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Rowe JH, Elia I, Shahid O, Gaudiano EF, Sifnugel NE, Johnson S, Reynolds AG, Fung ME, Joshi S, LaFleur MW, Park JS, Pauken KE, Rabinowitz JD, Freeman GJ, Haigis MC, Sharpe AH. Formate Supplementation Enhances Antitumor CD8+ T-cell Fitness and Efficacy of PD-1 Blockade. Cancer Discov 2023; 13:2566-2583. [PMID: 37728660 PMCID: PMC10843486 DOI: 10.1158/2159-8290.cd-22-1301] [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: 11/16/2022] [Revised: 08/10/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
The tumor microenvironment (TME) restricts antitumor CD8+ T-cell function and immunotherapy responses. Cancer cells compromise the metabolic fitness of CD8+ T cells within the TME, but the mechanisms are largely unknown. Here we demonstrate that one-carbon (1C) metabolism is enhanced in T cells in an antigen-specific manner. Therapeutic supplementation of 1C metabolism using formate enhances CD8+ T-cell fitness and antitumor efficacy of PD-1 blockade in B16-OVA tumors. Formate supplementation drives transcriptional alterations in CD8+ T-cell metabolism and increases gene signatures for cellular proliferation and activation. Combined formate and anti-PD-1 therapy increases tumor-infiltrating CD8+ T cells, which are essential for enhanced tumor control. Our data demonstrate that formate provides metabolic support to CD8+ T cells reinvigorated by anti-PD-1 to overcome a metabolic vulnerability in 1C metabolism in the TME to further improve T-cell function. SIGNIFICANCE This study identifies that deficiencies in 1C metabolism limit the efficacy of PD-1 blockade in B16-OVA tumors. Supplementing 1C metabolism with formate during anti-PD-1 therapy enhances CD8+ T-cell fitness in the TME and CD8+ T-cell-mediated tumor clearance. These findings demonstrate that formate supplementation can enhance exhausted CD8+ T-cell function. See related commentary by Lin et al., p. 2507. This article is featured in Selected Articles from This Issue, p. 2489.
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Affiliation(s)
- Jared H. Rowe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Ilaria Elia
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Osmaan Shahid
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Emily F. Gaudiano
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Natalia E. Sifnugel
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Sheila Johnson
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Amy G. Reynolds
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Megan E. Fung
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Shakchhi Joshi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Martin W. LaFleur
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Joon Seok Park
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Kristen E. Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Joshua D. Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215 USA
| | - Marcia C. Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Arlene H. Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Lay Institute of Immunology and Inflammation, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
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Abstract
MOTIVATION An observed metabolic response is the result of the coordinated activation and interaction between multiple genetic pathways. However, the complex structure of metabolism has meant that a compete understanding of which pathways are required to produce an observed metabolic response is not fully understood. In this article, we propose an approach that can identify the genetic pathways which dictate the response of metabolic network to specific experimental conditions. RESULTS Our approach is a combination of probabilistic models for pathway ranking, clustering and classification. First, we use a non-parametric pathway extraction method to identify the most highly correlated paths through the metabolic network. We then extract the defining structure within these top-ranked pathways using both Markov clustering and classification algorithms. Furthermore, we define detailed node and edge annotations, which enable us to track each pathway, not only with respect to its genetic dependencies, but also allow for an analysis of the interacting reactions, compounds and KEGG sub-networks. We show that our approach identifies biologically meaningful pathways within two microarray expression datasets using entire KEGG metabolic networks. AVAILABILITY AND IMPLEMENTATION An R package containing a full implementation of our proposed method is currently available from http://www.bic.kyoto-u.ac.jp/pathway/timhancock.
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Affiliation(s)
- Timothy Hancock
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan.
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Tsoi BM, Beckhouse AG, Gelling CL, Raftery MJ, Chiu J, Tsoi AM, Lauterbach L, Rogers PJ, Higgins VJ, Dawes IW. Essential role of one-carbon metabolism and Gcn4p and Bas1p transcriptional regulators during adaptation to anaerobic growth of Saccharomyces cerevisiae. J Biol Chem 2009; 284:11205-15. [PMID: 19224916 DOI: 10.1074/jbc.m809225200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The transcriptional activator Gcn4p is considered the master regulator of amino acid metabolism in Saccharomyces cerevisiae and is required for the transcriptional response to amino acid starvation. Here it is shown that Gcn4p plays a previously undescribed role in regulating adaptation to anaerobic growth. A gcn4 mutant exhibited a highly extended lag phase after a shift to anaerobiosis that was the result of l-serine depletion. In addition, the one-carbon metabolism and purine biosynthesis transcriptional regulator Bas1p were strictly required for anaerobic growth on minimal medium, and this was similarly due to l-serine limitation in bas1 mutants. The induction of one-carbon metabolism during anaerobiosis is needed to increase the supply of l-serine from the glycine and threonine pathways. Using a number of experimental approaches, we demonstrate that these transcription regulators play vital roles in regulating l-serine biosynthesis in the face of increased demand during adaptation to anaerobiosis. This increased l-serine requirement is most likely due to anaerobic remodeling of the cell wall, involving de novo synthesis of a large number of very serine-rich mannoproteins and an increase in the total serine content of the cell wall. During anaerobic starvation for l-serine, this essential amino acid is preferentially directed to the cell wall, indicating the existence of a regulatory mechanism to balance competing cellular demands.
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Affiliation(s)
- Bonny M Tsoi
- School of Biomedical and Health Sciences, University of Western Sydney, Penrith, New South Wales DC 1791, Australia
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Subramanian M, Qiao WB, Khanam N, Wilkins O, Der SD, Lalich JD, Bognar AL. Transcriptional regulation of the one-carbon metabolism regulon in Saccharomyces cerevisiae by Bas1p. Mol Microbiol 2005; 57:53-69. [PMID: 15948949 DOI: 10.1111/j.1365-2958.2005.04663.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanisms mediating responses to glycine withdrawal in budding yeast were studied using a genome-wide profiling approach. A striking pattern of repressed expression of genes with an enrichment for those involved in one-carbon metabolism and AMP biosynthesis was revealed. Sequence analysis of the promoters for the most severely repressed genes identified a conserved sequence, TGACTC, a known binding site for the transcription factors Gcn4p and Bas1p. Loss of BAS1 abolished or significantly reduced the repression of these genes in response to glycine removal but this phenotype was much less apparent in the absence of BAS2 or GCN4. Addition of a Bas1p-LexA fusion protein to a strain with a LexAop-LacZ fusion showed a strong glycine effect both in a BAS2 and a bas2 background. A Bas1p-VP16 fusion protein activated expression in a bas1bas2 strain but no glycine effect was observed while a Bas1p-Bas2p fusion protein activated expression to a lesser extent with a slight stimulation by glycine. These results suggest that glycine affects Bas1p activation of transcription rather than DNA binding and that Bas2p is not required for this affect. Glycine withdrawal repressed many of the same genes as addition of adenine, a process known to be dependent on Bas1p. However, the glycine response is independent of adenine repression, because glycine regulation occurs normally in ade strains. We did not see any difference in the degree of stimulation by glycine in the presence or absence of adenine even in Ade+ strains. Glycine regulation was also found to be dependent on an intact SHM2 gene, which encodes cytoplasmic serine hydroxymethyltransferase. A reporter plasmid containing a DNA sequence from the GCV2 promoter which confers glycine regulation on heterologous genes was introduced into the yeast deletion set to screen for genes required for glycine regulation. A number of genes, including BAS1 were required for activation by glycine but only the SHM2 gene was required for repression in the absence of glycine. We also showed that regulation of the SHM2 promoter by glycine requires Bas1p but not Bas2p or Gcn4p using a beta-galactosidase reporter. The response of the promoter to glycine required an intact SHM2 gene but was restored in a shm2 strain by addition of formate to the medium.
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Affiliation(s)
- Mohan Subramanian
- Department of Medical Genetics and Microbiology, University of Toronto, Medical Sciences Building Room 4383, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
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Teplyakov A, Obmolova G, Sarikaya E, Pullalarevu S, Krajewski W, Galkin A, Howard AJ, Herzberg O, Gilliland GL. Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism. J Bacteriol 2004; 186:7134-40. [PMID: 15489424 PMCID: PMC523196 DOI: 10.1128/jb.186.21.7134-7140.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ygfZ gene product of Escherichia coli represents a large protein family conserved in bacteria to eukaryotes. The members of this family are uncharacterized proteins with marginal sequence similarity to the T-protein (aminomethyltransferase) of the glycine cleavage system. To assist with the functional assignment of the YgfZ family, the crystal structure of the E. coli protein was determined by multiwavelength anomalous diffraction. The protein molecule has a three-domain architecture with a central hydrophobic channel. The structure is very similar to that of bacterial dimethylglycine oxidase, an enzyme of the glycine betaine pathway and a homolog of the T-protein. Based on structural superposition, a folate-binding site was identified in the central channel of YgfZ, and the ability of YgfZ to bind folate derivatives was confirmed experimentally. However, in contrast to dimethylglycine oxidase and T-protein, the YgfZ family lacks amino acid conservation at the folate site, which implies that YgfZ is not an aminomethyltransferase but is likely a folate-dependent regulatory protein involved in one-carbon metabolism.
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Affiliation(s)
- Alexey Teplyakov
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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Gelling CL, Piper MDW, Hong SP, Kornfeld GD, Dawes IW. Identification of a novel one-carbon metabolism regulon in Saccharomyces cerevisiae. J Biol Chem 2003; 279:7072-81. [PMID: 14645232 DOI: 10.1074/jbc.m309178200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycine specifically induces genes encoding subunits of the glycine decarboxylase complex (GCV1, GCV2, and GCV3), and this is mediated by a fall in cytoplasmic levels of 5,10-methylenetetrahydrofolate caused by inhibition of cytoplasmic serine hydroxymethyltransferase. Here it is shown that this control system extends to genes for other enzymes of one-carbon metabolism and de novo purine biosynthesis. Northern analysis of the response to glycine demonstrated that the induction of the GCV genes and the induction of other amino acid metabolism genes are temporally distinct. The genome-wide response to glycine revealed that several other genes are rapidly co-induced with the GCV genes, including SHM2, which encodes cytoplasmic serine hydroxymethyltransferase. These results were refined by examining transcript levels in an shm2Delta strain (in which cytoplasmic 5,10-methylenetetrahydrofolate levels are reduced) and a met13Delta strain, which lacks the main methylenetetrahydrofolate reductase activity of yeast and is effectively blocked at consumption of 5,10-methylene tetrahydrofolate for methionine synthesis. Glycine addition also caused a substantial transient disturbance to metabolism, including a sequence of changes in induction of amino acid biosynthesis and respiratory chain genes. Analysis of the glycine response in the shm2Delta strain demonstrated that apart from the one-carbon regulon, most of these transient responses were not contingent on a disturbance to one-carbon metabolism. The one-carbon response is distinct from the Bas1p purine biosynthesis regulon and thus represents the first example of transcriptional regulation in response to activated one-carbon status.
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Affiliation(s)
- Cristy L Gelling
- Ramaciotti Centre for Gene Function Analysis and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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Cowart LA, Okamoto Y, Pinto FR, Gandy JL, Almeida JS, Hannun YA. Roles for sphingolipid biosynthesis in mediation of specific programs of the heat stress response determined through gene expression profiling. J Biol Chem 2003; 278:30328-38. [PMID: 12740364 DOI: 10.1074/jbc.m300656200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies have demonstrated roles for de novo production of sphingolipids in Saccharomyces cerevisiae in the regulation of the transient cell cycle arrest and nutrient permease degradation associated with the heat stress response, suggesting multiple functions for yeast sphingolipids in this response. We, therefore, sought to determine the generalized involvement of sphingolipids in the heat stress response by using microarray hybridization of RNA isolated from heat-stressed cultures of the mutant strain lcb1-100, which is unable to produce sphingolipids in response to heat. Approximately 70 genes showed differential regulation during the first 15 min of heat stress in the lcb1-100 strain compared with the wild type strain, indicating a requirement for de novo sphingolipid biosynthesis for proper regulation of these genes during heat stress. Grouping these genes into functional categories revealed several pathways, including some in which sphingolipids were previously suspected to play a role, such as stress response pathways and cell cycle regulation. Hierarchical clustering analysis revealed sphingolipid involvement in regulation of tRNA synthesis and metabolic genes and transporters. Additionally, the microarray results demonstrated novel sphingolipid involvement in transcriptional regulation of pathways of translation and cell wall organization and biogenesis. Our results demonstrate a broad-reaching effect of sphingolipids in the yeast heat stress response and suggest that the mechanism of sphingolipid involvement in several cellular pathways occurs via sphingolipid-mediated regulation of message levels.
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Affiliation(s)
- L Ashley Cowart
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, 29403, USA
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Marks VD, van der Merwe GK, van Vuuren HJJ. Transcriptional profiling of wine yeast in fermenting grape juice: regulatory effect of diammonium phosphate. FEMS Yeast Res 2003; 3:269-87. [PMID: 12689635 DOI: 10.1016/s1567-1356(02)00201-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The nitrogen composition of grape musts affects fermentation kinetics and production of aroma and spoilage compounds in wine. It is common practice in wineries to supplement grape musts with diammonium phosphate (DAP) to prevent nitrogen-related fermentation problems. Laboratory strains of Saccharomyces cerevisiae preferentially use rich nitrogen sources, such as ammonia, over poor nitrogen sources. We used global gene expression analysis to monitor the effect of DAP addition on gene expression patterns in wine yeast in fermenting Riesling grape must. The expression of 350 genes in the commercial wine yeast strain VIN13 was affected; 185 genes were down-regulated and 165 genes were up-regulated in response to DAP. Genes that were down-regulated encode small molecule transporters and nitrogen catabolic enzymes, including those linked to the production of urea, a precursor of ethyl carbamate in wine. Genes involved in amino acid metabolism, assimilation of sulfate, de novo purine biosynthesis, tetrahydrofolate one-carbon metabolism, and protein synthesis were up-regulated. The expression level of 86 orphan genes was also affected by DAP.
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Affiliation(s)
- Virginia D Marks
- Wine Research Centre, Faculty of Agricultural Sciences, University of British Columbia, 2205 East Mall, Vancouver, BC, Canada V6T 1Z4
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Hanson AD, Roje S. ONE-CARBON METABOLISM IN HIGHER PLANTS. ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY 2001; 52:119-137. [PMID: 11337394 DOI: 10.1146/annurev.arplant.52.1.119] [Citation(s) in RCA: 274] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The metabolism of one-carbon (C1) units is essential to plants, and plant C1 metabolism has novel features not found in other organisms-plus some enigmas. Despite its centrality, uniqueness, and mystery, plant C1 biochemistry has historically been quite poorly explored, in part because its enzymes and intermediates tend to be labile and low in abundance. Fortunately, the integration of molecular and genetic approaches with biochemical ones is now driving rapid advances in knowledge of plant C1 enzymes and genes. An overview of these advances is presented. There has also been progress in measuring C1 metabolite fluxes and pool sizes, although this remains challenging and there are relatively few data. In the future, combining reverse genetics with flux and pool size determinations should lead to quantitative understanding of how plant C1 pathways function. This is a prerequisite for their rational engineering.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611; e-mail:
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