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Zaal EA, Jansen JWA, Berkers CR. Stable Isotope Tracing Experiments Using LC-MS. Methods Mol Biol 2025; 2855:103-116. [PMID: 39354303 DOI: 10.1007/978-1-0716-4116-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Metabolomics has emerged as a pivotal field in understanding cellular function, particularly in the context of disease. In numerous diseases, including cancer, alterations in metabolism play an essential role in disease progression and drug response. Hence, unraveling the metabolic rewiring is of importance to find novel diagnostic and therapeutic strategies. Isotope tracing is a powerful technique for delving deeper into the metabolic wiring of cells. By tracking an isotopically labeled substrate through biochemical reactions in the cell, this technique provides a dynamic understanding of cellular metabolism. This chapter outlines a robust isotope tracing protocol utilizing high-resolution mass spectrometry coupled to liquid chromatography in cell culture-based models. We cover essential aspects of experimental design and analyses, providing a valuable resource for researchers aiming to employ isotopic tracing.
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Affiliation(s)
- Esther A Zaal
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
- Metabolism Expertise Centre, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Jeroen W A Jansen
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Metabolism Expertise Centre, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Celia R Berkers
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Metabolism Expertise Centre, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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2
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Guillard J, Schwörer S. Metabolic control of collagen synthesis. Matrix Biol 2024; 133:43-56. [PMID: 39084474 PMCID: PMC11402592 DOI: 10.1016/j.matbio.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
The extracellular matrix (ECM) is present in all tissues and crucial in maintaining normal tissue homeostasis and function. Defects in ECM synthesis and remodeling can lead to various diseases, while overproduction of ECM components can cause severe conditions like organ fibrosis and influence cancer progression and therapy resistance. Collagens are the most abundant core ECM proteins in physiological and pathological conditions and are predominantly synthesized by fibroblasts. Previous efforts to target aberrant collagen synthesis in fibroblasts by inhibiting pro-fibrotic signaling cascades have been ineffective. More recently, metabolic rewiring downstream of pro-fibrotic signaling has emerged as a critical regulator of collagen synthesis in fibroblasts. Here, we propose that targeting the metabolic pathways involved in ECM biomass generation provides a novel avenue for treating conditions characterized by excessive collagen accumulation. This review summarizes the unique metabolic challenges collagen synthesis imposes on fibroblasts and discusses how underlying metabolic networks could be exploited to create therapeutic opportunities in cancer and fibrotic disease. Finally, we provide a perspective on open questions in the field and how conceptual and technical advances will help address them to unlock novel metabolic vulnerabilities of collagen synthesis in fibroblasts and beyond.
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Affiliation(s)
- Julien Guillard
- Section of Hematology/Oncology, Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, 60637, USA
| | - Simon Schwörer
- Section of Hematology/Oncology, Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, 60637, USA; Committee on Cancer Biology, Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL, 60637, USA.
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3
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Ji JX, Hoang LN, Cochrane DR, Lum A, Senz J, Farnell D, Tessier-Cloutier B, Huntsman DG, Klein Geltink RI. The unique metabolome of clear cell ovarian carcinoma. J Pathol 2024; 264:160-173. [PMID: 39096103 DOI: 10.1002/path.6329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/29/2024] [Accepted: 06/08/2024] [Indexed: 08/04/2024]
Abstract
Clear cell ovarian carcinoma (CCOC) is an aggressive malignancy affecting younger women. Despite ovarian cancer subtypes having diverse molecular and clinical characteristics, the mainstay of treatment for advanced stage disease remains cytotoxic chemotherapy. Late stage CCOC is resistant to conventional chemotherapy, which means a suboptimal outcome for patients affected. Despite detailed genomic, epigenomic, transcriptomic, and proteomic characterisation, subtype-specific treatment for CCOC has shown little progress. The unique glycogen accumulation defining CCOC suggests altered metabolic pathway activity and dependency. This study presents the first metabolomic landscape of ovarian cancer subtypes, including 42 CCOC, 20 high-grade serous and 21 endometrioid ovarian carcinomas, together comprising the three most common ovarian carcinoma subtypes. We describe a distinct metabolomic landscape of CCOC compared with other ovarian cancer subtypes, including alterations in energy utilisation and cysteine metabolism. In addition, we identify CCOC-specific alterations in metabolic pathways including serine biosynthesis and ROS-associated pathways that could serve as potential therapeutic targets. Our study provides the first in-depth study into the metabolome of ovarian cancers and a rich resource to support ongoing research efforts to identify subtype-specific therapeutic targets that could improve the dismal outcome for patients with this devastating malignancy. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lien N Hoang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Amy Lum
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Janine Senz
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Ramon I Klein Geltink
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
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4
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Lyons SA, McClelland GB. Commentary: Tracing the fate of metabolic substrates during changes in whole-body energy expenditure in mice. Comp Biochem Physiol B Biochem Mol Biol 2024; 274:111008. [PMID: 39059702 DOI: 10.1016/j.cbpb.2024.111008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 07/28/2024]
Abstract
For small mammals, such as mice, cannulation procedures can be quite challenging, limiting research associated with tracing isotopically labelled substrates at the whole-animal level. When cannulation in mice is possible, assessment of substrate use is further limited to when mice are either under anesthesia or are at rest, as there are no studies directly quantifying substrate use during exercise in mice. The use of isotopic tracer techniques has greatly advanced our knowledge in understanding how metabolic substrates (carbohydrates, amino acids, and fatty acids) contribute to whole-body metabolism. However, research regarding tissue-specific fuel use contributions to whole-body energy expenditure in mice at varying metabolic intensities (i.e., exercise) is lacking, despite the popularity of using mice in a variety of metabolic models. In this commentary, we briefly discuss the methodologies, advantages, and disadvantages of using radiolabelled, positron emission, and stable isotopes with a specific focus on fatty acids. We highlight recent mouse studies that have used creative experimental designs employing the use of isotopic tracer techniques and we briefly discuss how these methodologies can be further pursued to deepen our understanding of substrate use during exercise. Lastly, we show findings of a recent study we performed using a radiolabelled fatty acid tracer (14C-bromopalmitic acid) to determine fatty acid uptake in 16 muscles, two brown and two white adipose tissue depots during submaximal exercise in deer mice.
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Affiliation(s)
- Sulayman A Lyons
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Grant B McClelland
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
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5
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Britt EC, Qing X, Votava JA, Lika J, Wagner AS, Shen S, Arp NL, Khan H, Schieke SM, Fletcher CD, Huttenlocher A, Fan J. Activation induces shift in nutrient utilization that differentially impacts cell functions in human neutrophils. Proc Natl Acad Sci U S A 2024; 121:e2321212121. [PMID: 39284072 PMCID: PMC11441510 DOI: 10.1073/pnas.2321212121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 07/29/2024] [Indexed: 09/25/2024] Open
Abstract
Neutrophils utilize a variety of metabolic sources to support their crucial functions as the first responders in innate immunity. Here, through in vivo and ex vivo isotopic tracing, we examined the contributions of different nutrients to neutrophil metabolism under specific conditions. Human peripheral blood neutrophils, in contrast to a neutrophil-like cell line, rely on glycogen storage as a major metabolic source under resting state but rapidly switch to primarily using extracellular glucose upon activation with various stimuli. This shift is driven by a substantial increase in glucose uptake, enabled by rapidly increased GLUT1 on cell membrane, that dominates the simultaneous increase in gross glycogen cycling capacity. Shifts in nutrient utilization impact neutrophil functions in a function-specific manner: oxidative burst depends on glucose utilization, whereas NETosis and phagocytosis can be flexibly supported by either glucose or glycogen, and neutrophil migration and fungal control are enhanced by the shift from glycogen utilization to glucose utilization. This work provides a quantitative and dynamic understanding of fundamental features in neutrophil metabolism and elucidates how metabolic remodeling shapes neutrophil functions, which has broad health relevance.
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Affiliation(s)
- Emily C Britt
- Morgridge Institute for Research, Madison, WI 53715
- Nutrition and Metabolism Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Xin Qing
- Morgridge Institute for Research, Madison, WI 53715
- Nutrition and Metabolism Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Jorgo Lika
- Morgridge Institute for Research, Madison, WI 53715
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
| | - Andrew S Wagner
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Simone Shen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Nicholas L Arp
- Morgridge Institute for Research, Madison, WI 53715
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
| | - Hamidullah Khan
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53715
- Department of Dermatology, Georgetown University Medical Center Washington DC VA Medical Center, Washington, DC 20036
| | - Stefan M Schieke
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53715
- Department of Dermatology, Georgetown University Medical Center Washington DC VA Medical Center, Washington, DC 20036
| | | | - Anna Huttenlocher
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Carbone Cancer Center, Madison, WI 53792
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53792
| | - Jing Fan
- Morgridge Institute for Research, Madison, WI 53715
- Nutrition and Metabolism Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Carbone Cancer Center, Madison, WI 53792
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6
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Burr DJ, Drauschke J, Kanevche K, Kümmel S, Stryhanyuk H, Heberle J, Perfumo A, Elsaesser A. Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400289. [PMID: 38708804 DOI: 10.1002/smll.202400289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/16/2024] [Indexed: 05/07/2024]
Abstract
This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.
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Affiliation(s)
- David J Burr
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Janina Drauschke
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Katerina Kanevche
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Steffen Kümmel
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Amedea Perfumo
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Telegrafenberg, 14473, Potsdam, Germany
| | - Andreas Elsaesser
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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7
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VanSant-Webb C, Low HK, Kuramoto J, Stanley CE, Qiang H, Su AY, Ross AN, Cooper CG, Cox JE, Summers SA, Evason KJ, Ducker GS. Phospholipid isotope tracing suggests β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159514. [PMID: 38795827 DOI: 10.1016/j.bbalip.2024.159514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/08/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Activating mutations in the CTNNB1 gene encoding β-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). Profound alterations in lipid metabolism, including increases in fatty acid oxidation and transformation of the phospholipidome, occur in HCC with CTNNB1 mutations, but it is unclear what mechanisms give rise to these changes. We employed untargeted lipidomics and targeted isotope tracing to measure phospholipid synthesis activity in an inducible human liver cell line expressing mutant β-catenin, as well as in transgenic zebrafish with activated β-catenin-driven HCC. In both models, activated β-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid isotope tracing analysis in human cells revealed a reduction in phosphatidylcholine (PC) production rates as assayed by choline incorporation. We developed lipid isotope tracing analysis for zebrafish tumors and observed reductions in phosphatidylcholine synthesis by both the CDP-choline and PEMT pathways. The observed changes in the β-catenin-driven HCC phospholipidome suggest that zebrafish can recapitulate conserved features of HCC lipid metabolism and may serve as a model for identifying future HCC-specific lipid metabolic targets.
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Affiliation(s)
- Chad VanSant-Webb
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Hayden K Low
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Junko Kuramoto
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Claire E Stanley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Hantao Qiang
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Audrey Y Su
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexis N Ross
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Chad G Cooper
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, University of Utah College of Health, Salt Lake City, UT 84112, USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Gregory S Ducker
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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8
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Wu Z, Bezwada D, Cai F, Harris RC, Ko B, Sondhi V, Pan C, Vu HS, Nguyen PT, Faubert B, Cai L, Chen H, Martin-Sandoval M, Do D, Gu W, Zhang Y, Zhang Y, Brooks B, Kelekar S, Zacharias LG, Oaxaca KC, Patricio JS, Mathews TP, Garcia-Bermudez J, Ni M, DeBerardinis RJ. Electron transport chain inhibition increases cellular dependence on purine transport and salvage. Cell Metab 2024; 36:1504-1520.e9. [PMID: 38876105 PMCID: PMC11240302 DOI: 10.1016/j.cmet.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 03/11/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
Mitochondria house many metabolic pathways required for homeostasis and growth. To explore how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts from patients with various mitochondrial disorders and cancer cells with electron transport chain (ETC) blockade. These analyses revealed extensive perturbations in purine metabolism, and stable isotope tracing demonstrated that ETC defects suppress de novo purine synthesis while enhancing purine salvage. In human lung cancer, tumors with markers of low oxidative mitochondrial metabolism exhibit enhanced expression of the salvage enzyme hypoxanthine phosphoribosyl transferase 1 (HPRT1) and high levels of the HPRT1 product inosine monophosphate. Mechanistically, ETC blockade activates the pentose phosphate pathway, providing phosphoribosyl diphosphate to drive purine salvage supplied by uptake of extracellular bases. Blocking HPRT1 sensitizes cancer cells to ETC inhibition. These findings demonstrate how cells remodel purine metabolism upon ETC blockade and uncover a new metabolic vulnerability in tumors with low respiration.
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Affiliation(s)
- Zheng Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Divya Bezwada
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert C Harris
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bookyung Ko
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Varun Sondhi
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunxiao Pan
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Phong T Nguyen
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brandon Faubert
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ling Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongli Chen
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Misty Martin-Sandoval
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duyen Do
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuanyuan Zhang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bailey Brooks
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sherwin Kelekar
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - K Celeste Oaxaca
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joao S Patricio
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Javier Garcia-Bermudez
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Ni
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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9
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Theodoropoulos PC, Guo HH, Wang W, Crossley E, Rivera Cancel G, Fang M, Nguyen T, Baniasadi H, Williams NS, Ready JM, De Brabander JK, Nijhawan D. Thiophenyl Derivatives of Nicotinamide Are Metabolized by the NAD Salvage Pathway into Unnatural NAD Derivatives That Inhibit IMPDH and Are Toxic to Peripheral Nerve Cancers. ACS Chem Biol 2024; 19:1339-1350. [PMID: 38829020 DOI: 10.1021/acschembio.4c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
N-Pyridinylthiophene carboxamide (compound 21) displays activity against peripheral nerve sheath cancer cells and mouse xenografts by an unknown mechanism. Through medicinal chemistry, we identified a more active derivative, compound 9, and found that only analogues with structures similar to nicotinamide retained activity. Genetic screens using compound 9 found that both NAMPT and NMNAT1, enzymes in the NAD salvage pathway, are necessary for activity. Compound 9 is metabolized by NAMPT and NMNAT1 into an adenine dinucleotide (AD) derivative in a cell-free system, cultured cells, and mice, and inhibition of this metabolism blocked compound activity. AD analogues derived from compound 9 inhibit IMPDH in vitro and cause cell death by inhibiting IMPDH in cells. These findings nominate these compounds as preclinical candidates for the development of tumor-activated IMPDH inhibitors to treat neuronal cancers.
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Affiliation(s)
- Panayotis C Theodoropoulos
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Holly H Guo
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Wentian Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Eric Crossley
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Giomar Rivera Cancel
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Min Fang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Thu Nguyen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Hamid Baniasadi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Jef K De Brabander
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Deepak Nijhawan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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10
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Lopes EC, Shi F, Sawant A, Ibrahim M, Gomez-Jenkins M, Hu Z, Manchiraju P, Bhatt V, Wang W, Hinrichs CS, Wallace DC, Su X, Rabinowitz JD, Chan CS, Guo JY, Ganesan S, Lattime EC, White E. RESPIRATION DEFECTS LIMIT SERINE SYNTHESIS REQUIRED FOR LUNG CANCER GROWTH AND SURVIVAL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596339. [PMID: 38853873 PMCID: PMC11160605 DOI: 10.1101/2024.05.28.596339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mitochondrial function is important for both energetic and anabolic metabolism. Pathogenic mitochondrial DNA (mtDNA) mutations directly impact these functions, resulting in the detrimental consequences seen in human mitochondrial diseases. The role of pathogenic mtDNA mutations in human cancers is less clear; while pathogenic mtDNA mutations are observed in some cancer types, they are almost absent in others. We report here that the proofreading mutant DNA polymerase gamma ( PolG D256A ) induced a high mtDNA mutation burden in non-small-cell lung cancer (NSCLC), and promoted the accumulation of defective mitochondria, which is responsible for decreased tumor cell proliferation and viability and increased cancer survival. In NSCLC cells, pathogenic mtDNA mutations increased glycolysis and caused dependence on glucose. The glucose dependency sustained mitochondrial energetics but at the cost of a decreased NAD+/NADH ratio that inhibited de novo serine synthesis. Insufficient serine synthesis, in turn, impaired the downstream synthesis of GSH and nucleotides, leading to impaired tumor growth that increased cancer survival. Unlike tumors with intact mitochondrial function, NSCLC with pathogenic mtDNA mutations were sensitive to dietary serine and glycine deprivation. Thus, mitochondrial function in NSCLC is required specifically to sustain sufficient serine synthesis for nucleotide production and redox homeostasis to support tumor growth, explaining why these cancers preserve functional mtDNA. In brief High mtDNA mutation burden in non-small-cell lung cancer (NSCLC) leads to the accumulation of respiration-defective mitochondria and dependency on glucose and glycolytic metabolism. Defective respiratory metabolism causes a massive accumulation of cytosolic nicotinamide adenine dinucleotide + hydrogen (NADH), which impedes serine synthesis and, thereby, glutathione (GSH) and nucleotide synthesis, leading to impaired tumor growth and increased survival. Highlights Proofreading mutations in Polymerase gamma led to a high burden of mitochondrial DNA mutations, promoting the accumulation of mitochondria with respiratory defects in NSCLC.Defective respiration led to reduced proliferation and viability of NSCLC cells increasing survival to cancer.Defective respiration caused glucose dependency to fuel elevated glycolysis.Altered glucose metabolism is associated with high NADH that limits serine synthesis, leading to impaired GSH and nucleotide production.Mitochondrial respiration defects sensitize NSCLC to dietary serine/glycine starvation, further increasing survival. Abstract Figure
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11
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Hilovsky D, Hartsell J, Young JD, Liu X. Stable Isotope Tracing Analysis in Cancer Research: Advancements and Challenges in Identifying Dysregulated Cancer Metabolism and Treatment Strategies. Metabolites 2024; 14:318. [PMID: 38921453 PMCID: PMC11205609 DOI: 10.3390/metabo14060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer, driving the development of therapies targeting cancer metabolism. Stable isotope tracing has emerged as a widely adopted tool for monitoring cancer metabolism both in vitro and in vivo. Advances in instrumentation and the development of new tracers, metabolite databases, and data analysis tools have expanded the scope of cancer metabolism studies across these scales. In this review, we explore the latest advancements in metabolic analysis, spanning from experimental design in stable isotope-labeling metabolomics to sophisticated data analysis techniques. We highlight successful applications in cancer research, particularly focusing on ongoing clinical trials utilizing stable isotope tracing to characterize disease progression, treatment responses, and potential mechanisms of resistance to anticancer therapies. Furthermore, we outline key challenges and discuss potential strategies to address them, aiming to enhance our understanding of the biochemical basis of cancer metabolism.
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Affiliation(s)
- Dalton Hilovsky
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
| | - Joshua Hartsell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
| | - Jamey D. Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37212, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; (D.H.); (J.H.)
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12
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Chen L, Xu R, Zhu J. Lipidome isotope labelling of gut microbes (LILGM): A method of discovering endogenous microbial lipids. Talanta 2024; 271:125730. [PMID: 38310758 DOI: 10.1016/j.talanta.2024.125730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/22/2024] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
Lipidomics analysis of gut microbiome has become critical in recent surge of extensive human disease studies that investigate microbiome contributions. However, challenges remain in comprehending the origins of thousands of lipid species produced by the diverse microbes. Here, we proposed the development and utilization of a liquid chromatography-mass spectrometry-based approach, named lipidome isotope labelling of gut microbes (LILGM), which enables confident detection and identification of endogenous gut microbial lipidome via 13C/15N labeling strategy and high-resolution mass spectrometry. Our method leveraged in vitro microbial cultures and stable isotope-labeled 13C and 15N, allowing a reasonable degree of isotope incorporation into microbial lipids over short-term of inoculation. We then systematically detected the mass spectral patterns of 182 labeled lipid species by our in-house data analysis pipeline. Further bioinformatics analyses confidently identified biologically relevant microbial lipids from lipid classes such as diacylglycerols (DGs), fatty acids (FAs), phosphatidylglycerols (PGs), and phosphatidylethanolamines (PEs) that may have profound impacts to human physiology. Our study also demonstrated the application of LILGM by showcasing the confident detection of dysregulated microbial lipids post antibiotic perturbation. The debiased sparse partial correlation analysis provides insights into lipid metabolism intricacies. Overall, our method can provide unambiguous analyses to the endogenous microbial lipids in given biological context, and can also instantly reflect the lipidomic changes of gut microbes in response to environmental factors. We believe our LILGM approach has the potential to provide new body of knowledge by combining promising analytical approaches for sensitive and specific lipid detection to support functional microbiome studies.
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Affiliation(s)
- Li Chen
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH, 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Rui Xu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiangjiang Zhu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH, 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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13
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Meiser J, Frezza C. Presenting metabolomics analyses: what's in a number? EMBO J 2024:10.1038/s44318-024-00098-1. [PMID: 38664540 DOI: 10.1038/s44318-024-00098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/09/2024] Open
Affiliation(s)
- Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Christian Frezza
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University Hospital Cologne, Cologne, Germany.
- Institute of Genetics, Faculty of Mathematics and Natural Sciences, Faculty of Medicine, University of Cologne, Cologne, Germany.
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14
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Lu W, McBride MJ, Lee WD, Xing X, Xu X, Li X, Oschmann AM, Shen Y, Bartman C, Rabinowitz JD. Selected Ion Monitoring for Orbitrap-Based Metabolomics. Metabolites 2024; 14:184. [PMID: 38668312 PMCID: PMC11051813 DOI: 10.3390/metabo14040184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Matthew J. McBride
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Won Dong Lee
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
| | - Xi Xing
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Xincheng Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Xi Li
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Anna M. Oschmann
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Yihui Shen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline Bartman
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
- Rutgers Cancer Institute of New Jersey (CINJ), Rutgers University, New Brunswick, NJ 08901, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ 08544, USA
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15
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Peper CJ, Kilgore MD, Jiang Y, Xiu Y, Xia W, Wang Y, Shi M, Zhou D, Dumont AS, Wang X, Liu N. Tracing the path of disruption: 13C isotope applications in traumatic brain injury-induced metabolic dysfunction. CNS Neurosci Ther 2024; 30:e14693. [PMID: 38544365 PMCID: PMC10973562 DOI: 10.1111/cns.14693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/25/2024] [Accepted: 03/12/2024] [Indexed: 05/14/2024] Open
Abstract
Cerebral metabolic dysfunction is a critical pathological hallmark observed in the aftermath of traumatic brain injury (TBI), as extensively documented in clinical investigations and experimental models. An in-depth understanding of the bioenergetic disturbances that occur following TBI promises to reveal novel therapeutic targets, paving the way for the timely development of interventions to improve patient outcomes. The 13C isotope tracing technique represents a robust methodological advance, harnessing biochemical quantification to delineate the metabolic trajectories of isotopically labeled substrates. This nuanced approach enables real-time mapping of metabolic fluxes, providing a window into the cellular energetic state and elucidating the perturbations in key metabolic circuits. By applying this sophisticated tool, researchers can dissect the complexities of bioenergetic networks within the central nervous system, offering insights into the metabolic derangements specific to TBI pathology. Embraced by both animal studies and clinical research, 13C isotope tracing has bolstered our understanding of TBI-induced metabolic dysregulation. This review synthesizes current applications of isotope tracing and its transformative potential in evaluating and addressing the metabolic sequelae of TBI.
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Affiliation(s)
- Charles J. Peper
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Mitchell D. Kilgore
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Yinghua Jiang
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Yuwen Xiu
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Winna Xia
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Yingjie Wang
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Mengxuan Shi
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Di Zhou
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Aaron S. Dumont
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
| | - Xiaoying Wang
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Neuroscience Program, Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Ning Liu
- Clinical Neuroscience Research Center, Departments of Neurosurgery and NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Neuroscience Program, Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
- Tulane University Translational Sciences InstituteNew OrleansLouisianaUSA
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16
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Li S, Qian C, Wu XN, Zhou S. Carbon-Atom Exchange between [MC 2] + (M = Os and Ir) and Methane: on the Thermodynamic and Dynamic Aspects. J Phys Chem A 2024; 128:792-798. [PMID: 38239066 DOI: 10.1021/acs.jpca.3c07961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Gas-phase reactions of [OsC2]+ and [IrC2]+ with methane at ambient temperature have been studied using quadrupole-ion trap mass spectrometry combined with quantum chemical calculations. Both [OsC2]+ and [IrC2]+ undergo carbon-atom exchange reactions with methane. The associated mechanisms for the two systems are found to be similar. The differences in the rates of carbon isotope exchange reactions of methane with [MC2]+ (M = Os and Ir) are explained by several factors like the energy barrier for the initial H3C-H bond breaking processes, the molecular dynamics, orbital interactions, and the H-binding energies of the pivotal steps. Besides, the number of participating valence orbitals might be one of the keys to regulate the rate in the key step. The present findings may provide useful ideas and inspiration for designing similar processes.
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Affiliation(s)
- Shihan Li
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou 310027, P. R. China
- Zhejiang Provincial Innovation Center of Advanced Chemicals Technology, Institute of Zhejiang University - Quzhou, Quzhou 324000, P.R. China
| | - Chao Qian
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou 310027, P. R. China
- Zhejiang Provincial Innovation Center of Advanced Chemicals Technology, Institute of Zhejiang University - Quzhou, Quzhou 324000, P.R. China
| | - Xiao-Nan Wu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Shaodong Zhou
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou 310027, P. R. China
- Zhejiang Provincial Innovation Center of Advanced Chemicals Technology, Institute of Zhejiang University - Quzhou, Quzhou 324000, P.R. China
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17
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Farah C, Mignion L, Jordan BF. Metabolic Profiling to Assess Response to Targeted and Immune Therapy in Melanoma. Int J Mol Sci 2024; 25:1725. [PMID: 38339003 PMCID: PMC10855758 DOI: 10.3390/ijms25031725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
There is currently no consensus to determine which advanced melanoma patients will benefit from targeted therapy, immunotherapy, or a combination of both, highlighting the critical need to identify early-response biomarkers to advanced melanoma therapy. The goal of this review is to provide scientific rationale to highlight the potential role of metabolic imaging to assess response to targeted and/or immune therapy in melanoma cancer. For that purpose, a brief overview of current melanoma treatments is provided. Then, current knowledge with respect to melanoma metabolism is described with an emphasis on major crosstalks between melanoma cell metabolism and signaling pathways involved in BRAF-targeted therapy as well as in immune checkpoint inhibition therapies. Finally, preclinical and clinical studies using metabolic imaging and/or profiling to assess response to melanoma treatment are summarized with a particular focus on PET (Positron Emission Tomography) imaging and 13C-MRS (Magnetic Resonance Spectroscopy) methods.
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Affiliation(s)
- Chantale Farah
- Biomedical Magnetic Resonance Research Group, Louvain Drug Research Institute, Université Catholique de Louvain (UCLouvain), B-1200 Brussels, Belgium;
| | - Lionel Mignion
- Nuclear and Electron Spin Technologies (NEST) Platform, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), B-1200 Brussels, Belgium;
| | - Bénédicte F. Jordan
- Biomedical Magnetic Resonance Research Group, Louvain Drug Research Institute, Université Catholique de Louvain (UCLouvain), B-1200 Brussels, Belgium;
- Nuclear and Electron Spin Technologies (NEST) Platform, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), B-1200 Brussels, Belgium;
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18
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Lien EC, Vu N, Westermark AM, Danai LV, Lau AN, Gültekin Y, Kukurugya MA, Bennett BD, Vander Heiden MG. Effects of aging on glucose and lipid metabolism in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.17.572088. [PMID: 38187759 PMCID: PMC10769226 DOI: 10.1101/2023.12.17.572088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Aging is accompanied by multiple molecular changes that contribute to aging-associated pathologies, such as accumulation of cellular damage and mitochondrial dysfunction. Tissue metabolism can also change with age, in part because mitochondria are central to cellular metabolism. Moreover, the co-factor NAD+, which is reported to decline across multiple tissue types during aging, plays a central role in metabolic pathways such as glycolysis, the tricarboxylic acid cycle, and the oxidative synthesis of nucleotides, amino acids, and lipids. To further characterize how tissue metabolism changes with age, we intravenously infused [U-13C]-glucose into young and old C57BL/6J, WSB/EiJ, and Diversity Outbred mice to trace glucose fate into downstream metabolites within plasma, liver, gastrocnemius muscle, and brain tissues. We found that glucose incorporation into central carbon and amino acid metabolism was robust during healthy aging across these different strains of mice. We also observed that levels of NAD+, NADH, and the NAD+/NADH ratio were unchanged in these tissues with healthy aging. However, aging tissues, particularly brain, exhibited evidence of up-regulated fatty acid and sphingolipid metabolism reactions that regenerate NAD+ from NADH. Because mitochondrial respiration, a major source of NAD+ regeneration, is reported to decline with age, our data supports a model where NAD+-generating lipid metabolism reactions may buffer against changes in NAD+/NADH during healthy aging.
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Affiliation(s)
- Evan C. Lien
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ngoc Vu
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Anna M. Westermark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Laura V. Danai
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Allison N. Lau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yetiş Gültekin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Matthew G. Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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19
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Hattori Y, Andoh T, Kawabata S, Hu N, Michiue H, Nakamura H, Nomoto T, Suzuki M, Takata T, Tanaka H, Watanabe T, Ono K. Proposal of recommended experimental protocols for in vitro and in vivo evaluation methods of boron agents for neutron capture therapy. JOURNAL OF RADIATION RESEARCH 2023; 64:859-869. [PMID: 37717596 PMCID: PMC10665309 DOI: 10.1093/jrr/rrad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/19/2023] [Accepted: 08/19/2023] [Indexed: 09/19/2023]
Abstract
Recently, boron neutron capture therapy (BNCT) has been attracting attention as a minimally invasive cancer treatment. In 2020, the accelerator-based BNCT with L-BPA (Borofalan) as its D-sorbitol complex (Steboronine®) for head and neck cancers was approved by Pharmaceutical and Medical Devices Agency for the first time in the world. As accelerator-based neutron generation techniques are being developed in various countries, the development of novel tumor-selective boron agents is becoming increasingly important and desired. The Japanese Society of Neutron Capture Therapy believes it is necessary to propose standard evaluation protocols at each stage in the development of boron agents for BNCT. This review summarizes recommended experimental protocols for in vitro and in vivo evaluation methods of boron agents for BNCT based on our experience with L-BPA approval.
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Affiliation(s)
- Yoshihide Hattori
- Research Center for BNCT, Osaka Metropolitan University, 1-1 Gakuen-cho, Nakaku, Sakai 599-8531, Japan
| | - Tooru Andoh
- Laboratory of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Kobe 650-8586, Japan
| | - Shinji Kawabata
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki-shi, Osaka 569-8686, Japan
| | - Naonori Hu
- Kansai BNCT Medical Center, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki-shi, Osaka 569-8686, Japan
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun 590-0494 Japan
| | - Hiroyuki Michiue
- Neutron Therapy Research Center, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Takahiro Nomoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Minoru Suzuki
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun 590-0494 Japan
| | - Takushi Takata
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun 590-0494 Japan
| | - Hiroki Tanaka
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun 590-0494 Japan
| | - Tsubasa Watanabe
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun 590-0494 Japan
| | - Koji Ono
- Kansai BNCT Medical Center, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki-shi, Osaka 569-8686, Japan
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20
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Scott AJ, Correa LO, Edwards DM, Sun Y, Ravikumar V, Andren AC, Zhang L, Srinivasan S, Jairath N, Verbal K, Muraszko K, Sagher O, Carty SA, Hervey-Jumper S, Orringer D, Kim MM, Junck L, Umemura Y, Leung D, Venneti S, Camelo-Piragua S, Lawrence TS, Ippolito JE, Al-Holou WN, Chinnaiyan P, Heth J, Rao A, Lyssiotis CA, Wahl DR. Metabolomic Profiles of Human Glioma Inform Patient Survival. Antioxid Redox Signal 2023; 39:942-956. [PMID: 36852494 PMCID: PMC10655010 DOI: 10.1089/ars.2022.0085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
Aims: Targeting tumor metabolism may improve the outcomes for patients with glioblastoma (GBM). To further preclinical efforts targeting metabolism in GBM, we tested the hypothesis that brain tumors can be stratified into distinct metabolic groups with different patient outcomes. Therefore, to determine if tumor metabolites relate to patient survival, we profiled the metabolomes of human gliomas and correlated metabolic information with clinical data. Results: We found that isocitrate dehydrogenase-wildtype (IDHwt) GBMs are metabolically distinguishable from IDH mutated (IDHmut) astrocytomas and oligodendrogliomas. Survival of patients with IDHmut gliomas was expectedly more favorable than those with IDHwt GBM, and metabolic signatures can stratify IDHwt GBMs subtypes with varying prognoses. Patients whose GBMs were enriched in amino acids had improved survival, while those whose tumors were enriched for nucleotides, redox molecules, and lipid metabolites fared more poorly. These findings were recapitulated in validation cohorts using both metabolomic and transcriptomic data. Innovation: Our results suggest the existence of metabolic subtypes of GBM with differing prognoses, and further support the concept that metabolism may drive the aggressiveness of human gliomas. Conclusions: Our data show that metabolic signatures of human gliomas can inform patient survival. These findings may be used clinically to tailor novel metabolically targeted agents for GBM patients with different metabolic phenotypes. Antioxid. Redox Signal. 39, 942-956.
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Affiliation(s)
- Andrew J. Scott
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Luis O. Correa
- Department of Immunology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Donna M. Edwards
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yilun Sun
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Visweswaran Ravikumar
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony C. Andren
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Neil Jairath
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kait Verbal
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Karin Muraszko
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Oren Sagher
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Shannon A. Carty
- Department of Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Shawn Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Daniel Orringer
- Department of Neurosurgery, New York University Langone Health, New York, New York, USA
| | - Michelle M. Kim
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Larry Junck
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoshie Umemura
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Denise Leung
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sriram Venneti
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Theodore S. Lawrence
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph E. Ippolito
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Wajd N. Al-Holou
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Prakash Chinnaiyan
- Department of Radiation Oncology, Beaumont Health, Royal Oak, Michigan, USA
- Oakland University William Beaumont School of Medicine, Rochester, Michigan, USA
| | - Jason Heth
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Arvind Rao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Costas A. Lyssiotis
- Department of Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel R. Wahl
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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21
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Britt EC, Qing X, Votava JA, Lika J, Wagner A, Shen S, Arp NL, Khan H, Schieke SM, Fletcher CD, Huttenlocher A, Fan J. Activation induces shift in nutrient utilization that differentially impacts cell functions in human neutrophils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559385. [PMID: 37808750 PMCID: PMC10557599 DOI: 10.1101/2023.09.25.559385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Neutrophils - the first responders in innate immunity - perform a variety of effector functions associated with specific metabolic demand. To maintain fitness and support functions, neutrophils have been found to utilize extracellular glucose, intracellular glycogen, and other alternative substrates. However, the quantitative contribution of these nutrients under specific conditions and the relative dependence of various cell functions on specific nutrients remain unclear. Here, using ex vivo and in vivo isotopic tracing, we reveal that under resting condition, human peripheral blood neutrophils, in contrast to in vitro cultured human neutrophil-like cell lines, rely on glycogen as a major direct source of glycolysis and pentose phosphate pathway. Upon activation with a diversity of stimuli, neutrophils undergo a significant and often rapid nutrient preference shift, with glucose becoming the dominant metabolic source thanks to a multi-fold increase in glucose uptake mechanistically mediated by the phosphorylation and translocation of GLUT1. At the same time, cycling between gross glycogenesis and glycogenolysis is also substantially increased, while the net flux favors sustained or increased glycogen storage. The shift in nutrient utilization impacts neutrophil functions in a function-specific manner. The activation of oxidative burst specifically depends on the utilization of extracellular glucose rather than glycogen. In contrast, the release of neutrophil traps can be flexibly supported by either glucose or glycogen. Neutrophil migration and fungal control is promoted by the shift away from glycogen utilization. Together, these results quantitatively characterize fundamental features of neutrophil metabolism and elucidate how metabolic remodeling shapes neutrophil functions upon activation.
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Affiliation(s)
- Emily C. Britt
- Morgridge Institute for Research, Madison, WI, USA
- Department of Nutritional Sciences, University of Wisconsin–Madison, Madison, WI, USA
| | - Xin Qing
- Morgridge Institute for Research, Madison, WI, USA
- Department of Nutritional Sciences, University of Wisconsin–Madison, Madison, WI, USA
| | | | - Jorgo Lika
- Morgridge Institute for Research, Madison, WI, USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
| | - Andrew Wagner
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Simone Shen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicholas L. Arp
- Morgridge Institute for Research, Madison, WI, USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
| | - Hamidullah Khan
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA. Department of Dermatology, Georgetown University Medical Center and Washington DC VA Medical Center, Washington, D.C., USA
| | - Stefan M. Schieke
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA. Department of Dermatology, Georgetown University Medical Center and Washington DC VA Medical Center, Washington, D.C., USA
| | | | - Anna Huttenlocher
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jing Fan
- Morgridge Institute for Research, Madison, WI, USA
- Department of Nutritional Sciences, University of Wisconsin–Madison, Madison, WI, USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792
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22
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Scott AJ, Mittal A, Meghdadi B, Palavalasa S, Achreja A, O'Brien A, Kothari AU, Zhou W, Xu J, Lin A, Wilder-Romans K, Edwards DM, Wu Z, Feng J, Andren AC, Zhang L, Tarnal V, Redic KA, Qi N, Fischer J, Yang E, Regan MS, Stopka SA, Baquer G, Lawrence TS, Venneti S, Agar NYR, Lyssiotis CA, Al-Holou WN, Nagrath D, Wahl DR. Rewiring of cortical glucose metabolism fuels human brain cancer growth. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.24.23297489. [PMID: 37961582 PMCID: PMC10635194 DOI: 10.1101/2023.10.24.23297489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The brain avidly consumes glucose to fuel neurophysiology. Cancers of the brain, such as glioblastoma (GBM), lose aspects of normal biology and gain the ability to proliferate and invade healthy tissue. How brain cancers rewire glucose utilization to fuel these processes is poorly understood. Here we perform infusions of 13 C-labeled glucose into patients and mice with brain cancer to define the metabolic fates of glucose-derived carbon in tumor and cortex. By combining these measurements with quantitative metabolic flux analysis, we find that human cortex funnels glucose-derived carbons towards physiologic processes including TCA cycle oxidation and neurotransmitter synthesis. In contrast, brain cancers downregulate these physiologic processes, scavenge alternative carbon sources from the environment, and instead use glucose-derived carbons to produce molecules needed for proliferation and invasion. Targeting this metabolic rewiring in mice through dietary modulation selectively alters GBM metabolism and slows tumor growth. Significance This study is the first to directly measure biosynthetic flux in both glioma and cortical tissue in human brain cancer patients. Brain tumors rewire glucose carbon utilization away from oxidation and neurotransmitter production towards biosynthesis to fuel growth. Blocking these metabolic adaptations with dietary interventions slows brain cancer growth with minimal effects on cortical metabolism.
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23
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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24
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VanSant-Webb C, Low HK, Kuramoto J, Stanley CE, Qiang H, Su A, Ross AN, Cooper CG, Cox JE, Summers SA, Evason KJ, Ducker GS. Phospholipid isotope tracing reveals β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.12.562134. [PMID: 37904922 PMCID: PMC10614757 DOI: 10.1101/2023.10.12.562134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Background and Aims Activating mutations in the CTNNB1 gene encoding β-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). HCC with CTNNB1 mutations show profound alterations in lipid metabolism including increases in fatty acid oxidation and transformation of the phospholipidome, but it is unclear how these changes arise and whether they contribute to the oncogenic program in HCC. Methods We employed untargeted lipidomics and targeted isotope tracing to quantify phospholipid production fluxes in an inducible human liver cell line expressing mutant β-catenin, as well as in transgenic zebrafish with activated β-catenin-driven HCC. Results In both models, activated β-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid flux analysis in human cells revealed a large reduction in phosphatidylcholine (PC) production rates as assayed by choline tracer incorporation. We developed isotope tracing lipid flux analysis for zebrafish and observed similar reductions in phosphatidylcholine synthesis flux accomplished by sex-specific mechanisms. Conclusions The integration of isotope tracing with lipid abundances highlights specific lipid class transformations downstream of β-catenin signaling in HCC and suggests future HCC-specific lipid metabolic targets.
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Affiliation(s)
- Chad VanSant-Webb
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Hayden K Low
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Junko Kuramoto
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Claire E Stanley
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Hantao Qiang
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Audrey Su
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Alexis N Ross
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Chad G Cooper
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, University of Utah College of Health. Salt Lake City, UT 84112 USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
- Huntsman Cancer Institute, University of Utah. Salt Lake City UT, 84112 USA
| | - Gregory S Ducker
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
- Huntsman Cancer Institute, University of Utah. Salt Lake City UT, 84112 USA
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25
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Cai F, Bezwada D, Cai L, Mahar R, Wu Z, Chang MC, Pachnis P, Yang C, Kelekar S, Gu W, Brooks B, Ko B, Vu HS, Mathews TP, Zacharias LG, Martin-Sandoval M, Do D, Oaxaca KC, Jin ES, Margulis V, Malloy CR, Merritt ME, DeBerardinis RJ. Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples. Cell Metab 2023; 35:1830-1843.e5. [PMID: 37611583 PMCID: PMC10732579 DOI: 10.1016/j.cmet.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023]
Abstract
Stable isotopes are powerful tools to assess metabolism. 13C labeling is detected using nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS). MS has excellent sensitivity but generally cannot discriminate among different 13C positions (isotopomers), whereas NMR is less sensitive but reports some isotopomers. Here, we develop an MS method that reports all 16 aspartate and 32 glutamate isotopomers while requiring less than 1% of the sample used for NMR. This method discriminates between pathways that result in the same number of 13C labels in aspartate and glutamate, providing enhanced specificity over conventional MS. We demonstrate regional metabolic heterogeneity within human tumors, document the impact of fumarate hydratase (FH) deficiency in human renal cancers, and investigate the contributions of tricarboxylic acid (TCA) cycle turnover and CO2 recycling to isotope labeling in vivo. This method can accompany NMR or standard MS to provide outstanding sensitivity in isotope-labeling experiments, particularly in vivo.
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Affiliation(s)
- Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Divya Bezwada
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ling Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rohit Mahar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32603, USA
| | - Zheng Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mario C Chang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32603, USA
| | - Panayotis Pachnis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chendong Yang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sherwin Kelekar
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bailey Brooks
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bookyung Ko
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Misty Martin-Sandoval
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duyen Do
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - K Celeste Oaxaca
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eunsook S Jin
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Veterans Affairs North Texas Healthcare System, Dallas, TX 75216, USA
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32603, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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26
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MacPherson S, Duncan KD, Goodlett DR, Lum JJ. Strategies for uncovering stable isotope tracing patterns between cell populations. Curr Opin Biotechnol 2023; 83:102991. [PMID: 37619527 DOI: 10.1016/j.copbio.2023.102991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023]
Abstract
Despite practical complexities, isotope tracing studies in humans are becoming increasingly feasible. However, several technological challenges need to be addressed in order to take full advantage of human tracing studies. First, absolute metabolic flux measurements in mice are not so easily applied to human models, given that tissue resection is restricted to a single surgical time point. Second, isotope tracing has yet to be employed to detect metabolic differences between cells types in vivo. Here, we discuss the current models and propose an alternative, liquid tumor environment, that could overcome these limitations. Furthermore, we highlight current strategies used to maintain isotopolog enrichment following cell isolation techniques to facilitate cell-type-specific analysis.
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Affiliation(s)
- Sarah MacPherson
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC, Canada
| | - Kyle D Duncan
- Department of Chemistry, Vancouver Island University, Nanaimo, BC, Canada; Department of Chemistry, University of Victoria, Victoria, BC, Canada
| | - David R Goodlett
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Julian J Lum
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
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27
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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28
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Huang Y, Mohanty V, Dede M, Tsai K, Daher M, Li L, Rezvani K, Chen K. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux. Nat Commun 2023; 14:4883. [PMID: 37573313 PMCID: PMC10423258 DOI: 10.1038/s41467-023-40457-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/26/2023] [Indexed: 08/14/2023] Open
Abstract
Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements. Computational methods such as flux balance analysis (FBA) have been developed to estimate metabolic flux from bulk RNA-seq data and can potentially be extended to single-cell RNA-seq (scRNA-seq) data. However, it is unclear how reliable current methods are, particularly in TME characterization. Here, we present a computational framework METAFlux (METAbolic Flux balance analysis) to infer metabolic fluxes from bulk or single-cell transcriptomic data. Large-scale experiments using cell-lines, the cancer genome atlas (TCGA), and scRNA-seq data obtained from diverse cancer and immunotherapeutic contexts, including CAR-NK cell therapy, have validated METAFlux's capability to characterize metabolic heterogeneity and metabolic interaction amongst cell types.
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Affiliation(s)
- Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Biostatistics & Data Science, School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, 77030, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kyle Tsai
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Li Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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29
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El Shami M, Savani MR, Gattie LC, Smith B, Hicks WH, Rich JN, Richardson TE, McBrayer SK, Abdullah KG. Human plasma-like medium facilitates metabolic tracing and enables upregulation of immune signaling pathways in glioblastoma explants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542774. [PMID: 37398280 PMCID: PMC10312566 DOI: 10.1101/2023.05.29.542774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Purpose Metabolism within the tumor microenvironment (TME) represents an increasing area of interest to understand glioma initiation and progression. Stable isotope tracing is a technique critical to the study of tumor metabolism. Cell culture models of this disease are not routinely cultured under physiologically relevant nutrient conditions and do not retain cellular heterogeneity present in the parental TME. Moreover, in vivo, stable isotope tracing in intracranial glioma xenografts, the gold standard for metabolic investigation, is time consuming and technically challenging. To provide insights into glioma metabolism in the presence of an intact TME, we performed stable isotope tracing analysis of patient-derived, heterocellular Surgically eXplanted Organoid (SXO) glioma models in human plasma-like medium (HPLM). Methods Glioma SXOs were established and cultured in conventional media or transitioned to HPLM. We evaluated SXO cytoarchitecture and histology, then performed spatial transcriptomic profiling to identify cellular populations and differential gene expression patterns. We performed stable isotope tracing with 15N2-glutamine to evaluate intracellular metabolite labeling patterns. Results Glioma SXOs cultured in HPLM retain cytoarchitecture and cellular constituents. Immune cells in HPLM-cultured SXOs demonstrated increased transcription of immune-related signatures, including innate immune, adaptive immune, and cytokine signaling programs. 15N isotope enrichment from glutamine was observed in metabolites from diverse pathways, and labeling patterns were stable over time. Conclusion To enable ex vivo, tractable investigations of whole tumor metabolism, we developed an approach to conduct stable isotope tracing in glioma SXOs cultured under physiologically relevant nutrient conditions. Under these conditions, SXOs maintained viability, composition, and metabolic activity while exhibiting increased immune-related transcriptional programs.
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Affiliation(s)
- Mohamad El Shami
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Milan R Savani
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - Lauren C Gattie
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Bailey Smith
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - William H Hicks
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Jeremy N Rich
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Timothy E Richardson
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Samuel K McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75235, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
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30
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Wu Z, Bezwada D, Harris RC, Pan C, Nguyen PT, Faubert B, Cai L, Cai F, Vu HS, Chen H, Sandoval MM, Do D, Gu W, Zhang Y, Ko B, Brooks B, Kelekar S, Zhang Y, Zacharias LG, Oaxaca KC, Mathews TP, Garcia-Bermudez J, Ni M, DeBerardinis RJ. Electron transport chain inhibition increases cellular dependence on purine transport and salvage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540429. [PMID: 37214913 PMCID: PMC10197673 DOI: 10.1101/2023.05.11.540429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cancer cells reprogram their metabolism to support cell growth and proliferation in harsh environments. While many studies have documented the importance of mitochondrial oxidative phosphorylation (OXPHOS) in tumor growth, some cancer cells experience conditions of reduced OXPHOS in vivo and induce alternative metabolic pathways to compensate. To assess how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts and plasma from patients with inborn errors of mitochondrial metabolism, and in cancer cells subjected to inhibition of the electron transport chain (ETC). All these analyses revealed extensive perturbations in purine-related metabolites; in non-small cell lung cancer (NSCLC) cells, ETC blockade led to purine metabolite accumulation arising from a reduced cytosolic NAD + /NADH ratio (NADH reductive stress). Stable isotope tracing demonstrated that ETC deficiency suppressed de novo purine nucleotide synthesis while enhancing purine salvage. Analysis of NSCLC patients infused with [U- 13 C]glucose revealed that tumors with markers of low oxidative mitochondrial metabolism exhibited high expression of the purine salvage enzyme HPRT1 and abundant levels of the HPRT1 product inosine monophosphate (IMP). ETC blockade also induced production of ribose-5' phosphate (R5P) by the pentose phosphate pathway (PPP) and import of purine nucleobases. Blocking either HPRT1 or nucleoside transporters sensitized cancer cells to ETC inhibition, and overexpressing nucleoside transporters was sufficient to drive growth of NSCLC xenografts. Collectively, this study mechanistically delineates how cells compensate for suppressed purine metabolism in response to ETC blockade, and uncovers a new metabolic vulnerability in tumors experiencing NADH excess.
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31
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Clasen F, Nunes PM, Bidkhori G, Bah N, Boeing S, Shoaie S, Anastasiou D. Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer. iScience 2023; 26:106040. [PMID: 36844450 PMCID: PMC9947310 DOI: 10.1016/j.isci.2023.106040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/08/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Dietary nutrient availability and gene expression, together, influence tissue metabolic activity. Here, we explore whether altering dietary nutrient composition in the context of mouse liver cancer suffices to overcome chronic gene expression changes that arise from tumorigenesis and western-style diet (WD). We construct a mouse genome-scale metabolic model and estimate metabolic fluxes in liver tumors and non-tumoral tissue after computationally varying the composition of input diet. This approach, called Systematic Diet Composition Swap (SyDiCoS), revealed that, compared to a control diet, WD increases production of glycerol and succinate irrespective of specific tissue gene expression patterns. Conversely, differences in fatty acid utilization pathways between tumor and non-tumor liver are amplified with WD by both dietary carbohydrates and lipids together. Our data suggest that combined dietary component modifications may be required to normalize the distinctive metabolic patterns that underlie selective targeting of tumor metabolism.
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Affiliation(s)
- Frederick Clasen
- Cancer Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE1 9RT, UK
| | - Patrícia M. Nunes
- Cancer Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gholamreza Bidkhori
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE1 9RT, UK
| | - Nourdine Bah
- Bioinformatics and Biostatistics Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE1 9RT, UK
- Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
| | - Dimitrios Anastasiou
- Cancer Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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32
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Yu D, Zhou L, Liu X, Xu G. Stable isotope-resolved metabolomics based on mass spectrometry: Methods and their applications. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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33
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Chen Z, Bordieanu B, Kesavan R, Lesner NP, Venigalla SSK, Shelton SD, DeBerardinis RJ, Mishra P. Lactate metabolism is essential in early-onset mitochondrial myopathy. SCIENCE ADVANCES 2023; 9:eadd3216. [PMID: 36598990 PMCID: PMC9812384 DOI: 10.1126/sciadv.add3216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Myopathies secondary to mitochondrial electron transport chain (ETC) dysfunction can result in devastating disease. While the consequences of ETC defects have been extensively studied in culture, little in vivo data are available. Using a mouse model of severe, early-onset mitochondrial myopathy, we characterized the proteomic, transcriptomic, and metabolic characteristics of disease progression. Unexpectedly, ETC dysfunction in muscle results in reduced expression of glycolytic enzymes in our animal model and patient muscle biopsies. The decrease in glycolysis was mediated by loss of constitutive Hif1α signaling, down-regulation of the purine nucleotide cycle enzyme AMPD1, and activation of AMPK. In vivo isotope tracing experiments indicated that myopathic muscle relies on lactate import to supply central carbon metabolites. Inhibition of lactate import reduced steady-state levels of tricarboxylic acid cycle intermediates and compromised the life span of myopathic mice. These data indicate an unexpected mode of metabolic reprogramming in severe mitochondrial myopathy that regulates disease progression.
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Affiliation(s)
- Zhenkang Chen
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bogdan Bordieanu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rushendhiran Kesavan
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas P. Lesner
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Siva Sai Krishna Venigalla
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D. Shelton
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J. DeBerardinis
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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34
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Lackner M, Neef SK, Winter S, Beer-Hammer S, Nürnberg B, Schwab M, Hofmann U, Haag M. Untargeted stable isotope-resolved metabolomics to assess the effect of PI3Kβ inhibition on metabolic pathway activities in a PTEN null breast cancer cell line. Front Mol Biosci 2022; 9:1004602. [PMID: 36310598 PMCID: PMC9614656 DOI: 10.3389/fmolb.2022.1004602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
The combination of high-resolution LC-MS untargeted metabolomics with stable isotope-resolved tracing is a promising approach for the global exploration of metabolic pathway activities. In our established workflow we combine targeted isotopologue feature extraction with the non-targeted X13CMS routine. Metabolites, detected by X13CMS as differentially labeled between two biological conditions are subsequently integrated into the original targeted library. This strategy enables monitoring of changes in known pathways as well as the discovery of hitherto unknown metabolic alterations. Here, we demonstrate this workflow in a PTEN (phosphatase and tensin homolog) null breast cancer cell line (MDA-MB-468) exploring metabolic pathway activities in the absence and presence of the selective PI3Kβ inhibitor AZD8186. Cells were fed with [U-13C] glucose and treated for 1, 3, 6, and 24 h with 0.5 µM AZD8186 or vehicle, extracted by an optimized sample preparation protocol and analyzed by LC-QTOF-MS. Untargeted differential tracing of labels revealed 286 isotope-enriched features that were significantly altered between control and treatment conditions, of which 19 features could be attributed to known compounds from targeted pathways. Other 11 features were unambiguously identified based on data-dependent MS/MS spectra and reference substances. Notably, only a minority of the significantly altered features (11 and 16, respectively) were identified when preprocessing of the same data set (treatment vs. control in 24 h unlabeled samples) was performed with tools commonly used for label-free (i.e. w/o isotopic tracer) non-targeted metabolomics experiments (Profinder´s batch recursive feature extraction and XCMS). The structurally identified metabolites were integrated into the existing targeted isotopologue feature extraction workflow to enable natural abundance correction, evaluation of assay performance and assessment of drug-induced changes in pathway activities. Label incorporation was highly reproducible for the majority of isotopologues in technical replicates with a RSD below 10%. Furthermore, inter-day repeatability of a second label experiment showed strong correlation (Pearson R2 > 0.99) between tracer incorporation on different days. Finally, we could identify prominent pathway activity alterations upon PI3Kβ inhibition. Besides pathways in central metabolism, known to be changed our workflow revealed additional pathways, like pyrimidine metabolism or hexosamine pathway. All pathways identified represent key metabolic processes associated with cancer metabolism and therapy.
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Affiliation(s)
- Marcel Lackner
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Sylvia K. Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Sandra Beer-Hammer
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute for Experimental and Clinical Pharmacology and Pharmacogenomics, Interfaculty Center for Pharmacogenomics and Drug Research (ICePhA), University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
| | - Bernd Nürnberg
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute for Experimental and Clinical Pharmacology and Pharmacogenomics, Interfaculty Center for Pharmacogenomics and Drug Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
- Departments of Clinical Pharmacology and of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- *Correspondence: Mathias Haag,
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35
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Lesner NP, Wang X, Chen Z, Frank A, Menezes CJ, House S, Shelton SD, Lemoff A, McFadden DG, Wansapura J, DeBerardinis RJ, Mishra P. Differential requirements for mitochondrial electron transport chain components in the adult murine liver. eLife 2022; 11:e80919. [PMID: 36154948 PMCID: PMC9648974 DOI: 10.7554/elife.80919] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial electron transport chain (ETC) dysfunction due to mutations in the nuclear or mitochondrial genome is a common cause of metabolic disease in humans and displays striking tissue specificity depending on the affected gene. The mechanisms underlying tissue-specific phenotypes are not understood. Complex I (cI) is classically considered the entry point for electrons into the ETC, and in vitro experiments indicate that cI is required for basal respiration and maintenance of the NAD+/NADH ratio, an indicator of cellular redox status. This finding has largely not been tested in vivo. Here, we report that mitochondrial complex I is dispensable for homeostasis of the adult mouse liver; animals with hepatocyte-specific loss of cI function display no overt phenotypes or signs of liver damage, and maintain liver function, redox and oxygen status. Further analysis of cI-deficient livers did not reveal significant proteomic or metabolic changes, indicating little to no compensation is required in the setting of complex I loss. In contrast, complex IV (cIV) dysfunction in adult hepatocytes results in decreased liver function, impaired oxygen handling, steatosis, and liver damage, accompanied by significant metabolomic and proteomic perturbations. Our results support a model whereby complex I loss is tolerated in the mouse liver because hepatocytes use alternative electron donors to fuel the mitochondrial ETC.
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Affiliation(s)
- Nicholas P Lesner
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Xun Wang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Zhenkang Chen
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Anderson Frank
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - Cameron J Menezes
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sara House
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Spencer D Shelton
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - David G McFadden
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - Janaka Wansapura
- Advanced Imaging Research Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Prashant Mishra
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
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36
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Pal S, Kaplan JP, Nguyen H, Stopka SA, Savani MR, Regan MS, Nguyen QD, Jones KL, Moreau LA, Peng J, Dipiazza MG, Perciaccante AJ, Zhu X, Hunsel BR, Liu KX, Alexandrescu S, Drissi R, Filbin MG, McBrayer SK, Agar NYR, Chowdhury D, Haas-Kogan DA. A druggable addiction to de novo pyrimidine biosynthesis in diffuse midline glioma. Cancer Cell 2022; 40:957-972.e10. [PMID: 35985342 PMCID: PMC9575661 DOI: 10.1016/j.ccell.2022.07.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 12/18/2022]
Abstract
Diffuse midline glioma (DMG) is a uniformly fatal pediatric cancer driven by oncohistones that do not readily lend themselves to drug development. To identify druggable targets for DMG, we conducted a genome-wide CRISPR screen that reveals a DMG selective dependency on the de novo pathway for pyrimidine biosynthesis. This metabolic vulnerability reflects an elevated rate of uridine/uracil degradation that depletes DMG cells of substrates for the alternate salvage pyrimidine biosynthesis pathway. A clinical stage inhibitor of DHODH (rate-limiting enzyme in the de novo pathway) diminishes uridine-5'-phosphate (UMP) pools, generates DNA damage, and induces apoptosis through suppression of replication forks-an "on-target" effect, as shown by uridine rescue. Matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy imaging demonstrates that this DHODH inhibitor (BAY2402234) accumulates in the brain at therapeutically relevant concentrations, suppresses de novo pyrimidine biosynthesis in vivo, and prolongs survival of mice bearing intracranial DMG xenografts, highlighting BAY2402234 as a promising therapy against DMGs.
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Affiliation(s)
- Sharmistha Pal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jakub P Kaplan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Kristen L Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Lisa A Moreau
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingyu Peng
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marina G Dipiazza
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew J Perciaccante
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Xiaoting Zhu
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Bradley R Hunsel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kevin X Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Sanda Alexandrescu
- Department of Pathology, Harvard Medical School Boston, Boston Children's Hospital, 300 Longwood Avenue, Bader 104, Boston, MA 02115, USA
| | - Rachid Drissi
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daphne A Haas-Kogan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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37
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Shi DD, Savani MR, Levitt MM, Wang AC, Endress JE, Bird CE, Buehler J, Stopka SA, Regan MS, Lin YF, Puliyappadamba VT, Gao W, Khanal J, Evans L, Lee JH, Guo L, Xiao Y, Xu M, Huang B, Jennings RB, Bonal DM, Martin-Sandoval MS, Dang T, Gattie LC, Cameron AB, Lee S, Asara JM, Kornblum HI, Mak TW, Looper RE, Nguyen QD, Signoretti S, Gradl S, Sutter A, Jeffers M, Janzer A, Lehrman MA, Zacharias LG, Mathews TP, Losman JA, Richardson TE, Cahill DP, DeBerardinis RJ, Ligon KL, Xu L, Ly P, Agar NYR, Abdullah KG, Harris IS, Kaelin WG, McBrayer SK. De novo pyrimidine synthesis is a targetable vulnerability in IDH mutant glioma. Cancer Cell 2022; 40:939-956.e16. [PMID: 35985343 PMCID: PMC9515386 DOI: 10.1016/j.ccell.2022.07.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022]
Abstract
Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they seem to be less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1-mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH-mutant gliomas. Mechanistically, this reflects an obligate dependence of glioma cells on the de novo pyrimidine synthesis pathway and mutant IDH's ability to sensitize to DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.
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Affiliation(s)
- Diana D Shi
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA 02215, USA; Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael M Levitt
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam C Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer E Endress
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Cylaina E Bird
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Joseph Buehler
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Fen Lin
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vinesh T Puliyappadamba
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhua Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Januka Khanal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Laura Evans
- Bayer HealthCare Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Joyce H Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Xiao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bofu Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Rebecca B Jennings
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Misty S Martin-Sandoval
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tammie Dang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren C Gattie
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Amy B Cameron
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Sungwoo Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harley I Kornblum
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Behavioral Sciences, and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2M9, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ryan E Looper
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Gradl
- Bayer AG, Muellerstrasse 178, 13353 Berlin, Germany
| | | | - Michael Jeffers
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ 07981, USA
| | | | - Mark A Lehrman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Timothy E Richardson
- Department of Pathology, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
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Salvador AF, Shyu CR, Parks EJ. Measurement of lipid flux to advance translational research: evolution of classic methods to the future of precision health. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1348-1353. [PMID: 36075949 PMCID: PMC9534914 DOI: 10.1038/s12276-022-00838-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 02/08/2023]
Abstract
Over the past 70 years, the study of lipid metabolism has led to important discoveries in identifying the underlying mechanisms of chronic diseases. Advances in the use of stable isotopes and mass spectrometry in humans have expanded our knowledge of target molecules that contribute to pathologies and lipid metabolic pathways. These advances have been leveraged within two research paths, leading to the ability (1) to quantitate lipid flux to understand the fundamentals of human physiology and pathology and (2) to perform untargeted analyses of human blood and tissues derived from a single timepoint to identify lipidomic patterns that predict disease. This review describes the physiological and analytical parameters that influence these measurements and how these issues will propel the coming together of the two fields of metabolic tracing and lipidomics. The potential of data science to advance these fields is also discussed. Future developments are needed to increase the precision of lipid measurements in human samples, leading to discoveries in how individuals vary in their production, storage, and use of lipids. New techniques are critical to support clinical strategies to prevent disease and to identify mechanisms by which treatments confer health benefits with the overall goal of reducing the burden of human disease. Personalized tracking of how lipid (fat) metabolism changes over time could lead to improvements in the diagnosis and treatment of several diseases. Elizabeth Parks and colleagues from the University of Missouri, Columbia, USA, discuss the ways in which researchers use stable isotope labeling to monitor the kinetics of fatty acids and other lipids in the body. Usually, lipid quantities are measured only at a single timepoint, however the tracking of lipid turnover over time provides further diagnostic information. Aided by new techniques such as high-throughput mass spectrometry and machine learning, researchers are now able to continuously map total lipid contents in individual patients. The transition of measurements of lipid flux from the research laboratory to the doctor’s office will likely play a role in a new era of precision medicine.
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Affiliation(s)
- Amadeo F Salvador
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, 65212, USA.,Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.,Department of Electrical Engineering and Computer Science, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Chi-Ren Shyu
- Department of Electrical Engineering and Computer Science, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Elizabeth J Parks
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, 65212, USA. .,Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
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Freeman BA, Jaro S, Park T, Keene S, Tansey W, Reznik E. MIRTH: Metabolite Imputation via Rank-Transformation and Harmonization. Genome Biol 2022; 23:184. [PMID: 36050754 PMCID: PMC9438248 DOI: 10.1186/s13059-022-02738-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/23/2022] [Indexed: 12/12/2022] Open
Abstract
Out of the thousands of metabolites in a given specimen, most metabolomics experiments measure only hundreds, with poor overlap across experimental platforms. Here, we describe Metabolite Imputation via Rank-Transformation and Harmonization (MIRTH), a method to impute unmeasured metabolite abundances by jointly modeling metabolite covariation across datasets which have heterogeneous coverage of metabolite features. MIRTH successfully recovers masked metabolite abundances both within single datasets and across multiple, independently-profiled datasets. MIRTH demonstrates that latent information about otherwise unmeasured metabolites is embedded within existing metabolomics data, and can be used to generate novel hypotheses and simplify existing metabolomic workflows.
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Affiliation(s)
- Benjamin A Freeman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Sophie Jaro
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA.,Electrical Engineering Department, The Cooper Union, New York, USA
| | - Tricia Park
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Sam Keene
- Electrical Engineering Department, The Cooper Union, New York, USA
| | - Wesley Tansey
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Ed Reznik
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA.
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40
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Bae H, Lam K, Jang C. Metabolic flux between organs measured by arteriovenous metabolite gradients. Exp Mol Med 2022; 54:1354-1366. [PMID: 36075951 PMCID: PMC9534916 DOI: 10.1038/s12276-022-00803-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 12/15/2022] Open
Abstract
Mammalian organs convert dietary nutrients into circulating metabolites and share them to maintain whole-body metabolic homeostasis. While the concentrations of circulating metabolites have been frequently measured in a variety of pathophysiological conditions, the exchange flux of circulating metabolites between organs is not easily measurable due to technical difficulties. Isotope tracing is useful for measuring such fluxes for a metabolite of interest, but the shuffling of isotopic atoms between metabolites requires mathematical modeling. Arteriovenous metabolite gradient measurements can complement isotope tracing to infer organ-specific net fluxes of many metabolites simultaneously. Here, we review the historical development of arteriovenous measurements and discuss their advantages and limitations with key example studies that have revealed metabolite exchange flux between organs in diverse pathophysiological contexts.
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Affiliation(s)
- Hosung Bae
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Katie Lam
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
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41
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Chang XL, Chen L, Liu B, Yang ST, Wang H, Cao A, Chen C. Stable isotope labeling of nanomaterials for biosafety evaluation and drug development. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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42
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Franco CN, Noe MM, Albrecht LV. Metabolism and Endocrine Disorders: What Wnt Wrong? Front Endocrinol (Lausanne) 2022; 13:887037. [PMID: 35600583 PMCID: PMC9120667 DOI: 10.3389/fendo.2022.887037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
A fundamental question in cell biology underlies how nutrients are regenerated to maintain and renew tissues. Physiologically, the canonical Wnt signaling is a vital pathway for cell growth, tissue remodeling, and organ formation; pathologically, Wnt signaling contributes to the development of myriad human diseases such as cancer. Despite being the focus of intense research, how Wnt intersects with the metabolic networks to promote tissue growth and remodeling has remained mysterious. Our understanding of metabolism has been revolutionized by technological advances in the fields of chemical biology, metabolomics, and live microscopy that have now made it possible to visualize and manipulate metabolism in living cells and tissues. The application of these toolsets to innovative model systems have propelled the Wnt field into new realms at the forefront answering the most pressing paradigms of cell metabolism in health and disease states. Elucidating the basis of Wnt signaling and metabolism in a cell-type and tissue-specific manner will provide a powerful base of knowledge for both basic biomedical fields and clinician scientists, and has the promise to generate new, transformative therapies in disease and even processes of aging.
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Affiliation(s)
- Carolina N. Franco
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California Irvine, Irvine, CA, United States
| | - May M. Noe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California Irvine, Irvine, CA, United States
| | - Lauren V. Albrecht
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California Irvine, Irvine, CA, United States
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, United States
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Abstract
Metabolism has been studied mainly in cultured cells or at the level of whole tissues or whole organisms in vivo. Consequently, our understanding of metabolic heterogeneity among cells within tissues is limited, particularly when it comes to rare cells with biologically distinct properties, such as stem cells. Stem cell function, tissue regeneration and cancer suppression are all metabolically regulated, although it is not yet clear whether there are metabolic mechanisms unique to stem cells that regulate their activity and function. Recent work has, however, provided evidence that stem cells do have a metabolic signature that is distinct from that of restricted progenitors and that metabolic changes influence tissue homeostasis and regeneration. Stem cell maintenance throughout life in many tissues depends upon minimizing anabolic pathway activation and cell division. Consequently, stem cell activation by tissue injury is associated with changes in mitochondrial function, lysosome activity and lipid metabolism, potentially at the cost of eroding self-renewal potential. Stem cell metabolism is also regulated by the environment: stem cells metabolically interact with other cells in their niches and are able to sense and adapt to dietary changes. The accelerating understanding of stem cell metabolism is revealing new aspects of tissue homeostasis with the potential to promote tissue regeneration and cancer suppression.
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44
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Alarcon-Barrera JC, Kostidis S, Ondo-Mendez A, Giera M. Recent advances in metabolomics analysis for early drug development. Drug Discov Today 2022; 27:1763-1773. [PMID: 35218927 DOI: 10.1016/j.drudis.2022.02.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022]
Abstract
The pharmaceutical industry adapted proteomics and other 'omics technologies for drug research early following their initial introduction. Although metabolomics lacked behind in this development, it has now become an accepted and widely applied approach in early drug development. Over the past few decades, metabolomics has evolved from a pure exploratory tool to a more mature and quantitative biochemical technology. Several metabolomics-based platforms are now applied during the early phases of drug discovery. Metabolomics analysis assists in the definition of the physiological response and target engagement (TE) markers as well as elucidation of the mode of action (MoA) of drug candidates under investigation. In this review, we highlight recent examples and novel developments of metabolomics analyses applied during early drug development.
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Affiliation(s)
- Juan Carlos Alarcon-Barrera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands; Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Alejandro Ondo-Mendez
- Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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