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Traversa P, Ferraz de Arruda G, Vazquez A, Moreno Y. Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1537. [PMID: 37998229 PMCID: PMC10670216 DOI: 10.3390/e25111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/04/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here, we propose a directed hypergraph with edge-dependent vertex weight as a novel framework to represent metabolic networks. This hypergraph-based representation captures higher-order interactions among metabolites and reactions, as well as the directionalities of reactions and stoichiometric weights, preserving all essential information. Within this framework, we propose the communicability and the search information as metrics to quantify the robustness and complexity of directed hypergraphs. We explore the implications of network directionality on these measures and illustrate a practical example by applying them to a small-scale E. coli core model. Additionally, we compare the robustness and the complexity of 30 different models of metabolism, connecting structural and biological properties. Our findings show that antibiotic resistance is associated with high structural robustness, while the complexity can distinguish between eukaryotic and prokaryotic organisms.
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Affiliation(s)
- Pietro Traversa
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, 50018 Zaragoza, Spain
- CENTAI Institute, 10138 Turin, Italy
| | | | - Alexei Vazquez
- Nodes & Links Ltd., Salisbury House, Station Road, Cambridge CB1 2LA, UK
| | - Yamir Moreno
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, 50018 Zaragoza, Spain
- CENTAI Institute, 10138 Turin, Italy
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Camargo FDG, Santamaria-Torres M, Cala MP, Guevara-Suarez M, Restrepo SR, Sánchez-Camargo A, Fernández-Niño M, Corujo M, Gallo Molina AC, Cifuentes J, Serna JA, Cruz JC, Muñoz-Camargo C, Gonzalez Barrios AF. Genome-Scale Metabolic Reconstruction, Non-Targeted LC-QTOF-MS Based Metabolomics Data, and Evaluation of Anticancer Activity of Cannabis sativa Leaf Extracts. Metabolites 2023; 13:788. [PMID: 37512495 PMCID: PMC10385671 DOI: 10.3390/metabo13070788] [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: 05/12/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Over the past decades, Colombia has suffered complex social problems related to illicit crops, including forced displacement, violence, and environmental damage, among other consequences for vulnerable populations. Considerable effort has been made in the regulation of illicit crops, predominantly Cannabis sativa, leading to advances such as the legalization of medical cannabis and its derivatives, the improvement of crops, and leaving an open window to the development of scientific knowledge to explore alternative uses. It is estimated that C. sativa can produce approximately 750 specialized secondary metabolites. Some of the most relevant due to their anticancer properties, besides cannabinoids, are monoterpenes, sesquiterpenoids, triterpenoids, essential oils, flavonoids, and phenolic compounds. However, despite the increase in scientific research on the subject, it is necessary to study the primary and secondary metabolism of the plant and to identify key pathways that explore its great metabolic potential. For this purpose, a genome-scale metabolic reconstruction of C. sativa is described and contextualized using LC-QTOF-MS metabolic data obtained from the leaf extract from plants grown in the region of Pesca-Boyaca, Colombia under greenhouse conditions at the Clever Leaves facility. A compartmentalized model with 2101 reactions and 1314 metabolites highlights pathways associated with fatty acid biosynthesis, steroids, and amino acids, along with the metabolism of purine, pyrimidine, glucose, starch, and sucrose. Key metabolites were identified through metabolomic data, such as neurine, cannabisativine, cannflavin A, palmitoleic acid, cannabinoids, geranylhydroquinone, and steroids. They were analyzed and integrated into the reconstruction, and their potential applications are discussed. Cytotoxicity assays revealed high anticancer activity against gastric adenocarcinoma (AGS), melanoma cells (A375), and lung carcinoma cells (A549), combined with negligible impact against healthy human skin cells.
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Affiliation(s)
- Fidias D González Camargo
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
- Applied Genomics Research Group Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Mary Santamaria-Torres
- Metabolomics Core Facility-MetCore Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Mónica P Cala
- Metabolomics Core Facility-MetCore Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Marcela Guevara-Suarez
- Applied Genomics Research Group Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Silvia Restrepo Restrepo
- Laboratory of Mycology and Phytopathology (LAMFU), Department of Biological Sciences and Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Andrea Sánchez-Camargo
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Miguel Fernández-Niño
- Leibniz-Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, 06110 Halle, Germany
| | - María Corujo
- Ecomedics S.A.S., Commercially Known as Clever Leaves, Calle 95 # 11A-94, Bogota 110221, Colombia
| | - Ada Carolina Gallo Molina
- Chemical and Biochemical Processes Group, Department of Chemical and Environmental Engineering, National University of Colombia, Bogotá 11001, Colombia
| | - Javier Cifuentes
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Julian A Serna
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Juan C Cruz
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Carolina Muñoz-Camargo
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Andrés F Gonzalez Barrios
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
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Dusad V, Thiel D, Barahona M, Keun HC, Oyarzún DA. Opportunities at the Interface of Network Science and Metabolic Modeling. Front Bioeng Biotechnol 2021; 8:591049. [PMID: 33569373 PMCID: PMC7868444 DOI: 10.3389/fbioe.2020.591049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022] Open
Abstract
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key to understand how cells respond to genetic, environmental, or therapeutic perturbations. Here we discuss the roles of two complementary strategies for the analysis of genome-scale metabolic models: Flux Balance Analysis (FBA) and network science. While FBA estimates metabolic flux on the basis of an optimization principle, network approaches reveal emergent properties of the global metabolic connectivity. We highlight how the integration of both approaches promises to deliver insights on the structure and function of metabolic systems with wide-ranging implications in discovery science, precision medicine and industrial biotechnology.
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Affiliation(s)
- Varshit Dusad
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Denise Thiel
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Hector C. Keun
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Diego A. Oyarzún
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
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