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Dasgupta S. Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024. [PMID: 38856681 DOI: 10.1089/omi.2024.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.
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Çubuk C, Loucera C, Peña-Chilet M, Dopazo J. Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer. Int J Mol Sci 2023; 24:ijms24087450. [PMID: 37108611 PMCID: PMC10138666 DOI: 10.3390/ijms24087450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The reprogramming of metabolism is a recognized cancer hallmark. It is well known that different signaling pathways regulate and orchestrate this reprogramming that contributes to cancer initiation and development. However, recent evidence is accumulating, suggesting that several metabolites could play a relevant role in regulating signaling pathways. To assess the potential role of metabolites in the regulation of signaling pathways, both metabolic and signaling pathway activities of Breast invasive Carcinoma (BRCA) have been modeled using mechanistic models. Gaussian Processes, powerful machine learning methods, were used in combination with SHapley Additive exPlanations (SHAP), a recent methodology that conveys causality, to obtain potential causal relationships between the production of metabolites and the regulation of signaling pathways. A total of 317 metabolites were found to have a strong impact on signaling circuits. The results presented here point to the existence of a complex crosstalk between signaling and metabolic pathways more complex than previously was thought.
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Affiliation(s)
- Cankut Çubuk
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Carlos Loucera
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, 41013 Sevilla, Spain
| | - María Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Sevilla, Spain
- FPS, ELIXIR-es, Hospital Virgen del Rocío, 42013 Sevilla, Spain
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Sevilla, Spain
- FPS, ELIXIR-es, Hospital Virgen del Rocío, 42013 Sevilla, Spain
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Costa MN, Silva RN. Cytotoxic activity of l-lysine alpha-oxidase against leukemia cells. Semin Cancer Biol 2022; 86:590-599. [PMID: 34606983 DOI: 10.1016/j.semcancer.2021.09.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/27/2023]
Abstract
Cancer cells exhibit higher proliferation rates than normal cells, and as a consequence, a higher nutritional demand for metabolites such as amino acids. Such cells demonstrate high expression of amino acid transporters and are significantly dependent on the external uptake of amino acids. Moreover, some types of cancer cells exhibit oncogenic mutations that render them auxotrophic to certain amino acids. This metabolic difference between tumor and normal cells has been explored for developing anticancer drugs. Enzymes capable of depleting certain amino acids in the bloodstream can be employed to inhibit the proliferation of cancer cells and promote cell death. Certain microbial enzymes, such as l-asparaginase and l-amino acid oxidases, have been studied for this purpose. In this paper, we discuss the role of l-asparaginase, the only enzyme currently used as a chemotherapeutic agent. We also review the studies on a new potential antineoplastic agent, l-lysine α-oxidase, an enzyme of l-amino acid oxidase family.
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Affiliation(s)
- Mariana N Costa
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP, 14049-900, Brazil.
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Li H, Ma L, Li W, Zheng B, Wang J, Chen S, Wang Y, Ge F, Qin B, Zheng X, Deng Y, Zeng R. Proline metabolism reprogramming of trained macrophages induced by early respiratory infection combined with allergen sensitization contributes to development of allergic asthma in childhood of mice. Front Immunol 2022; 13:977235. [PMID: 36211408 PMCID: PMC9533174 DOI: 10.3389/fimmu.2022.977235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Background Infants with respiratory syncytial virus (RSV)-associated bronchiolitis are at increased risk of childhood asthma. Recent studies demonstrated that certain infections induce innate immune memory (also termed trained immunity), especially in macrophages, to respond more strongly to future stimuli with broad specificity, involving in human inflammatory diseases. Metabolic reprogramming increases the capacity of the innate immune cells to respond to a secondary stimulation, is a crucial step for the induction of trained immunity. We hypothesize that specific metabolic reprogramming of lung trained macrophages induced by neonatal respiratory infection is crucial for childhood allergic asthma. Objective To address the role of metabolic reprogramming in lung trained macrophages induced by respiratory virus infection in allergic asthma. Methods Neonatal mice were infected and sensitized by the natural rodent pathogen Pneumonia virus of mice (PVM), a mouse equivalent strain of human RSV, combined with ovalbumin (OVA). Lung CD11b+ macrophages in the memory phase were re-stimulated to investigate trained immunity and metabonomics. Adoptive transfer, metabolic inhibitor and restore experiments were used to explore the role of specific metabolic reprogramming in childhood allergic asthma. Results PVM infection combined with OVA sensitization in neonatal mice resulted in non-Th2 (Th1/Th17) type allergic asthma following OVA challenge in childhood of mice. Lung CD11b+ macrophages in the memory phage increased, and showed enhanced inflammatory responses following re-stimulation, suggesting trained macrophages. Adoptive transfer of the trained macrophages mediated the allergic asthma in childhood. The trained macrophages showed metabolic reprogramming after re-stimulation. Notably, proline biosynthesis remarkably increased. Inhibition of proline biosynthesis suppressed the development of the trained macrophages as well as the Th1/Th17 type allergic asthma, while supplement of proline recovered the trained macrophages as well as the allergic asthma. Conclusion Proline metabolism reprogramming of trained macrophages induced by early respiratory infection combined with allergen sensitization contributes to development of allergic asthma in childhood. Proline metabolism could be a well target for prevention of allergic asthma in childhood.
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Affiliation(s)
- Hanglin Li
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Linyan Ma
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Wenjian Li
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Boyang Zheng
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
- The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Junhai Wang
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Shunyan Chen
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Yang Wang
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Fei Ge
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Beibei Qin
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
- Clinical Lab, Hebei Provincial People’s Hospital, Shijiazhuang, China
| | - Xiaoqing Zheng
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Yuqing Deng
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Ruihong Zeng
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Ruihong Zeng,
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Hendriks LEL, van Meerbeeck J, Cadranel J. Targeted adjuvant therapy in non-small cell lung cancer: trick or treat? Eur Respir J 2021; 58:58/4/2101637. [PMID: 34711606 DOI: 10.1183/13993003.01637-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/31/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Lizza E L Hendriks
- Dept of Pulmonary Diseases, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Jan van Meerbeeck
- Dept of Thoracic Oncology, CORE- Antwerp University Hospital and Antwerp University, Antwerp, Belgium
| | - Jacques Cadranel
- Dept of Pulmonology and Thoracic Oncology, Assistance Publique Hôpitaux de Paris, Hôpital Tenon and GRC 04 Theranoscan, Sorbonne Université, Paris, France
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Lukasheva EV, Babayeva G, Karshieva SS, Zhdanov DD, Pokrovsky VS. L-Lysine α-Oxidase: Enzyme with Anticancer Properties. Pharmaceuticals (Basel) 2021; 14:1070. [PMID: 34832852 PMCID: PMC8618108 DOI: 10.3390/ph14111070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022] Open
Abstract
L-lysine α-oxidase (LO), one of L-amino acid oxidases, deaminates L-lysine with the yield of H2O2, ammonia, and α-keto-ε-aminocaproate. Multiple in vitro and in vivo studies have reported cytotoxic, antitumor, antimetastatic, and antitumor activity of LO. Unlike asparaginase, LO has a dual mechanism of action: depletion of L-lysine and formation of H2O2, both targeting tumor growth. Prominent results were obtained on murine and human tumor models, including human colon cancer xenografts HCT 116, LS174T, and T47D with maximum T/C 12, 37, and 36%, respectively. The data obtained from human cancer xenografts in immunodeficient mice confirm the potential of LO as an agent for colon cancer treatment. In this review, we discuss recently discovered molecular mechanisms of biological action and the potential of LO as anticancer enzyme.
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Affiliation(s)
- Elena V. Lukasheva
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho—Maklaya Street 6, 117198 Moscow, Russia; (E.V.L.); (G.B.)
| | - Gulalek Babayeva
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho—Maklaya Street 6, 117198 Moscow, Russia; (E.V.L.); (G.B.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia;
| | - Saida Sh. Karshieva
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia;
| | - Dmitry D. Zhdanov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10/8, 119121 Moscow, Russia;
| | - Vadim S. Pokrovsky
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho—Maklaya Street 6, 117198 Moscow, Russia; (E.V.L.); (G.B.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia;
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Federal Territory Sirius, 1 Olimpiisky Prospect, 354340 Sochi, Russia
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