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Kirchmair A, Nemati N, Lamberti G, Trefny M, Krogsdam A, Siller A, Hörtnagl P, Schumacher P, Sopper S, Sandbichler A, Zippelius A, Ghesquière B, Trajanoski Z. 13C tracer analysis reveals the landscape of metabolic checkpoints in human CD8 + T cell differentiation and exhaustion. Front Immunol 2023; 14:1267816. [PMID: 37928527 PMCID: PMC10620935 DOI: 10.3389/fimmu.2023.1267816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Naïve T cells remain in an actively maintained state of quiescence until activation by antigenic signals, upon which they start to proliferate and generate effector cells to initiate a functional immune response. Metabolic reprogramming is essential to meet the biosynthetic demands of the differentiation process, and failure to do so can promote the development of hypofunctional exhausted T cells. Methods Here we used 13C metabolomics and transcriptomics to study the metabolism of CD8+ T cells in their complete course of differentiation from naïve over stem-like memory to effector cells and in exhaustion-inducing conditions. Results The quiescence of naïve T cells was evident in a profound suppression of glucose oxidation and a decreased expression of ENO1, downstream of which no glycolytic flux was detectable. Moreover, TCA cycle activity was low in naïve T cells and associated with a downregulation of SDH subunits. Upon stimulation and exit from quiescence, the initiation of cell growth and proliferation was accompanied by differential expression of metabolic enzymes and metabolic reprogramming towards aerobic glycolysis with high rates of nutrient uptake, respiration and lactate production. High flux in anabolic pathways imposed a strain on NADH homeostasis, which coincided with engagement of the proline cycle for mitochondrial redox shuttling. With acquisition of effector functions, cells increasingly relied on glycolysis as opposed to oxidative phosphorylation, which was, however, not linked to changes in mitochondrial abundance. In exhaustion, decreased effector function concurred with a reduction in mitochondrial metabolism, glycolysis and amino acid import, and an upregulation of quiescence-associated genes, TXNIP and KLF2, and the T cell suppressive metabolites succinate and itaconate. Discussion Overall, these results identify multiple metabolic features that regulate quiescence, proliferation and effector function, but also exhaustion of CD8+ T cells during differentiation. Thus, targeting these metabolic checkpoints may be a promising therapeutic strategy for both prevention of exhaustion and promotion of stemness of anti-tumor T cells.
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Affiliation(s)
- Alexander Kirchmair
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Niloofar Nemati
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Giorgia Lamberti
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Marcel Trefny
- Department of Biomedicine, Cancer Immunology, University and University Hospital of Basel, Basel, Switzerland
| | - Anne Krogsdam
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- NGS Core Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anita Siller
- Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria
| | - Paul Hörtnagl
- Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria
| | - Petra Schumacher
- Core Facility FACS Sorting, University Clinic for Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Core Facility FACS Sorting, University Clinic for Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Alfred Zippelius
- Department of Biomedicine, Cancer Immunology, University and University Hospital of Basel, Basel, Switzerland
| | - Bart Ghesquière
- Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Metabolomics Core Facility Leuven, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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Guo K, Glatter T, Paczia N, Liesack W. Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress. Appl Environ Microbiol 2023; 89:e0011323. [PMID: 37184406 PMCID: PMC10305061 DOI: 10.1128/aem.00113-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
Methylocystis spp. are known to have a low salt tolerance (≤1.0% NaCl). Therefore, we tested various amino acids and other well-known osmolytes for their potential to act as an osmoprotectant under otherwise growth-inhibiting NaCl conditions. Adjustment of the medium to 10 mM asparagine had the greatest osmoprotective effect under severe salinity (1.50% NaCl), leading to partial growth recovery of strain SC2. The intracellular concentration of asparagine increased to 264 ± 57 mM, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine specifically induced major proteome rearrangements related to the KEGG level 3 categories of "methane metabolism," "pyruvate metabolism," "amino acid turnover," and "cell division." In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exometabolome and the 13C-labeling pattern suggest that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in central metabolic pathway activity and the sizes of free amino acid pools. In consequence, asparagine acted, in part, as a carbon source for the growth recovery of strain SC2 under severe salinity. IMPORTANCE Methylocystis spp. play a major role in reducing methane emissions into the atmosphere from methanogenic wetlands. In addition, they contribute to atmospheric methane oxidation in upland soils. Although these bacteria are typical soil inhabitants, Methylocystis spp. are thought to have limited capacity to acclimate to salt stress. This called for a thorough study into potential osmoprotectants, which revealed asparagine as the most promising candidate. Intriguingly, asparagine was taken up quantitatively and acted, at least in part, as an intracellular carbon source under severe salt stress. The effect of asparagine as an osmoprotectant for Methylocystis spp. is an unexpected finding. It may provide Methylocystis spp. with an ecological advantage in wetlands, where these methanotrophs colonize the roots of submerged vascular plants. Collectively, our study offers a new avenue into research on compounds that may increase the resilience of Methylocystis spp. to environmental change.
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Affiliation(s)
- Kangli Guo
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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MacPherson S, Keyes S, Kilgour MK, Smazynski J, Chan V, Sudderth J, Turcotte T, Devlieger A, Yu J, Huggler KS, Cantor JR, DeBerardinis RJ, Siatskas C, Lum JJ. Clinically relevant T cell expansion media activate distinct metabolic programs uncoupled from cellular function. Mol Ther Methods Clin Dev 2022; 24:380-393. [PMID: 35284590 PMCID: PMC8897702 DOI: 10.1016/j.omtm.2022.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/11/2022] [Indexed: 12/17/2022]
Abstract
Ex vivo expansion conditions used to generate T cells for immunotherapy are thought to adopt metabolic phenotypes that impede therapeutic efficacy in vivo. The comparison of five different culture media used for clinical T cell expansion revealed unique optima based on different output variables, including proliferation, differentiation, function, activation, and mitochondrial phenotypes. The extent of proliferation and function depended on the culture media rather than stimulation conditions. Moreover, the expanded T cell end products adapted their metabolism when switched to a different media formulation, as shown by glucose and glutamine uptake and patterns of glucose isotope labeling. However, adoption of these metabolic phenotypes was uncoupled to T cell function. Expanded T cell products cultured in ascites from ovarian cancer patients displayed suppressed mitochondrial activity and function irrespective of the ex vivo expansion media. Thus, ex vivo T cell expansion media have profound impacts on metabolism and function.
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Affiliation(s)
- Sarah MacPherson
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC V8R6V5, Canada
| | - Sarah Keyes
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC V8R6V5, Canada
| | - Marisa K Kilgour
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC V8R6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Julian Smazynski
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC V8R6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Vanessa Chan
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC V8R6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jessica Sudderth
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Jessie Yu
- Stemcell Technologies Canada Inc., Vancouver, BC, Canada
| | - Kimberly S Huggler
- Morgridge Institute for Research, Madison, WI, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason R Cantor
- Morgridge Institute for Research, Madison, WI, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.,University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Julian J Lum
- Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, BC V8R6V5, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Abstract
Metastasis formation is the leading cause of death in cancer patients. It has recently emerged that cancer cells adapt their metabolism to successfully transition through the metastatic cascade. Consequently, measuring and analyzing the in vivo metabolism of metastases has the potential to reveal novel treatment strategies to prevent metastasis formation. Here, we describe two different metastasis mouse models and how their metabolism can be analyzed with metabolomics and 13C tracer analysis.
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Affiliation(s)
- Patricia Altea-Manzano
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Dorien Broekaert
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - João A G Duarte
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Juan Fernández-García
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Mélanie Planque
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.
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Maralingannavar V, Parmar D, Panchagnula V, Gadgil M. Superfluous glutamine synthetase activity in Chinese Hamster Ovary cells selected under glutamine limitation is growth limiting in glutamine-replete conditions and can be inhibited by serine. Biotechnol Prog 2019; 35:e2856. [PMID: 31148368 DOI: 10.1002/btpr.2856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/08/2019] [Accepted: 05/25/2019] [Indexed: 11/08/2022]
Abstract
Passaging and expansion of animal cells in lean maintenance medium could result in periods of limitation of some nutrients. Over time, such stresses could possibly result in selection of cells with metabolic changes and contribute to heterogeneity. Here, we investigate whether selection of Chinese Hamster Ovary (CHO) cells under glutamine limitation results in changes in growth under glutamine-replete conditions. In glutamine-limiting medium, compared to control cells passaged in glutamine-rich medium, the selected cells showed higher glutamine synthetase (GS) activity and attained a higher peak viable cell density (PVCD). Surprisingly, in glutamine-replete conditions, selected cells still showed a higher GS activity but a lower PVCD. We show that in glutamine-replete medium, PVCD of selected cells was restored on (a) inhibition of GS activity with methionine sulfoximine, (b) supplementation of aspartate-without affecting GS activity, and (c) supplementation of serine, which is reported to inhibit GS in vitro. Consistent with the reported effect of serine, inhibition of GS activity was observed upon serine supplementation along with reduced growth of cells under glutamine-limiting conditions. The latter observation is important for the design of glutamine-free culture medium and feed used for GS-CHO and GS-NS0. In summary, we show that CHO cells selected under glutamine limitation have superfluous GS activity in glutamine-replete medium, which negatively affects their PVCD. This may be due to its effect on availability of aspartate which was the limiting nutrient for the growth of selected cells in glutamine-replete conditions.
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Affiliation(s)
- Vishwanathgouda Maralingannavar
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, Uttar Pradesh, India
| | - Dharmeshkumar Parmar
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, Uttar Pradesh, India
| | - Venkateswarlu Panchagnula
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, Uttar Pradesh, India
| | - Mugdha Gadgil
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, Uttar Pradesh, India
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Fu Y, He L, Reeve J, Beck DAC, Lidstrom ME. Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph Methylomicrobium buryatense 5GB1. mBio 2019; 10:e00406-19. [PMID: 30967465 DOI: 10.1128/mBio.00406-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One-carbon compounds such as methane and methanol are of increasing interest as sustainable substrates for biological production of fuels and industrial chemicals. The bacteria that carry out these conversions have been studied for many decades, but gaps exist in our knowledge of their metabolic pathways. One such gap is the difference between growth on methane and growth on methanol. Understanding such metabolism is important, since each has advantages and disadvantages as a feedstock for production of chemicals and fuels. The significance of our research is in the demonstration that the metabolic network is substantially altered in each case and in the delineation of these changes. The resulting new insights into the core metabolism of this bacterium now provide an improved basis for future strain design. Methylomicrobium buryatense 5GB1 is an obligate methylotroph which grows on methane or methanol with similar growth rates. It has long been assumed that the core metabolic pathways must be similar on the two substrates, but recent studies of methane metabolism in this bacterium suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach and a 13C tracer approach were taken to understand core carbon metabolism in M. buryatense 5GB1 during growth on methanol and to determine whether such differences occur. Our results suggest a systematic shift of active core metabolism in which increased flux occurred through both the Entner-Doudoroff (ED) pathway and the partial serine cycle, while the tricarboxylic acid (TCA) cycle was incomplete, in contrast to growth on methane. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol, and the results are consistent with predictions based on ATP and NADH changes. Transcriptomics analysis suggested that the changes in fluxes and metabolite levels represented results of posttranscriptional regulation. The combination of flux balance analysis of the genome-scale model and the flux ratio from 13C data changed the solution space for a better prediction of cell behavior and demonstrated the significant differences in physiology between growth on methane and growth on methanol.
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Abstract
Immune cell function is tightly regulated by cellular metabolism, which in turn is strongly linked to the nutrient availability in the microenvironment surrounding the cells. This link is critical for effector CD8+ T cells which, after activation, must migrate from nutrient-rich environments into nutrient-scarce regions such as the tumor microenvironment. Assessing how nutrient availability modulates the metabolism of effector CD8+ T cells is thus key for understanding how harsh environments may impair their proliferation and effector function. Here, we describe an approach to systematically study the impact of the nutrient microenvironment on the metabolism of effector CD8+ T cells, based on performing stable 13C isotope labeling measurements on in vitro-differentiated murine effector CD8+ T cells.
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Affiliation(s)
- Juan Fernández-García
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium.
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Abstract
Metabolic alterations are a hallmark of cancer. While determining metabolic changes in vitro has delivered valuable insight into the metabolism of cancer cells, it emerges that determining the in vivo metabolism adds an additional layer of information. Here, we therefore describe how to measure the in vivo metabolism of cancer tissue using 13C glucose infusions in mice.
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Affiliation(s)
- Dorien Broekaert
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium.
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