemic metabolism and neuroprotection via gut-brain axis in mice with human APOE ϵ3 and ϵ4 alleles. METHOD We performed experiments with young mice expressing the human APOE3 (E3FAD mice and APOE4 gene (E4FAD mice). We fed mice with either inulin or control diet for 16 weeks starting from 3 months of age. We determined gut microbiome diversity and composition using16s rRNA sequencing, systemic metabolism using in vivo MRI and metabolomics, and blood-brain barrier (BBB) tight junction expression using Western blot. RESULTS In both E3FAD and E4FAD mice, inulin altered the alpha and beta diversity of the gut microbiome, increased beneficial taxa of bacteria and elevated cecal short chain fatty acid and hippocampal scyllo-inositol. E3FAD mice had altered metabolism related to tryptophan and tyrosine, while E4FAD mice had changes in the tricarboxylic acid cycle, pentose phosphate pathway, and bile acids. Differences were found in levels of brain metabolites related to oxidative stress, and levels of Claudin-1 and Claudin-5 BBB tight junction expression. DISCUSSION We found that inulin had many similar beneficial effects in the gut and brain for both E3FAD and E4FAD mice, which may be protective for brain functions and reduce risk for neurodegeneration. . E3FAD and E4FAD mice also had distinct responses in several metabolic pathways, suggesting an APOE-dependent nutrigenetic effects in modulating systemic metabolism and neuroprotection.
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Affiliation(s)
- Lucille M Yanckello
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, USA
| | - Jared D Hoffman
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, USA
| | - Ya-Hsuan Chang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, USA
| | - Penghui Lin
- Center for Environmental Systems Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Geetika Nehra
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - George Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Tyler C Hammond
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA.,Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA
| | - Andrew T Yackzan
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - Andrew N Lane
- Center for Environmental Systems 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
| | - Stefan J Green
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Anika M S Hartz
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, USA
| | - Ai-Ling Lin
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, USA.,Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA.,F. Joseph Halcomb III, M.D. Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky, USA
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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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Merino MJ, Ricketts CJ, Moreno V, Yang Y, Fan TW, Lane AN, Meltzer PS, Vocke CD, Crooks DR, Linehan WM. Multifocal Renal Cell Carcinomas With Somatic IDH2 Mutation: Report of a Previously Undescribed Neoplasm. Am J Surg Pathol 2021; 45:137-142. [PMID: 33165095 PMCID: PMC7736215 DOI: 10.1097/pas.0000000000001611] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Renal cell carcinoma (RCC) is a heterogenous disease composed of several different cancer types characterized by distinct histologies and genetic alterations, including mutation of the Krebs cycle enzyme genes for fumarate hydratase and succinate dehydrogenase (SDH). This report describes a patient with multifocal renal tumors that presented with a novel, biphasic histologic morphology with one component consisting of small cells growing in a diffuse pattern occasionally forming glandular and cystic structures, reminiscent of type 1 papillary RCC, and the other component having larger cells with abundant eosinophilic and clear cytoplasm and appearing in a solid pattern of growth. Genetic analysis of multiple tumors showed that all had a somatic mutation of the IDH2 gene that created the known pathogenic, gain-of-function p.R172M alteration that results in abnormal accumulation of the oncometabolite 2-hydroxyglutarate (2-HG). Analysis of multiple tumors demonstrated highly elevated levels of 2-HG and a CpG island methylator phenotype that is characteristic of 2-HG-related inhibition of the Ten-eleven translocation (TET) family of DNA demethylases. In combination with fumarate hydratase-deficient and succinate dehydrogenase-deficient RCCs that have increased levels of the fumarate and succinate oncometabolites, respectively, the mutation of isocitrate dehydrogenase 2 represents the third Krebs cycle enzyme alteration to be associated with oncometabolite-induced RCC tumorigenesis. This study associates the discovery of a new histologic presentation of RCC with the first report of an IDH2 gain-of-function mutation in RCC.
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Affiliation(s)
- Maria J. Merino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christopher J. Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vanessa Moreno
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ye Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, 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, 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
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cathy D. Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel R. Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - W. Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Chang Y, Hoffman JD, Yanckello LM, McCulloch SD, Lin P, Lane AN, Chlipala G, Green SJ, Lin A. Apolipoprotein E genotype‐dependent nutrigenetic effects to prebiotic inulin for reducing risk for Alzheimer’s disease in a mouse model. Alzheimers Dement 2020. [DOI: 10.1002/alz.041175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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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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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: 129] [Impact Index Per Article: 32.3] [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] [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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Lane AN, Higashi RM, Fan TWM. Metabolic reprogramming in tumors: Contributions of the tumor microenvironment. Genes Dis 2020; 7:185-198. [PMID: 32215288 PMCID: PMC7083762 DOI: 10.1016/j.gendis.2019.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/06/2019] [Accepted: 10/16/2019] [Indexed: 12/22/2022] Open
Abstract
The genetic alterations associated with cell transformation are in large measure expressed in the metabolic phenotype as cancer cells proliferate and change their local environment, and prepare for metastasis. Qualitatively, the fundamental biochemistry of cancer cells is generally the same as in the untransformed cells, but the cancer cells produce a local environment, the TME, that is hostile to the stromal cells, and compete for nutrients. In order to proliferate, cells need sufficient nutrients, either those that cannot be made by the cells themselves, or must be made from simpler precursors. However, in solid tumors, the nutrient supply is often limiting given the potential for rapid proliferation, and the poor quality of the vasculature. Thus, cancer cells may employ a variety of strategies to obtain nutrients for survival, growth and metastasis. Although much has been learned using established cell lines in standard culture conditions, it is becoming clear from in vivo metabolic studies that this can also be misleading, and which nutrients are used for energy production versus building blocks for synthesis of macromolecules can vary greatly from tumor to tumor, and even within the same tumor. Here we review the operation of metabolic networks, and how recent understanding of nutrient supply in the TME and utilization are being revealed using stable isotope tracers in vivo as well as in vitro.
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Key Words
- 2OG, 2-oxoglutarate
- ACO1,2, aconitase 1,2
- CP-MAS, Cross polarization Magic Angle Spinning
- Cancer metabolism
- DMEM, Dulbeccos Modified Eagles Medium
- ECAR, extracellular acidification rate
- ECM, extracellular matrix
- EMP, Embden-Meyerhof Pathway
- IDH1,2, isocitrate dehydrogenase 1,2 (NADP+dependent)
- IF, interstitial fluid
- ME, malic enzyme
- Metabolic flux
- Nutrient supply
- RPMI, Roswell Park Memorial Institute
- SIRM, Stable Isotope Resolved Metabolomics
- Stable isotope resolved metabolomics
- TIL, tumor infiltrating lymphocyte
- TIM/TPI, triose phosphate isomerase
- TME, Tumor Micro Environment
- Tumor microenvironment
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Affiliation(s)
- Andrew N. Lane
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, USA
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Zhang Y, Zhang X, Lane AN, Fan TWM, Liu J. Inferring Gene Regulatory Networks of Metabolic Enzymes Using Gradient Boosted Trees. IEEE J Biomed Health Inform 2020; 24:1528-1536. [DOI: 10.1109/jbhi.2019.2931997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Hardwick JS, Haugland MM, El-Sagheer AH, Ptchelkine D, Beierlein FR, Lane AN, Brown T, Lovett JE, Anderson EA. 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis. Nucleic Acids Res 2020; 48:2830-2840. [PMID: 32052020 PMCID: PMC7102949 DOI: 10.1093/nar/gkaa086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/28/2020] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2' position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2'-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation.
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Affiliation(s)
- Jack S Hardwick
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marius M Haugland
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Denis Ptchelkine
- Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Frank R Beierlein
- Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry and Department of Toxicology & Cancer Biology, The University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, USA
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, UK
| | - Edward A Anderson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Venugopalan A, Nguyen K, Lynberg M, Maity T, Qi Y, Roper N, Cultraro C, Chan K, Misra V, Thorkell A, Zhang X, Crooks D, Linehan WM, Lane AN, Guha U. Epigenetic Reprogramming Driven By Metabolic Alterations As A Mechanism Of EGFR – Tyrosine Kinase Inhibitor Resistance In Human Lung Adenocarcinoma. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Yue Qi
- National Cancer Institute
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39
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Gonzalez A, Deng Y, Lane AN, Benkeser D, Cui X, Staimez LR, Ford CN, Khan FN, Markley Webster SC, Leong A, Wilson PWF, Phillips LS, Rhee MK. Impact of mismatches in HbA 1c vs glucose values on the diagnostic classification of diabetes and prediabetes. Diabet Med 2020; 37:689-696. [PMID: 31721287 DOI: 10.1111/dme.14181] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/11/2019] [Indexed: 12/18/2022]
Abstract
AIMS To determine whether HbA1c mismatches (HbA1c levels that are higher or lower than expected for the average glucose levels in different individuals) could lead to errors if diagnostic classification is based only on HbA1c levels. METHODS In a cross-sectional study, 3106 participants without known diabetes underwent a 75-g oral glucose tolerance test (fasting glucose and 2-h glucose) and a 50-g glucose challenge test (1-h glucose) on separate days. They were classified by oral glucose tolerance test results as having: normal glucose metabolism; prediabetes; or diabetes. Predicted HbA1c was determined from the linear regression modelling the relationship between observed HbA1c and average glucose (mean of fasting glucose and 2-h glucose from the oral glucose tolerance test, and 1-h glucose from the glucose challenge test) within oral glucose tolerance test groups. The haemoglobin glycation index was calculated as [observed - predicted HbA1c ], and divided into low, intermediate and high haemoglobin glycation index mismatch tertiles. RESULTS Those participants with higher mismatches were more likely to be black, to be men, to be older, and to have higher BMI (all P<0.001). Using oral glucose tolerance test criteria, the distribution of normal glucose metabolism, prediabetes and diabetes was similar across mismatch tertiles; however, using HbA1c criteria, the participants with low mismatches were classified as 97% normal glucose metabolism, 3% prediabetes and 0% diabetes, i.e. mostly normal, while those with high mismatches were classified as 13% normal glucose metabolism, 77% prediabetes and 10% diabetes, i.e. mostly abnormal (P<0.001). CONCLUSIONS Measuring only HbA1c could lead to under-diagnosis in people with low mismatches and over-diagnosis in those with high mismatches. Additional oral glucose tolerance tests and/or fasting glucose testing to complement HbA1c in diagnostic classification should be performed in most individuals.
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Affiliation(s)
- A Gonzalez
- Atlanta VA Health Care System, Decatur, GA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Y Deng
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - A N Lane
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - D Benkeser
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - X Cui
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - L R Staimez
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - C N Ford
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - F N Khan
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, University of Washington, Seattle, WA, USA
| | - S C Markley Webster
- Atlanta VA Health Care System, Decatur, GA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - A Leong
- Endocrine Unit, Diabetes Unit, Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - P W F Wilson
- Atlanta VA Health Care System, Decatur, GA, USA
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - L S Phillips
- Atlanta VA Health Care System, Decatur, GA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - M K Rhee
- Atlanta VA Health Care System, Decatur, GA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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40
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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: 202] [Impact Index Per Article: 50.5] [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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41
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Sun Q, Fan TWM, Lane AN, Higashi RM. Applications of Chromatography-Ultra High-Resolution MS for Stable Isotope-Resolved Metabolomics (SIRM) Reconstruction of Metabolic Networks. Trends Analyt Chem 2020; 123:115676. [PMID: 32483395 PMCID: PMC7263348 DOI: 10.1016/j.trac.2019.115676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolism is a complex network of compartmentalized and coupled chemical reactions, which often involve transfers of substructures of biomolecules, thus requiring metabolite substructures to be tracked. Stable isotope resolved metabolomics (SIRM) enables pathways reconstruction, even among chemically identical metabolites, by tracking the provenance of stable isotope-labeled substructures using NMR and ultrahigh resolution (UHR) MS. The latter can resolve and count isotopic labels in metabolites and can identify isotopic enrichment in substructures when operated in tandem MS mode. However, MS2 is difficult to implement with chromatography-based UHR-MS due to lengthy MS1 acquisition time that is required to obtain the molecular isotopologue count, which is further exacerbated by the numerous isotopologue source ions to fragment. We review here recent developments in tandem MS applications of SIRM to obtain more detailed information about isotopologue distributions in metabolites and their substructures.
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Affiliation(s)
- Qiushi Sun
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, KY, 40539, USA
| | - Teresa W-M. Fan
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, KY, 40539, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40539, USA
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, KY, 40539, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40539, USA
| | - Richard M. Higashi
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, KY, 40539, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40539, USA
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42
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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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43
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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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44
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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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45
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Li Y, Fan TWM, Lane AN, Kang WY, Arnold SM, Stromberg AJ, Wang C, Chen L. SDA: a semi-parametric differential abundance analysis method for metabolomics and proteomics data. BMC Bioinformatics 2019; 20:501. [PMID: 31623550 PMCID: PMC6798423 DOI: 10.1186/s12859-019-3067-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/19/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022] Open
Abstract
Background Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficult because the data may not be normally distributed and there is often a large fraction of zero values. Although several statistical methods have been proposed, they either require the data normality assumption or are inefficient. Results We propose a new semi-parametric differential abundance analysis (SDA) method for metabolomics and proteomics data from MS. The method considers a two-part model, a logistic regression for the zero proportion and a semi-parametric log-linear model for the possibly non-normally distributed non-zero values, to characterize data from each feature. A kernel-smoothed likelihood method is developed to estimate model coefficients and a likelihood ratio test is constructed for differential abundant analysis. The method has been implemented into an R package, SDAMS, which is available at https://www.bioconductor.org/packages/release/bioc/html/SDAMS.html. Conclusion By introducing the two-part semi-parametric model, SDA is able to handle both non-normally distributed data and large fraction of zero values in a MS dataset. It also allows for adjustment of covariates. Simulations and real data analyses demonstrate that SDA outperforms existing methods.
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Affiliation(s)
- Yuntong Li
- Department of Statistics, University of Kentucky, Lexington, 40536, USA
| | - Teresa W M Fan
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Woo-Young Kang
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.,Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.,Department of Medicine, University of Kentucky, Lexington, 40536, USA
| | | | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA. .,Department of Biostatistics, University of Kentucky, Lexington, 40536, USA.
| | - Li Chen
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA. .,Department of Biostatistics, University of Kentucky, Lexington, 40536, USA.
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46
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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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47
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Kishimoto S, Brender JR, Crooks DR, Matsumoto S, Seki T, Oshima N, Merkle H, Lin P, Reed G, Chen AP, Ardenkjaer-Larsen JH, Munasinghe J, Saito K, Yamamoto K, Choyke PL, Mitchell J, Lane AN, Fan TWM, Linehan WM, Krishna MC. Imaging of glucose metabolism by 13C-MRI distinguishes pancreatic cancer subtypes in mice. eLife 2019; 8:e46312. [PMID: 31408004 PMCID: PMC6706239 DOI: 10.7554/elife.46312] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 02/23/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022] Open
Abstract
Metabolic differences among and within tumors can be an important determinant in cancer treatment outcome. However, methods for determining these differences non-invasively in vivo is lacking. Using pancreatic ductal adenocarcinoma as a model, we demonstrate that tumor xenografts with a similar genetic background can be distinguished by their differing rates of the metabolism of 13C labeled glucose tracers, which can be imaged without hyperpolarization by using newly developed techniques for noise suppression. Using this method, cancer subtypes that appeared to have similar metabolic profiles based on steady state metabolic measurement can be distinguished from each other. The metabolic maps from 13C-glucose imaging localized lactate production and overall glucose metabolism to different regions of some tumors. Such tumor heterogeneity would not be not detectable in FDG-PET.
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Affiliation(s)
- Shun Kishimoto
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Jeffrey R Brender
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, NCI, NIHBethesdaUnited States
| | - Shingo Matsumoto
- Graduate School of Information Science and Technology, Division of Bioengineering and BioinformaticsHokkaido UniversitySapporoJapan
- JST, PRESTSaitamaJapan
| | - Tomohiro Seki
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Nobu Oshima
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | | | - Penghui Lin
- Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUnited States
| | | | | | - Jan Henrik Ardenkjaer-Larsen
- GE HealthCareChicagoUnited States
- Department of Electrical EngineeringTechnical University of DenmarkKongens LyngbyDenmark
| | | | - Keita Saito
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Kazutoshi Yamamoto
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Peter L Choyke
- Molecular Imaging Program, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - James Mitchell
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Andrew N Lane
- Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUnited States
- Markey Cancer CenterUniversity of KentuckyLexingtonUnited States
| | - Teresa WM Fan
- Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUnited States
- Markey Cancer CenterUniversity of KentuckyLexingtonUnited States
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, NCI, NIHBethesdaUnited States
| | - Murali C Krishna
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
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48
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Fan TWM, Bruntz RC, Yang Y, Song H, Chernyavskaya Y, Deng P, Zhang Y, Shah PP, Beverly LJ, Qi Z, Mahan AL, Higashi RM, Dang CV, Lane AN. De novo synthesis of serine and glycine fuels purine nucleotide biosynthesis in human lung cancer tissues. J Biol Chem 2019; 294:13464-13477. [PMID: 31337706 DOI: 10.1074/jbc.ra119.008743] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/06/2019] [Indexed: 11/06/2022] Open
Abstract
Nucleotide synthesis is essential to proliferating cells, but the preferred precursors for de novo biosynthesis are not defined in human cancer tissues. We have employed multiplexed stable isotope-resolved metabolomics to track the metabolism of [13C6]glucose, D2-glycine, [13C2]glycine, and D3-serine into purine nucleotides in freshly resected cancerous and matched noncancerous lung tissues from nonsmall cell lung cancer (NSCLC) patients, and we compared the metabolism with established NSCLC PC9 and A549 cell lines in vitro Surprisingly, [13C6]glucose was the best carbon source for purine synthesis in human NSCLC tissues, in contrast to the noncancerous lung tissues from the same patient, which showed lower mitotic indices and MYC expression. We also observed that D3-Ser was preferentially incorporated into purine rings over D2-glycine in both tissues and cell lines. MYC suppression attenuated [13C6]glucose, D3-serine, and [13C2]glycine incorporation into purines and reduced proliferation in PC9 but not in A549 cells. Using detailed kinetic modeling, we showed that the preferred use of glucose as a carbon source for purine ring synthesis in NSCLC tissues involves cytoplasmic activation/compartmentation of the glucose-to-serine pathway and enhanced reversed one-carbon fluxes that attenuate exogenous serine incorporation into purines. Our findings also indicate that the substrate for de novo nucleotide synthesis differs profoundly between cancer cell lines and fresh human lung cancer tissues; the latter preferred glucose to exogenous serine or glycine but not the former. This distinction in substrate utilization in purine synthesis in human cancer tissues should be considered when targeting one-carbon metabolism for cancer therapy.
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Affiliation(s)
- Teresa W M Fan
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536.
| | - Ronald C Bruntz
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Ye Yang
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Huan Song
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Yelena Chernyavskaya
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Pan Deng
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Yan Zhang
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Parag P Shah
- J. G. Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Levi J Beverly
- J. G. Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Zhen Qi
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Angela L Mahan
- Department of Surgery and Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536
| | - Chi V Dang
- Ludwig Institute for Cancer Research, New York, New York 10017; Wistar Institute, Philadelphia, Pennsylvania 19104
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry (CESB)/Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536.
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49
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Kang WY, Thompson PT, El-Amouri SS, Fan TWM, Lane AN, Higashi RM. Improved segmented-scan spectral stitching for stable isotope resolved metabolomics (SIRM) by ultra-high-resolution Fourier transform mass spectrometry. Anal Chim Acta 2019; 1080:104-115. [PMID: 31409459 DOI: 10.1016/j.aca.2019.06.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/11/2018] [Revised: 05/30/2019] [Accepted: 06/08/2019] [Indexed: 12/25/2022]
Abstract
We have implemented a linear ion trap (LIT)-based SIM-stitching method for ultra-high-resolution Fourier transform mass spectrometry (FTMS) that increases the S/N over a wide m/z range compared to non-segmented wide full-scan (WFS) spectra. Here we described an improved segmented spectral scan stitching method that was based on quadrupole mass filter (QMF)-SIM, which overcame previous limitations of ion signal loss in LIT. This allowed for accurate representation of isotopologue distributions, both at natural abundance and in stable isotope-resolved metabolomics (SIRM)-based experiments. We also introduced a new spectral binning method that provided more precise and resolution-independent bins for irreversibly noise-suppressed FTMS spectra. We demonstrated a substantial improvement in S/N and sensitivity (typically > 10-fold) for 13C labeled lipid extracts of human macrophages grown as three-dimensional (3D) cell culture, with detection of an increased number of 13C isotopologue ions. The method also enabled analysis of extracts from very limited biological samples.
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Affiliation(s)
- Woo-Young Kang
- Center for Environmental and Systems Biochemistry (CESB), Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, United States
| | - Patrick T Thompson
- Center for Environmental and Systems Biochemistry (CESB), Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, United States
| | - Salim S El-Amouri
- Center for Environmental and Systems Biochemistry (CESB), Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, United States
| | - Teresa W M Fan
- Center for Environmental and Systems Biochemistry (CESB), Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, United States
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry (CESB), Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, United States
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry (CESB), Markey Cancer Center, Department of Toxicology and Cancer Biology, University of Kentucky, United States.
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50
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Kulkarni RA, Briney CA, Crooks DR, Bergholtz SE, Mushti C, Lockett SJ, Lane AN, Fan TW, Swenson RE, Marston Linehan W, Meier JL. Cover Feature: Photoinducible Oncometabolite Detection (ChemBioChem 3/2019). Chembiochem 2019. [DOI: 10.1002/cbic.201900008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chloe A. Briney
- Chemical Biology LaboratoryNational Cancer InstituteNIH Frederick MD 21702 USA
| | - Daniel R. Crooks
- Urologic Oncology BranchNational Cancer InstituteNIH Bethesda MD 20817 USA
| | - Sarah E. Bergholtz
- Chemical Biology LaboratoryNational Cancer InstituteNIH Frederick MD 21702 USA
| | - Chandrasekhar Mushti
- Imaging Probe Development CenterNational Heart Lung and Blood InstituteNIH Rockville MD 20850 USA
| | - Stephen J. Lockett
- Optical Microscopy and Analysis LaboratoryFrederick National Laboratory for Cancer ResearchLeidos Biomedical Research, Inc. Frederick MD 21702 USA
| | - Andrew N. Lane
- Center for Environmental and Systems BiochemistryDepartment of Toxicology and Cancer Biology, andMarkey Cancer CenterUniversity of Kentucky Lexington KY 40536 USA
| | - Teresa W.‐M. Fan
- Center for Environmental and Systems BiochemistryDepartment of Toxicology and Cancer Biology, andMarkey Cancer CenterUniversity of Kentucky Lexington KY 40536 USA
| | - Rolf E. Swenson
- Imaging Probe Development CenterNational Heart Lung and Blood InstituteNIH Rockville MD 20850 USA
| | - W. Marston Linehan
- Urologic Oncology BranchNational Cancer InstituteNIH Bethesda MD 20817 USA
| | - Jordan L. Meier
- Chemical Biology LaboratoryNational Cancer InstituteNIH Frederick MD 21702 USA
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