1
|
Curvello R, Berndt N, Hauser S, Loessner D. Recreating metabolic interactions of the tumour microenvironment. Trends Endocrinol Metab 2024; 35:518-532. [PMID: 38212233 DOI: 10.1016/j.tem.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Tumours are heterogeneous tissues containing diverse populations of cells and an abundant extracellular matrix (ECM). This tumour microenvironment prompts cancer cells to adapt their metabolism to survive and grow. Besides epigenetic factors, the metabolism of cancer cells is shaped by crosstalk with stromal cells and extracellular components. To date, most experimental models neglect the complexity of the tumour microenvironment and its relevance in regulating the dynamics of the metabolism in cancer. We discuss emerging strategies to model cellular and extracellular aspects of cancer metabolism. We highlight cancer models based on bioengineering, animal, and mathematical approaches to recreate cell-cell and cell-matrix interactions and patient-specific metabolism. Combining these approaches will improve our understanding of cancer metabolism and support the development of metabolism-targeting therapies.
Collapse
Affiliation(s)
- Rodrigo Curvello
- Department of Chemical and Biological Engineering, Faculty of Engineering, Monash University, Melbourne, Victoria, Australia
| | - Nikolaus Berndt
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany; Institute of Computer-assisted Cardiovascular Medicine, Deutsches Herzzentrum der Charité, Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra Hauser
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Department of Radiopharmaceutical and Chemical Biology, Dresden, Germany
| | - Daniela Loessner
- Department of Chemical and Biological Engineering, Faculty of Engineering, Monash University, Melbourne, Victoria, Australia; Leibniz Institute of Polymer Research Dresden e.V., Max Bergmann Center of Biomaterials, Dresden, Germany; Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Melbourne, Victoria, Australia; Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Science, Monash University, Melbourne, Victoria, Australia.
| |
Collapse
|
2
|
Zhang BC, Laursen MF, Hu L, Hazrati H, Narita R, Jensen LS, Hansen AS, Huang J, Zhang Y, Ding X, Muyesier M, Nilsson E, Banasik A, Zeiler C, Mogensen TH, Etzerodt A, Agger R, Johannsen M, Kofod-Olsen E, Paludan SR, Jakobsen MR. Cholesterol-binding motifs in STING that control endoplasmic reticulum retention mediate anti-tumoral activity of cholesterol-lowering compounds. Nat Commun 2024; 15:2760. [PMID: 38553448 PMCID: PMC10980718 DOI: 10.1038/s41467-024-47046-5] [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: 05/24/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
The cGAS-STING pathway plays a crucial role in anti-tumoral responses by activating inflammation and reprogramming the tumour microenvironment. Upon activation, STING traffics from the endoplasmic reticulum (ER) to Golgi, allowing signalling complex assembly and induction of interferon and inflammatory cytokines. Here we report that cGAMP stimulation leads to a transient decline in ER cholesterol levels, mediated by Sterol O-Acyltransferase 1-dependent cholesterol esterification. This facilitates ER membrane curvature and STING trafficking to Golgi. Notably, we identify two cholesterol-binding motifs in STING and confirm their contribution to ER-retention of STING. Consequently, depletion of intracellular cholesterol levels enhances STING pathway activation upon cGAMP stimulation. In a preclinical tumour model, intratumorally administered cholesterol depletion therapy potentiated STING-dependent anti-tumoral responses, which, in combination with anti-PD-1 antibodies, promoted tumour remission. Collectively, we demonstrate that ER cholesterol sets a threshold for STING signalling through cholesterol-binding motifs in STING and we propose that this could be exploited for cancer immunotherapy.
Collapse
Affiliation(s)
- Bao-Cun Zhang
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Marlene F Laursen
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Lili Hu
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Hossein Hazrati
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
- Department of Forensic Medicine, Aarhus University, DK-8200, Aarhus N, Denmark
| | - Ryo Narita
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Lea S Jensen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Aida S Hansen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jinrong Huang
- Department of Biology, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - Yan Zhang
- Department of Engineering, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Xiangning Ding
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | | | - Emil Nilsson
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Agnieszka Banasik
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Christina Zeiler
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, DK-8200, Aarhus N, Denmark
| | - Anders Etzerodt
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Ralf Agger
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University, DK-8200, Aarhus N, Denmark
| | - Emil Kofod-Olsen
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Martin R Jakobsen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark.
| |
Collapse
|
3
|
Gustafsson J, Roshanzamir F, Hagnestål A, Patel SM, Daudu OI, Becker DF, Robinson JL, Nielsen J. Metabolic collaboration between cells in the tumor microenvironment has a negligible effect on tumor growth. Innovation (N Y) 2024; 5:100583. [PMID: 38445018 PMCID: PMC10912649 DOI: 10.1016/j.xinn.2024.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
The tumor microenvironment is composed of a complex mixture of different cell types interacting under conditions of nutrient deprivation, but the metabolism therein is not fully understood due to difficulties in measuring metabolic fluxes and exchange of metabolites between different cell types in vivo. Genome-scale metabolic modeling enables estimation of such exchange fluxes as well as an opportunity to gain insight into the metabolic behavior of individual cell types. Here, we estimated the availability of nutrients and oxygen within the tumor microenvironment using concentration measurements from blood together with a metabolite diffusion model. In addition, we developed an approach to efficiently apply enzyme usage constraints in a comprehensive metabolic model of human cells. The combined modeling reproduced severe hypoxic conditions and the Warburg effect, and we found that limitations in enzymatic capacity contribute to cancer cells' preferential use of glutamine as a substrate to the citric acid cycle. Furthermore, we investigated the common hypothesis that some stromal cells are exploited by cancer cells to produce metabolites useful for the cancer cells. We identified over 200 potential metabolites that could support collaboration between cancer cells and cancer-associated fibroblasts, but when limiting to metabolites previously identified to participate in such collaboration, no growth advantage was observed. Our work highlights the importance of enzymatic capacity limitations for cell behaviors and exemplifies the utility of enzyme-constrained models for accurate prediction of metabolism in cells and tumor microenvironments.
Collapse
Affiliation(s)
- Johan Gustafsson
- Department of Life Sciences, Chalmers University of Technology, SE- 412 96 Gothenburg, Sweden
| | - Fariba Roshanzamir
- Department of Life Sciences, Chalmers University of Technology, SE- 412 96 Gothenburg, Sweden
| | | | - Sagar M. Patel
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Oseeyi I. Daudu
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Donald F. Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jonathan L. Robinson
- Department of Life Sciences, Chalmers University of Technology, SE- 412 96 Gothenburg, Sweden
- BioInnovation Institute, DK2200 Copenhagen, Denmark
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE- 412 96 Gothenburg, Sweden
- BioInnovation Institute, DK2200 Copenhagen, Denmark
| |
Collapse
|
4
|
Jenkins SV, Shruti Shah, Jamshidi-Parsian A, Mortazavi A, Kristian H, Boysen G, Vang KB, Griffin RJ, Rajaram N, Dings RP. Acquired Radiation Resistance Induces Thiol-dependent Cisplatin Cross-resistance. Radiat Res 2024; 201:174-187. [PMID: 38329819 PMCID: PMC10993299 DOI: 10.1667/rade-23-00005.1] [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: 01/06/2023] [Accepted: 11/22/2023] [Indexed: 02/10/2024]
Abstract
Resistance to radiation remains a significant clinical challenge in non-small cell lung carcinoma (NSCLC). It is therefore important to identify the underlying molecular and cellular features that drive acquired resistance. We generated genetically matched NSCLC cell lines to investigate characteristics of acquired resistance. Murine Lewis lung carcinoma (LLC) and human A549 cells acquired an approximate 1.5-2.5-fold increase in radiation resistance as compared to their parental match, which each had unique intrinsic radio-sensitivities. The radiation resistance (RR) was reflected in higher levels of DNA damage and repair marker γH2AX and reduced apoptosis induction after radiation. Morphologically, we found that radiation resistance A549 (A549-RR) cells exhibited a greater nucleus-to-cytosol (N/C) ratio as compared to its parental counterpart. Since the N/C ratio is linked to the differentiation state, we next investigated the epithelial-to-mesenchymal transition (EMT) phenotype and cellular plasticity. We found that A549 cells had a greater radiation-induced plasticity, as measured by E-cadherin, vimentin and double-positive (DP) modulation, as compared to LLC. Additionally, migration was suppressed in A549-RR cells, as compared to A549 cells. Subsequently, we confirmed in vivo that the LLC-RR and A549-RR cells are also more resistance to radiation than their isogenic-matched counterpart. Moreover, we found that the acquired radiation resistance also induced resistance to cisplatin, but not carboplatin or oxaliplatin. This cross-resistance was attributed to induced elevation of thiol levels. Gamma-glutamylcysteine synthetase inhibitor buthionine sulfoximine (BSO) sensitized the resistant cells to cisplatin by decreasing the amount of thiols to levels prior to obtaining acquired radiation resistance. By generating radiation-resistance genetically matched NSCLC we were able to identify and overcome cisplatin cross-resistance. This is an important finding arguing for combinatorial treatment regimens including glutathione pathway disruptors in patients with the potential of improving clinical outcomes in the future.
Collapse
Affiliation(s)
- Samir V. Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Shruti Shah
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Amir Mortazavi
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Hailey Kristian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Gunnar Boysen
- Environment Health Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Kieng B. Vang
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Robert J. Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Narasimhan Rajaram
- Department for Biomedical Engineering, University of Arkansas, University of Arkansas at Fayetteville, Fayetteville, Arkansas 72701
| | - Ruud P.M. Dings
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| |
Collapse
|
5
|
Liu Y, Westerhoff HV. 'Social' versus 'asocial' cells-dynamic competition flux balance analysis. NPJ Syst Biol Appl 2023; 9:53. [PMID: 37898597 PMCID: PMC10613221 DOI: 10.1038/s41540-023-00313-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/09/2023] [Indexed: 10/30/2023] Open
Abstract
In multicellular organisms cells compete for resources or growth factors. If any one cell type wins, the co-existence of diverse cell types disappears. Existing dynamic Flux Balance Analysis (dFBA) does not accommodate changes in cell density caused by competition. Therefore we here develop 'dynamic competition Flux Balance Analysis' (dcFBA). With total biomass synthesis as objective, lower-growth-yield cells were outcompeted even when cells synthesized mutually required nutrients. Signal transduction between cells established co-existence, which suggests that such 'socialness' is required for multicellularity. Whilst mutants with increased specific growth rate did not outgrow the other cell types, loss of social characteristics did enable a mutant to outgrow the other cells. We discuss that 'asocialness' rather than enhanced growth rates, i.e., a reduced sensitivity to regulatory factors rather than enhanced growth rates, may characterize cancer cells and organisms causing ecological blooms. Therapies reinforcing cross-regulation may therefore be more effective than those targeting replication rates.
Collapse
Affiliation(s)
- Yanhua Liu
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans V Westerhoff
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
- Molecular Cell Biology, A-Life, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600, South Africa.
| |
Collapse
|
6
|
Ran M, Zhou Y, Guo Y, Huang D, Zhang SL, Tam KY. Cytosolic malic enzyme and glucose-6-phosphate dehydrogenase modulate redox balance in NSCLC with acquired drug resistance. FEBS J 2023; 290:4792-4809. [PMID: 37410361 DOI: 10.1111/febs.16897] [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: 12/27/2022] [Revised: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
Lung cancer cells often show elevated levels of reactive oxygen species (ROS) and nicotinamide adenine dinucleotide phosphate (NADPH). However, the connections between deregulated redox homeostasis in different subtypes of lung cancer and acquired drug resistance in lung cancer have not yet been fully established. Herein, we analyzed different subtypes of lung cancer data reported in the Cancer Cell Line Encyclopedia (CCLE) database, the Cancer Genome Atlas program (TCGA), and the sequencing data obtained from a gefitinib-resistant non-small-cell lung cancer (NSCLC) cell line (H1975GR). Using flux balance analysis (FBA) model integrated with multiomics data and gene expression profiles, we identified cytosolic malic enzyme 1 (ME1) and glucose-6-phosphate dehydrogenase as the major contributors to the significantly upregulated NADPH flux in NSCLC tissues as compared with normal lung tissues, and gefitinib-resistant NSCLC cell line as compared with the parental cell line. Silencing the gene expression of either of these two enzymes in two osimertinib-resistant NSCLC cell lines (H1975OR and HCC827OR) exhibited strong antiproliferative effects. Our findings not only underscored the pivotal roles of cytosolic ME1 and glucose-6-phosphate dehydrogenase in regulating redox states in NSCLC cells but also provided novel insights into their potential roles in drug-resistant NSCLC cells with disturbed redox states.
Collapse
Affiliation(s)
- Maoxin Ran
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, China
| | - Yan Zhou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, China
| | - Yizhen Guo
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, China
| | - Ding Huang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, China
| | - Shao-Lin Zhang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, China
| | - Kin Yip Tam
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida de Universidade, China
| |
Collapse
|
7
|
Strain B, Morrissey J, Antonakoudis A, Kontoravdi C. How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic models? Biotechnol Bioeng 2023; 120:2460-2478. [PMID: 36866411 PMCID: PMC10952175 DOI: 10.1002/bit.28366] [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: 09/02/2022] [Revised: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/04/2023]
Abstract
Genome-scale metabolic models (GEMs) possess the power to revolutionize bioprocess and cell line engineering workflows thanks to their ability to predict and understand whole-cell metabolism in silico. Despite this potential, it is currently unclear how accurately GEMs can capture both intracellular metabolic states and extracellular phenotypes. Here, we investigate this knowledge gap to determine the reliability of current Chinese hamster ovary (CHO) cell metabolic models. We introduce a new GEM, iCHO2441, and create CHO-S and CHO-K1 specific GEMs. These are compared against iCHO1766, iCHO2048, and iCHO2291. Model predictions are assessed via comparison with experimentally measured growth rates, gene essentialities, amino acid auxotrophies, and 13 C intracellular reaction rates. Our results highlight that all CHO cell models are able to capture extracellular phenotypes and intracellular fluxes, with the updated GEM outperforming the original CHO cell GEM. Cell line-specific models were able to better capture extracellular phenotypes but failed to improve intracellular reaction rate predictions in this case. Ultimately, this work provides an updated CHO cell GEM to the community and lays a foundation for the development and assessment of next-generation flux analysis techniques, highlighting areas for model improvements.
Collapse
Affiliation(s)
- Benjamin Strain
- Department of Chemical EngineeringImperial College LondonLondonUK
| | - James Morrissey
- Department of Chemical EngineeringImperial College LondonLondonUK
| | | | - Cleo Kontoravdi
- Department of Chemical EngineeringImperial College LondonLondonUK
| |
Collapse
|
8
|
Sen P, Orešič M. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine. Metabolites 2023; 13:855. [PMID: 37512562 PMCID: PMC10383060 DOI: 10.3390/metabo13070855] [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: 06/15/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Recent advancements in omics technologies have generated a wealth of biological data. Integrating these data within mathematical models is essential to fully leverage their potential. Genome-scale metabolic models (GEMs) provide a robust framework for studying complex biological systems. GEMs have significantly contributed to our understanding of human metabolism, including the intrinsic relationship between the gut microbiome and the host metabolism. In this review, we highlight the contributions of GEMs and discuss the critical challenges that must be overcome to ensure their reproducibility and enhance their prediction accuracy, particularly in the context of precision medicine. We also explore the role of machine learning in addressing these challenges within GEMs. The integration of omics data with GEMs has the potential to lead to new insights, and to advance our understanding of molecular mechanisms in human health and disease.
Collapse
Affiliation(s)
- Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| |
Collapse
|
9
|
Sweatt AJ, Griffiths CD, Paudel BB, Janes KA. Proteome-wide copy-number estimation from transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548432. [PMID: 37503057 PMCID: PMC10369941 DOI: 10.1101/2023.07.10.548432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein copy numbers constrain systems-level properties of regulatory networks, but absolute proteomic data remain scarce compared to transcriptomics obtained by RNA sequencing. We addressed this persistent gap by relating mRNA to protein statistically using best-available data from quantitative proteomics-transcriptomics for 4366 genes in 369 cell lines. The approach starts with a central estimate of protein copy number and hierarchically appends mRNA-protein and mRNA-mRNA dependencies to define an optimal gene-specific model that links mRNAs to protein. For dozens of independent cell lines and primary prostate samples, these protein inferences from mRNA outmatch stringent null models, a count-based protein-abundance repository, and empirical protein-to-mRNA ratios. The optimal mRNA-to-protein relationships capture biological processes along with hundreds of known protein-protein interaction complexes, suggesting mechanistic relationships are embedded. We use the method to estimate viral-receptor abundances of CD55-CXADR from human heart transcriptomes and build 1489 systems-biology models of coxsackievirus B3 infection susceptibility. When applied to 796 RNA sequencing profiles of breast cancer from The Cancer Genome Atlas, inferred copy-number estimates collectively reclassify 26% of Luminal A and 29% of Luminal B tumors. Protein-based reassignments strongly involve a pharmacologic target for luminal breast cancer (CDK4) and an α-catenin that is often undetectable at the mRNA level (CTTNA2). Thus, by adopting a gene-centered perspective of mRNA-protein covariation across different biological contexts, we achieve accuracies comparable to the technical reproducibility limits of contemporary proteomics. The collection of gene-specific models is assembled as a web tool for users seeking mRNA-guided predictions of absolute protein abundance (http://janeslab.shinyapps.io/Pinferna).
Collapse
Affiliation(s)
- Andrew J. Sweatt
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
| | - Cameron D. Griffiths
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
| | - B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908
| |
Collapse
|
10
|
Lee G, Lee SM, Kim HU. A contribution of metabolic engineering to addressing medical problems: Metabolic flux analysis. Metab Eng 2023; 77:283-293. [PMID: 37075858 DOI: 10.1016/j.ymben.2023.04.008] [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: 02/04/2023] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Metabolic engineering has served as a systematic discipline for industrial biotechnology as it has offered systematic tools and methods for strain development and bioprocess optimization. Because these metabolic engineering tools and methods are concerned with the biological network of a cell with emphasis on metabolic network, they have also been applied to a range of medical problems where better understanding of metabolism has also been perceived to be important. Metabolic flux analysis (MFA) is a unique systematic approach initially developed in the metabolic engineering community, and has proved its usefulness and potential when addressing a range of medical problems. In this regard, this review discusses the contribution of MFA to addressing medical problems. For this, we i) provide overview of the milestones of MFA, ii) define two main branches of MFA, namely constraint-based reconstruction and analysis (COBRA) and isotope-based MFA (iMFA), and iii) present successful examples of their medical applications, including characterizing the metabolism of diseased cells and pathogens, and identifying effective drug targets. Finally, synergistic interactions between metabolic engineering and biomedical sciences are discussed with respect to MFA.
Collapse
Affiliation(s)
- GaRyoung Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
11
|
Raddatz AD, Furdui CM, Bey EA, Kemp ML. Single-Cell Kinetic Modeling of β-Lapachone Metabolism in Head and Neck Squamous Cell Carcinoma. Antioxidants (Basel) 2023; 12:741. [PMID: 36978989 PMCID: PMC10045120 DOI: 10.3390/antiox12030741] [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: 01/30/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) cells are highly heterogeneous in their metabolism and typically experience elevated reactive oxygen species (ROS) levels such as superoxide and hydrogen peroxide (H2O2) in the tumor microenvironment. Tumor cells survive under these chronic oxidative conditions by upregulating antioxidant systems. To investigate the heterogeneity of cellular responses to chemotherapeutic H2O2 generation in tumor and healthy tissue, we leveraged single-cell RNA-sequencing (scRNA-seq) data to perform redox systems-level simulations of quinone-cycling β-lapachone treatment as a source of NQO1-dependent rapid superoxide and hydrogen peroxide (H2O2) production. Transcriptomic data from 10 HNSCC patient tumors was used to populate over 4000 single-cell antioxidant enzymatic network models of drug metabolism. The simulations reflected significant systems-level differences between the redox states of healthy and cancer cells, demonstrating in some patient samples a targetable cancer cell population or in others statistically indistinguishable effects between non-malignant and malignant cells. Subsequent multivariate analyses between healthy and malignant cellular models pointed to distinct contributors of redox responses between these phenotypes. This model framework provides a mechanistic basis for explaining mixed outcomes of NAD(P)H:quinone oxidoreductase 1 (NQO1)-bioactivatable therapeutics despite the tumor specificity of these drugs as defined by NQO1/catalase expression and highlights the role of alternate antioxidant components in dictating drug-induced oxidative stress.
Collapse
Affiliation(s)
- Andrew D. Raddatz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Erik A. Bey
- Wood Hudson Cancer Research Laboratory, Newport, KY 41071, USA
| | - Melissa L. Kemp
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA
| |
Collapse
|
12
|
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci U S A 2023; 120:e2217868120. [PMID: 36719923 PMCID: PMC9963017 DOI: 10.1073/pnas.2217868120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Single-cell RNA sequencing combined with genome-scale metabolic models (GEMs) has the potential to unravel the differences in metabolism across both cell types and cell states but requires new computational methods. Here, we present a method for generating cell-type-specific genome-scale models from clusters of single-cell RNA-Seq profiles. Specifically, we developed a method to estimate the minimum number of cells required to pool to obtain stable models, a bootstrapping strategy for estimating statistical inference, and a faster version of the task-driven integrative network inference for tissues algorithm for generating context-specific GEMs. In addition, we evaluated the effect of different RNA-Seq normalization methods on model topology and differences in models generated from single-cell and bulk RNA-Seq data. We applied our methods on data from mouse cortex neurons and cells from the tumor microenvironment of lung cancer and in both cases found that almost every cell subtype had a unique metabolic profile. In addition, our approach was able to detect cancer-associated metabolic differences between cancer cells and healthy cells, showcasing its utility. We also contextualized models from 202 single-cell clusters across 19 human organs using data from Human Protein Atlas and made these available in the web portal Metabolic Atlas, thereby providing a valuable resource to the scientific community. With the ever-increasing availability of single-cell RNA-Seq datasets and continuously improved GEMs, their combination holds promise to become an important approach in the study of human metabolism.
Collapse
|
13
|
Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023; 5:80-95. [PMID: 36717752 PMCID: PMC9886552 DOI: 10.1038/s42255-022-00720-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/01/2022] [Indexed: 01/31/2023]
Abstract
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic causes and a poorly understood pathogenesis, leading to the absence of effective causal treatments. Here we employ multi-layered omics profiling combined with biochemical and clinical features of individuals with MMA to reveal a molecular diagnosis for 177 out of 210 (84%) cases, the majority (148) of whom display pathogenic variants in methylmalonyl-CoA mutase (MMUT). Stratification of these data layers by disease severity shows dysregulation of the tricarboxylic acid cycle and its replenishment (anaplerosis) by glutamine. The relevance of these disturbances is evidenced by multi-organ metabolomics of a hemizygous Mmut mouse model as well as through identification of physical interactions between MMUT and glutamine anaplerotic enzymes. Using stable-isotope tracing, we find that treatment with dimethyl-oxoglutarate restores deficient tricarboxylic acid cycling. Our work highlights glutamine anaplerosis as a potential therapeutic intervention point in MMA.
Collapse
Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ximena Bonilla
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - David Lamparter
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Wenguang Shao
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Tanja Plessl
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Frei
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Bingisser
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandra Goetze
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Audrey van Drogen
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Patrick G A Pedrioli
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | | | - Martin Poms
- Division of Clinical Chemistry, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Florian Traversi
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Cherkaoui
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | - Raphael J Morscher
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luke Simmons
- Division of Child Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Merima Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ioannis Xenarios
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Agora Center, Lausanne, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Gunnar Rätsch
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Medical Informatics Unit, University Hospital Zurich, Zurich, Switzerland.
- AI Center, ETH Zurich, Zurich, Switzerland.
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland.
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
| | - Bernd Wollscheid
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
14
|
Foguet C, Xu Y, Ritchie SC, Lambert SA, Persyn E, Nath AP, Davenport EE, Roberts DJ, Paul DS, Di Angelantonio E, Danesh J, Butterworth AS, Yau C, Inouye M. Genetically personalised organ-specific metabolic models in health and disease. Nat Commun 2022; 13:7356. [PMID: 36446790 PMCID: PMC9708841 DOI: 10.1038/s41467-022-35017-7] [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: 05/05/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding how genetic variants influence disease risk and complex traits (variant-to-function) is one of the major challenges in human genetics. Here we present a model-driven framework to leverage human genome-scale metabolic networks to define how genetic variants affect biochemical reaction fluxes across major human tissues, including skeletal muscle, adipose, liver, brain and heart. As proof of concept, we build personalised organ-specific metabolic flux models for 524,615 individuals of the INTERVAL and UK Biobank cohorts and perform a fluxome-wide association study (FWAS) to identify 4312 associations between personalised flux values and the concentration of metabolites in blood. Furthermore, we apply FWAS to identify 92 metabolic fluxes associated with the risk of developing coronary artery disease, many of which are linked to processes previously described to play in role in the disease. Our work demonstrates that genetically personalised metabolic models can elucidate the downstream effects of genetic variants on biochemical reactions involved in common human diseases.
Collapse
Affiliation(s)
- Carles Foguet
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Elodie Persyn
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Artika P Nath
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | | | - David J Roberts
- BRC Haematology Theme, Radcliffe Department of Medicine, and NHSBT-Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, John Radcliffe Hospital, Oxford, UK
| | - Dirk S Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Science Centre, Human Technopole, Milan, Italy
| | - John Danesh
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Adam S Butterworth
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Christopher Yau
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, OX3 9DU, UK
- Health Data Research UK, Gibbs Building, 215 Euston Road, London, NW1 2BE, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- The Alan Turing Institute, London, UK.
| |
Collapse
|
15
|
Radiotherapy Side Effects: Comprehensive Proteomic Study Unraveled Neural Stem Cell Degenerative Differentiation upon Ionizing Radiation. Biomolecules 2022; 12:biom12121759. [PMID: 36551187 PMCID: PMC9775306 DOI: 10.3390/biom12121759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Cranial radiation therapy is one of the most effective treatments for childhood brain cancers. Despite the ameliorated survival rate of juvenile patients, radiation exposure-induced brain neurogenic region injury could markedly impair patients' cognitive functions and even their quality of life. Determining the mechanism underlying neural stem cells (NSCs) response to irradiation stress is a crucial therapeutic strategy for cognitive impairment. The present study demonstrated that X-ray irradiation arrested NSCs' cell cycle and impacted cell differentiation. To further characterize irradiation-induced molecular alterations in NSCs, two-dimensional high-resolution mass spectrometry-based quantitative proteomics analyses were conducted to explore the mechanism underlying ionizing radiation's influence on stem cell differentiation. We observed that ionizing radiation suppressed intracellular protein transport, neuron projection development, etc., particularly in differentiated cells. Redox proteomics was performed for the quantification of cysteine thiol modifications in order to profile the oxidation-reduction status of proteins in stem cells that underwent ionizing radiation treatment. Via conjoint screening of protein expression abundance and redox status datasets, several significantly expressed and oxidized proteins were identified in differentiating NSCs subjected to X-ray irradiation. Among these proteins, succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (sdha) and the acyl carrier protein, mitochondrial (Ndufab1) were highly related to neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, and Huntington's disease, illustrating the dual-character of NSCs in cell differentiation: following exposure to ionizing radiation, the normal differentiation of NSCs was compromised, and the upregulated oxidized proteins implied a degenerative differentiation trajectory. These findings could be integrated into research on neurodegenerative diseases and future preventive strategies.
Collapse
|
16
|
Li G, Wu X, Ma X. Artificial intelligence in radiotherapy. Semin Cancer Biol 2022; 86:160-171. [PMID: 35998809 DOI: 10.1016/j.semcancer.2022.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022]
Abstract
Radiotherapy is a discipline closely integrated with computer science. Artificial intelligence (AI) has developed rapidly over the past few years. With the explosive growth of medical big data, AI promises to revolutionize the field of radiotherapy through highly automated workflow, enhanced quality assurance, improved regional balances of expert experiences, and individualized treatment guided by multi-omics. In addition to independent researchers, the increasing number of large databases, biobanks, and open challenges significantly facilitated AI studies on radiation oncology. This article reviews the latest research, clinical applications, and challenges of AI in each part of radiotherapy including image processing, contouring, planning, quality assurance, motion management, and outcome prediction. By summarizing cutting-edge findings and challenges, we aim to inspire researchers to explore more future possibilities and accelerate the arrival of AI radiotherapy.
Collapse
Affiliation(s)
- Guangqi Li
- Division of Biotherapy, Cancer Center, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, No. 37 GuoXue Alley, Chengdu 610041, China
| | - Xin Wu
- Head & Neck Oncology ward, Division of Radiotherapy Oncology, Cancer Center, West China Hospital, Sichuan University, No. 37 GuoXue Alley, Chengdu 610041, China
| | - Xuelei Ma
- Division of Biotherapy, Cancer Center, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, No. 37 GuoXue Alley, Chengdu 610041, China.
| |
Collapse
|
17
|
Mittal A, Nenwani M, Sarangi I, Achreja A, Lawrence TS, Nagrath D. Radiotherapy-induced metabolic hallmarks in the tumor microenvironment. Trends Cancer 2022; 8:855-869. [PMID: 35750630 DOI: 10.1016/j.trecan.2022.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 10/17/2022]
Abstract
Radiation is frequently administered for cancer treatment, but resistance or remission remains common. Cancer cells alter their metabolism after radiotherapy to reduce its cytotoxic effects. The influence of altered cancer metabolism extends to the tumor microenvironment (TME), where components of the TME exchange metabolites to support tumor growth. Combining radiotherapy with metabolic targets in the TME can improve therapy response. We review the metabolic rewiring of cancer cells following radiotherapy and put these observations in the context of the TME to describe the metabolic hallmarks of radiotherapy in the TME.
Collapse
Affiliation(s)
- Anjali Mittal
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Minal Nenwani
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Itisam Sarangi
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Abhinav Achreja
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Theodore S Lawrence
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Deepak Nagrath
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
18
|
Jawalagatti V, Kirthika P, Lee JH. Targeting primary and metastatic tumor growth in an aggressive breast cancer by engineered tryptophan auxotrophic Salmonella Typhimurium. MOLECULAR THERAPY - ONCOLYTICS 2022; 25:350-363. [PMID: 35694447 PMCID: PMC9163429 DOI: 10.1016/j.omto.2022.05.004] [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: 12/07/2021] [Accepted: 05/07/2022] [Indexed: 11/26/2022]
Abstract
The global cancer burden is growing and accounted for 10 million deaths in 2020. The resurgence of chemo- and radiation resistance have contributed to the treatment failures in many cancer types. Therefore, alternative strategies are desired for the effective cancer therapy. Bacteria-mediated cancer therapy presents an attarctive alternative option for the treatment and diagnosis of cancers. Herein, we describe an engineered Salmonella Typhimurium (ST) auxotrophic for tryptophan as a cancer therapeutic. The tryptophan auxotrophy was sufficient to render ST avirulent and highly safe to mice. The auxotroph recovered from the infected tumors had improved ability to target and colonize the tumors. We show that tryptophan auxotrophy reduced the fitness of ST in healthy tissues, but not in the tumors. We evaluated the auxotroph in highly aggressive metastatic 4T1 breast cancer model to inhibit primary tumor growth and lung metastases. The therapy greatly suppressed the primary growth with tumor-free survival of 40% mice. Importantly, therapy abolished the metastatic dissemination of tumor to lungs. Further, therapy markedly diminished the macrophage population in the tumors that may have contributed to the therapeutic benefit recorded. Collectively, results highlight the therapeutic efficacy of the tryptophan auxotrophic ST in an aggressive metastatic cancer model.
Collapse
|
19
|
Kutay M, Gozuacik D, Çakır T. Cancer Recurrence and Omics: Metabolic Signatures of Cancer Dormancy Revealed by Transcriptome Mapping of Genome-Scale Networks. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:270-279. [PMID: 35394340 DOI: 10.1089/omi.2022.0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A major problem in medicine and oncology is cancer recurrence through the activation of dormant cancer cells. A system scale examination of metabolic dysregulations associated with the cancer dormancy offers promise for the discovery of novel molecular targets for cancer precision medicine, and importantly, for the prevention of cancer recurrence. In this study, we mapped the total mRNA sequencing-based transcriptomic data from dormant cancer cell lines and nondormant cancer controls onto a human genome-scale metabolic network by using a graph-based approach, and two mass balance-based approaches with one based on reaction activity/inactivity and the other one on flux changes. The gene expression datasets were accessed from Gene Expression Omnibus (GSE83142 and GSE114012). This analysis included two diverse cancer types, a liquid and a solid cancer, namely, acute lymphoblastic leukemia and colorectal cancer. For the dormant cancer state, we observed changes in major adenosine triphosphate-producing pathways, including the citric acid cycle, oxidative phosphorylation, and glycolysis/gluconeogenesis, indicating a reprogramming in the metabolism of dormant cells away from Warburg-based energy metabolism. All three computational approaches unanimously predicted that folate metabolism, pyruvate metabolism, and glutamate metabolism, as well as valine/leucine/isoleucine metabolism are likely dysregulated in cancer dormancy. These findings provide new insights and molecular pathway targets on cancer dormancy, comprehensively catalog dormancy-associated metabolic pathways, and inform future research aimed at prevention of cancer recurrence in particular.
Collapse
Affiliation(s)
- Merve Kutay
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Devrim Gozuacik
- Koç University Research Center for Translational Medicine (KUTTAM) and Koc, University School of Medicine, Istanbul, Turkey
- Sabancı University Nanotechnology Research and Application Center (SUNUM), Istanbul, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| |
Collapse
|
20
|
Palsson BO, Yurkovich JT. Is the kinetome conserved? Mol Syst Biol 2022; 18:e10782. [PMID: 35188334 PMCID: PMC8859747 DOI: 10.15252/msb.202110782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bernhard O Palsson
- Department of Bioengineering University of California San Diego La Jolla CA USA
| | - James T Yurkovich
- Department of Bioengineering University of California San Diego La Jolla CA USA
| |
Collapse
|
21
|
Read GH, Bailleul J, Vlashi E, Kesarwala AH. Metabolic response to radiation therapy in cancer. Mol Carcinog 2022; 61:200-224. [PMID: 34961986 PMCID: PMC10187995 DOI: 10.1002/mc.23379] [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: 08/11/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 11/11/2022]
Abstract
Tumor metabolism has emerged as a hallmark of cancer and is involved in carcinogenesis and tumor growth. Reprogramming of tumor metabolism is necessary for cancer cells to sustain high proliferation rates and enhanced demands for nutrients. Recent studies suggest that metabolic plasticity in cancer cells can decrease the efficacy of anticancer therapies by enhancing antioxidant defenses and DNA repair mechanisms. Studying radiation-induced metabolic changes will lead to a better understanding of radiation response mechanisms as well as the identification of new therapeutic targets, but there are few robust studies characterizing the metabolic changes induced by radiation therapy in cancer. In this review, we will highlight studies that provide information on the metabolic changes induced by radiation and oxidative stress in cancer cells and the associated underlying mechanisms.
Collapse
Affiliation(s)
- Graham H. Read
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Justine Bailleul
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Erina Vlashi
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
| | - Aparna H. Kesarwala
- Department of Radiation Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| |
Collapse
|
22
|
Lee SM, Lee G, Kim HU. Machine learning-guided evaluation of extraction and simulation methods for cancer patient-specific metabolic models. Comput Struct Biotechnol J 2022; 20:3041-3052. [PMID: 35782748 PMCID: PMC9218235 DOI: 10.1016/j.csbj.2022.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/11/2022] [Accepted: 06/12/2022] [Indexed: 11/30/2022] Open
Abstract
Genome-scale metabolic model (GEM) has been established as an important tool to study cellular metabolism at a systems level by predicting intracellular fluxes. With the advent of generic human GEMs, they have been increasingly applied to a range of diseases, often for the objective of predicting effective metabolic drug targets. Cancer is a representative disease where the use of GEMs has proved to be effective, partly due to the massive availability of patient-specific RNA-seq data. When using a human GEM, so-called context-specific GEM needs to be developed first by using cell-specific RNA-seq data. Biological validity of a context-specific GEM highly depends on both model extraction method (MEM) and model simulation method (MSM). However, while MEMs have been thoroughly examined, MSMs have not been systematically examined, especially, when studying cancer metabolism. In this study, the effects of pairwise combinations of three MEMs and five MSMs were evaluated by examining biological features of the resulting cancer patient-specific GEMs. For this, a total of 1,562 patient-specific GEMs were reconstructed, and subjected to machine learning-guided and biological evaluations to draw robust conclusions. Noteworthy observations were made from the evaluation, including the high performance of two MEMs, namely rank-based ‘task-driven Integrative Network Inference for Tissues’ (tINIT) or ‘Gene Inactivity Moderated by Metabolism and Expression’ (GIMME), paired with least absolute deviation (LAD) as a MSM, and relatively poorer performance of flux balance analysis (FBA) and parsimonious FBA (pFBA). Insights from this study can be considered as a reference when studying cancer metabolism using patient-specific GEMs.
Collapse
|
23
|
Barata T, Vieira V, Rodrigues R, Neves RPD, Rocha M. Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells. Comput Biol Med 2021; 142:105177. [PMID: 35026576 DOI: 10.1016/j.compbiomed.2021.105177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023]
Abstract
Cancer Stem Cells (CSCs) contribute to cancer aggressiveness, metastasis, chemo/radio-therapy resistance, and tumor recurrence. Recent studies emphasized the importance of metabolic reprogramming of CSCs for the maintenance and progression of the cancer phenotype through both the fulfillment of the energetic requirements and the supply of substrates fundamental for fast-cell growth, as well as through metabolite-induced epigenetic regulation. Therefore, it is of paramount importance to develop therapeutic strategies tailored to target the metabolism of CSCs. In this work, we built computational Genome-Scale Metabolic Models (GSMMs) for CSCs of different tissues. Flux simulations were then used to predict metabolic phenotypes, identify potential therapeutic targets, and spot already-known Transcription Factors (TFs), miRNAs and antimetabolites that could be used as part of drug repurposing strategies against cancer. Results were in accordance with experimental evidence, provided insights of new metabolic mechanisms for already known agents, and allowed for the identification of potential new targets and compounds that could be interesting for further in vitro and in vivo validation.
Collapse
Affiliation(s)
- Tânia Barata
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal
| | - Vítor Vieira
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Rúben Rodrigues
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal.
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; Department of Informatics, University of Minho.
| |
Collapse
|
24
|
Rocca A, Kholodenko BN. Can Systems Biology Advance Clinical Precision Oncology? Cancers (Basel) 2021; 13:6312. [PMID: 34944932 PMCID: PMC8699328 DOI: 10.3390/cancers13246312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Precision oncology is perceived as a way forward to treat individual cancer patients. However, knowing particular cancer mutations is not enough for optimal therapeutic treatment, because cancer genotype-phenotype relationships are nonlinear and dynamic. Systems biology studies the biological processes at the systems' level, using an array of techniques, ranging from statistical methods to network reconstruction and analysis, to mathematical modeling. Its goal is to reconstruct the complex and often counterintuitive dynamic behavior of biological systems and quantitatively predict their responses to environmental perturbations. In this paper, we review the impact of systems biology on precision oncology. We show examples of how the analysis of signal transduction networks allows to dissect resistance to targeted therapies and inform the choice of combinations of targeted drugs based on tumor molecular alterations. Patient-specific biomarkers based on dynamical models of signaling networks can have a greater prognostic value than conventional biomarkers. These examples support systems biology models as valuable tools to advance clinical and translational oncological research.
Collapse
Affiliation(s)
- Andrea Rocca
- Hygiene and Public Health, Local Health Unit of Romagna, 47121 Forlì, Italy
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
25
|
Lee SM, Kim HU. Development of computational models using omics data for the identification of effective cancer metabolic biomarkers. Mol Omics 2021; 17:881-893. [PMID: 34608924 DOI: 10.1039/d1mo00337b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Identification of novel biomarkers has been an active area of study for the effective diagnosis, prognosis and treatment of cancers. Among various types of cancer biomarkers, metabolic biomarkers, including enzymes, metabolites and metabolic genes, deserve attention as they can serve as a reliable source for diagnosis, prognosis and treatment of cancers. In particular, efforts to identify novel biomarkers have been greatly facilitated by a rapid increase in the volume of multiple omics data generated for a range of cancer cells. These omics data in turn serve as ingredients for developing computational models that can help derive deeper insights into the biology of cancer cells, and identify metabolic biomarkers. In this review, we provide an overview of omics data generated for cancer cells, and discuss recent studies on computational models that were developed using omics data in order to identify effective cancer metabolic biomarkers.
Collapse
Affiliation(s)
- Sang Mi Lee
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Hyun Uk Kim
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. .,KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea.,BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
| |
Collapse
|
26
|
Jung HD, Sung YJ, Kim HU. Omics and Computational Modeling Approaches for the Effective Treatment of Drug-Resistant Cancer Cells. Front Genet 2021; 12:742902. [PMID: 34691155 PMCID: PMC8527086 DOI: 10.3389/fgene.2021.742902] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Chemotherapy is a mainstream cancer treatment, but has a constant challenge of drug resistance, which consequently leads to poor prognosis in cancer treatment. For better understanding and effective treatment of drug-resistant cancer cells, omics approaches have been widely conducted in various forms. A notable use of omics data beyond routine data mining is to use them for computational modeling that allows generating useful predictions, such as drug responses and prognostic biomarkers. In particular, an increasing volume of omics data has facilitated the development of machine learning models. In this mini review, we highlight recent studies on the use of multi-omics data for studying drug-resistant cancer cells. We put a particular focus on studies that use computational models to characterize drug-resistant cancer cells, and to predict biomarkers and/or drug responses. Computational models covered in this mini review include network-based models, machine learning models and genome-scale metabolic models. We also provide perspectives on future research opportunities for combating drug-resistant cancer cells.
Collapse
Affiliation(s)
- Hae Deok Jung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Yoo Jin Sung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,KAIST Institute for Artificial Intelligence, KAIST, Daejeon, South Korea.,BioProcess Engineering Research Center and BioInformatics Research Center KAIST, Daejeon, South Korea
| |
Collapse
|
27
|
Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance. Nat Commun 2021; 12:2700. [PMID: 33976213 PMCID: PMC8113601 DOI: 10.1038/s41467-021-22989-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
Resistance to ionizing radiation, a first-line therapy for many cancers, is a major clinical challenge. Personalized prediction of tumor radiosensitivity is not currently implemented clinically due to insufficient accuracy of existing machine learning classifiers. Despite the acknowledged role of tumor metabolism in radiation response, metabolomics data is rarely collected in large multi-omics initiatives such as The Cancer Genome Atlas (TCGA) and consequently omitted from algorithm development. In this study, we circumvent the paucity of personalized metabolomics information by characterizing 915 TCGA patient tumors with genome-scale metabolic Flux Balance Analysis models generated from transcriptomic and genomic datasets. Metabolic biomarkers differentiating radiation-sensitive and -resistant tumors are predicted and experimentally validated, enabling integration of metabolic features with other multi-omics datasets into ensemble-based machine learning classifiers for radiation response. These multi-omics classifiers show improved classification accuracy, identify clinical patient subgroups, and demonstrate the utility of personalized blood-based metabolic biomarkers for radiation sensitivity. The integration of machine learning with genome-scale metabolic modeling represents a significant methodological advancement for identifying prognostic metabolite biomarkers and predicting radiosensitivity for individual patients.
Collapse
|