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Xie AX, Tansey W, Reznik E. UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307903. [PMID: 38826234 PMCID: PMC11142294 DOI: 10.1101/2024.05.24.24307903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Comprehensively studying metabolism requires the measurement of metabolite levels. However, in contrast to the broad availability of gene expression data, metabolites are rarely measured in large molecularly-defined cohorts of tissue samples. To address this basic barrier to metabolic discovery, we propose a Bayesian framework ("UnitedMet") which leverages the empirical strength of RNA-metabolite covariation to impute otherwise unmeasured metabolite levels from widely available transcriptomic data. We demonstrate that UnitedMet is equally capable of imputing whole pool sizes as well as the outcomes of isotope tracing experiments. We apply UnitedMet to investigate the metabolic impact of driver mutations in kidney cancer, identifying a novel association between BAP1 and a highly oxidative tumor phenotype. We similarly apply UnitedMet to determine that advanced kidney cancers upregulate oxidative phosphorylation relative to early-stage disease, that oxidative metabolism in kidney cancer is associated with inferior outcomes to combination therapy, and that kidney cancer metastases themselves demonstrate elevated oxidative phosphorylation relative to primary tumors. UnitedMet therefore enables the assessment of metabolic phenotypes in contexts where metabolite measurements were not taken or are otherwise infeasible, opening new avenues for the generation and evaluation of metabolite-centered hypotheses. UnitedMet is open source and publicly available (https://github.com/reznik-lab/UnitedMet).
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Affiliation(s)
- Amy X. Xie
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
- Biochemistry, Structural Biology, Cell Biology, Developmental Biology and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY
| | - Wesley Tansey
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
| | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
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Calhoon D, Sang L, Bezwada D, Kim N, Basu A, Hsu SC, Pimentel A, Brooks B, La K, Serrano AP, Cassidy DL, Cai L, Toffessi-Tcheuyap V, Margulis V, Cai F, Brugarolas J, Weiss RJ, DeBerardinis RJ, Birsoy K, Garcia-Bermudez J. Glycosaminoglycan-mediated lipoprotein uptake protects cancer cells from ferroptosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593939. [PMID: 38765991 PMCID: PMC11101130 DOI: 10.1101/2024.05.13.593939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Lipids are essential for tumours because of their structural, energetic, and signaling roles. While many cancer cells upregulate lipid synthesis, growing evidence suggests that tumours simultaneously intensify the uptake of circulating lipids carried by lipoproteins. Which mechanisms promote the uptake of extracellular lipids, and how this pool of lipids contributes to cancer progression, are poorly understood. Here, using functional genetic screens, we find that lipoprotein uptake confers resistance to lipid peroxidation and ferroptotic cell death. Lipoprotein supplementation robustly inhibits ferroptosis across numerous cancer types. Mechanistically, cancer cells take up lipoproteins through a pathway dependent on sulfated glycosaminoglycans (GAGs) linked to cell-surface proteoglycans. Tumour GAGs are a major determinant of the uptake of both low and high density lipoproteins. Impairment of glycosaminoglycan synthesis or acute degradation of surface GAGs decreases the uptake of lipoproteins, sensitizes cells to ferroptosis and reduces tumour growth in mice. We also find that human clear cell renal cell carcinomas, a distinctively lipid-rich tumour type, display elevated levels of lipoprotein-derived antioxidants and the GAG chondroitin sulfate than non-malignant human kidney. Altogether, our work identifies lipoprotein uptake as an essential anti-ferroptotic mechanism for cancer cells to overcome lipid oxidative stress in vivo, and reveals GAG biosynthesis as an unexpected mediator of this process.
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Affiliation(s)
- Dylan Calhoon
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- These authors contributed equally to this work
| | - Lingjie Sang
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- These authors contributed equally to this work
| | - Divya Bezwada
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nathaniel Kim
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amrita Basu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sheng-Chieh Hsu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anastasia Pimentel
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bailey Brooks
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Konnor La
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Ana Paulina Serrano
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel L Cassidy
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ling Cai
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O’Donnell School of Public Health, University of Texas Southwestern, Dallas, TX, USA
| | - Vanina Toffessi-Tcheuyap
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Feng Cai
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James Brugarolas
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ryan J Weiss
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 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
| | - Kivanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Javier Garcia-Bermudez
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Coffey NJ, Simon MC. Metabolic alterations in hereditary and sporadic renal cell carcinoma. Nat Rev Nephrol 2024; 20:233-250. [PMID: 38253811 PMCID: PMC11165401 DOI: 10.1038/s41581-023-00800-2] [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] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Kidney cancer is the seventh leading cause of cancer in the world, and its incidence is on the rise. Renal cell carcinoma (RCC) is the most common form and is a heterogeneous disease comprising three major subtypes that vary in their histology, clinical course and driver mutations. These subtypes include clear cell RCC, papillary RCC and chromophobe RCC. Molecular analyses of hereditary and sporadic forms of RCC have revealed that this complex and deadly disease is characterized by metabolic pathway alterations in cancer cells that lead to deregulated oxygen and nutrient sensing, as well as impaired tricarboxylic acid cycle activity. These metabolic changes facilitate tumour growth and survival. Specifically, studies of the metabolic features of RCC have led to the discovery of oncometabolites - fumarate and succinate - that can promote tumorigenesis, moonlighting functions of enzymes, and substrate auxotrophy owing to the disruption of pathways that enable the production of arginine and cholesterol. These metabolic alterations within RCC can be exploited to identify new therapeutic targets and interventions, in combination with novel approaches that minimize the systemic toxicity of metabolic inhibitors and reduce the risk of drug resistance owing to metabolic plasticity.
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Affiliation(s)
- Nathan J Coffey
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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Bischoff ME, Shamsaei B, Yang J, Secic D, Vemuri B, Reisz JA, D'Alessandro A, Bartolacci C, Adamczak R, Schmidt L, Wang J, Martines A, Biesiada J, Vest KE, Scaglioni PP, Plas DR, Patra KC, Gulati S, Figueroa JAL, Meller J, Cunningham JT, Czyzyk-Krzeska MF. Copper drives remodeling of metabolic state and progression of clear cell renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575895. [PMID: 38293110 PMCID: PMC10827129 DOI: 10.1101/2024.01.16.575895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Copper (Cu) is an essential trace element required for mitochondrial respiration. Late-stage clear cell renal cell carcinoma (ccRCC) accumulates Cu and allocates it to mitochondrial cytochrome c oxidase. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis, promoting tumor growth and progression of ccRCC. Specifically, Cu induces TCA cycle-dependent oxidation of glucose and its utilization for glutathione biosynthesis to protect against H 2 O 2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection. scRNA-seq determined that ccRCC progression involves increased expression of subunits of respiratory complexes, genes in glutathione and Cu metabolism, and NRF2 targets, alongside a decrease in HIF activity, a hallmark of ccRCC. Spatial transcriptomics identified that proliferating cancer cells are embedded in clusters of cells with oxidative metabolism supporting effects of metabolic states on ccRCC progression. Our work establishes novel vulnerabilities with potential for therapeutic interventions in ccRCC. Accumulation of copper is associated with progression and relapse of ccRCC and drives tumor growth.Cu accumulation and allocation to cytochrome c oxidase (CuCOX) remodels metabolism coupling energy production and nucleotide biosynthesis with maintenance of redox homeostasis.Cu induces oxidative phosphorylation via alterations in the mitochondrial proteome and lipidome necessary for the formation of the respiratory supercomplexes. Cu stimulates glutathione biosynthesis and glutathione derived specifically from glucose is necessary for survival of Cu Hi cells. Biosynthesis of glucose-derived glutathione requires activity of glutamyl pyruvate transaminase 2, entry of glucose-derived pyruvate to mitochondria via alanine, and the glutamate exporter, SLC25A22. Glutathione derived from glucose maintains redox homeostasis in Cu-treated cells, reducing Cu-H 2 O 2 Fenton-like reaction mediated cell death. Progression of human ccRCC is associated with gene expression signature characterized by induction of ETC/OxPhos/GSH/Cu-related genes and decrease in HIF/glycolytic genes in subpopulations of cancer cells. Enhanced, concordant expression of genes related to ETC/OxPhos, GSH, and Cu characterizes metabolically active subpopulations of ccRCC cells in regions adjacent to proliferative subpopulations of ccRCC cells, implicating oxidative metabolism in supporting tumor growth.
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Bartman CR, Faubert B, Rabinowitz JD, DeBerardinis RJ. Metabolic pathway analysis using stable isotopes in patients with cancer. Nat Rev Cancer 2023; 23:863-878. [PMID: 37907620 PMCID: PMC11161207 DOI: 10.1038/s41568-023-00632-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 11/02/2023]
Abstract
Metabolic reprogramming is central to malignant transformation and cancer cell growth. How tumours use nutrients and the relative rates of reprogrammed pathways are areas of intense investigation. Tumour metabolism is determined by a complex and incompletely defined combination of factors intrinsic and extrinsic to cancer cells. This complexity increases the value of assessing cancer metabolism in disease-relevant microenvironments, including in patients with cancer. Stable-isotope tracing is an informative, versatile method for probing tumour metabolism in vivo. It has been used extensively in preclinical models of cancer and, with increasing frequency, in patients with cancer. In this Review, we describe approaches for using in vivo isotope tracing to define fuel preferences and pathway engagement in tumours, along with some of the principles that have emerged from this work. Stable-isotope infusions reported so far have revealed that in humans, tumours use a diverse set of nutrients to supply central metabolic pathways, including the tricarboxylic acid cycle and amino acid synthesis. Emerging data suggest that some activities detected by stable-isotope tracing correlate with poor clinical outcomes and may drive cancer progression. We also discuss current challenges in isotope tracing, including comparisons of in vivo and in vitro models, and opportunities for future discovery in tumour metabolism.
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Affiliation(s)
- Caroline R Bartman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Brandon Faubert
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Ralph J DeBerardinis
- Howard Hughes Medical Institute and Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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