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Laevskaya A, Borovjagin A, Timashev PS, Lesniak MS, Ulasov I. Metabolome-Driven Regulation of Adenovirus-Induced Cell Death. Int J Mol Sci 2021; 22:ijms22010464. [PMID: 33466472 PMCID: PMC7796492 DOI: 10.3390/ijms22010464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/26/2020] [Accepted: 12/27/2020] [Indexed: 02/06/2023] Open
Abstract
A viral infection that involves virus invasion, protein synthesis, and virion assembly is typically accompanied by sharp fluctuations in the intracellular levels of metabolites. Under certain conditions, dramatic metabolic shifts can result in various types of cell death. Here, we review different types of adenovirus-induced cell death associated with changes in metabolic profiles of the infected cells. As evidenced by experimental data, in most cases changes in the metabolome precede cell death rather than represent its consequence. In our previous study, the induction of autophagic cell death was observed following adenovirus-mediated lactate production, acetyl-CoA accumulation, and ATP release, while apoptosis was demonstrated to be modulated by alterations in acetate and asparagine metabolism. On the other hand, adenovirus-induced ROS production and ATP depletion were demonstrated to play a significant role in the process of necrotic cell death. Interestingly, the accumulation of ceramide compounds was found to contribute to the induction of all the three types of cell death mentioned above. Eventually, the characterization of metabolite analysis could help in uncovering the molecular mechanism of adenovirus-mediated cell death induction and contribute to the development of efficacious oncolytic adenoviral vectors.
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Affiliation(s)
- Anastasia Laevskaya
- Group of Experimental Biotherapy and Diagnostic, Institute for Regenerative Medicine, World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Anton Borovjagin
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Peter S. Timashev
- Institute for Regenerative Medicine, World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Department of Polymers and Composites, N.N.Semenov Institute of Chemical Physics, 4 Kosygin St., 119991 Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russia
| | - Maciej S. Lesniak
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60601, USA;
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostic, Institute for Regenerative Medicine, World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Correspondence:
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Urman JM, Herranz JM, Uriarte I, Rullán M, Oyón D, González B, Fernandez-Urién I, Carrascosa J, Bolado F, Zabalza L, Arechederra M, Alvarez-Sola G, Colyn L, Latasa MU, Puchades-Carrasco L, Pineda-Lucena A, Iraburu MJ, Iruarrizaga-Lejarreta M, Alonso C, Sangro B, Purroy A, Gil I, Carmona L, Cubero FJ, Martínez-Chantar ML, Banales JM, Romero MR, Macias RI, Monte MJ, Marín JJG, Vila JJ, Corrales FJ, Berasain C, Fernández-Barrena MG, Avila MA. Pilot Multi-Omic Analysis of Human Bile from Benign and Malignant Biliary Strictures: A Machine-Learning Approach. Cancers (Basel) 2020; 12:cancers12061644. [PMID: 32575903 PMCID: PMC7352944 DOI: 10.3390/cancers12061644] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022] Open
Abstract
Cholangiocarcinoma (CCA) and pancreatic adenocarcinoma (PDAC) may lead to the development of extrahepatic obstructive cholestasis. However, biliary stenoses can also be caused by benign conditions, and the identification of their etiology still remains a clinical challenge. We performed metabolomic and proteomic analyses of bile from patients with benign (n = 36) and malignant conditions, CCA (n = 36) or PDAC (n = 57), undergoing endoscopic retrograde cholangiopancreatography with the aim of characterizing bile composition in biliopancreatic disease and identifying biomarkers for the differential diagnosis of biliary strictures. Comprehensive analyses of lipids, bile acids and small molecules were carried out using mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (1H-NMR) in all patients. MS analysis of bile proteome was performed in five patients per group. We implemented artificial intelligence tools for the selection of biomarkers and algorithms with predictive capacity. Our machine-learning pipeline included the generation of synthetic data with properties of real data, the selection of potential biomarkers (metabolites or proteins) and their analysis with neural networks (NN). Selected biomarkers were then validated with real data. We identified panels of lipids (n = 10) and proteins (n = 5) that when analyzed with NN algorithms discriminated between patients with and without cancer with an unprecedented accuracy.
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Affiliation(s)
- Jesús M. Urman
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - José M. Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Iker Uriarte
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - María Rullán
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Daniel Oyón
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Belén González
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Ignacio Fernandez-Urién
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - Juan Carrascosa
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - Federico Bolado
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - Lucía Zabalza
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
| | - María Arechederra
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Gloria Alvarez-Sola
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Leticia Colyn
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - María U. Latasa
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Leonor Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
- Program of Molecular Therapeutics, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - María J. Iraburu
- Department of Biochemistry and Genetics, School of Sciences; University of Navarra, 31008 Pamplona, Spain;
| | | | - Cristina Alonso
- OWL Metabolomics, Bizkaia Technology Park, 48160 Derio, Spain; (M.I.-L.); (C.A.)
| | - Bruno Sangro
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Hepatology Unit, Department of Internal Medicine, University of Navarra Clinic, 31008 Pamplona, Spain
| | - Ana Purroy
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- Navarrabiomed Biobank Unit, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Isabel Gil
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- Navarrabiomed Biobank Unit, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Lorena Carmona
- Proteomics Unit, Centro Nacional de Biotecnología (CNB) Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Francisco Javier Cubero
- Department of Immunology, Ophtalmology & Ear, Nose and Throat (ENT), Complutense University School of Medicine and 12 de Octubre Health Research Institute (Imas12), 28040 Madrid, Spain;
| | - María L. Martínez-Chantar
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Jesús M. Banales
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, 20014 San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Marta R. Romero
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Rocio I.R. Macias
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Maria J. Monte
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Jose J. G. Marín
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Juan J. Vila
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, 31008 Pamplona, Spain; (J.M.U.); (M.R.); (D.O.); (B.G.); (I.F.-U.); (J.C.); (F.B.); (L.Z.); (J.J.V.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
| | - Fernando J. Corrales
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Proteomics Unit, Centro Nacional de Biotecnología (CNB) Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Carmen Berasain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Maite G. Fernández-Barrena
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
| | - Matías A. Avila
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain; (M.A.); (B.S.); (A.P.); (I.G.); (C.B.); (M.G.F.-B.)
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, 28029 Madrid, Spain; (J.M.H.); (I.U.); (G.A.-S.); (M.L.M.-C.); (J.M.B.); (M.R.R.); (R.I.R.M.); (M.J.M.); (J.J.G.M.); (F.J.C.)
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (L.C.); (M.U.L.)
- Correspondence: ; Tel.: +34-948-194700 (ext. 4003)
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Caseiro AR, Santos Pedrosa S, Ivanova G, Vieira Branquinho M, Almeida A, Faria F, Amorim I, Pereira T, Maurício AC. Mesenchymal Stem/ Stromal Cells metabolomic and bioactive factors profiles: A comparative analysis on the umbilical cord and dental pulp derived Stem/ Stromal Cells secretome. PLoS One 2019; 14:e0221378. [PMID: 31774816 PMCID: PMC6881058 DOI: 10.1371/journal.pone.0221378] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/21/2019] [Indexed: 12/21/2022] Open
Abstract
Mesenchymal Stem/ Stromal Cells assume a supporting role to the intrinsic mechanisms of tissue regeneration, a feature mostly assigned to the contents of their secretome. A comparative study on the metabolomic and bioactive molecules/factors content of the secretome of Mesenchymal Stem/ Stromal Cells derived from two expanding sources: the umbilical cord stroma and the dental pulp is presented and discussed. The metabolic profile (Nuclear Magnetic Resonance Spectroscopy) evidenced some differences in the metabolite dynamics through the conditioning period, particularly on the glucose metabolism. Despite, overall similar profiles are suggested. More prominent differences are highlighted for the bioactive factors (Multiplexing Laser Bear Analysis), in which Follistatin, Growth Regulates Protein, Hepatocyte Growth Factor, Interleukin-8 and Monocyte Chemotactic Protein-1 dominate in Umbilical Cord Mesenchymal Stem/ Stromal Cells secretion, while in Dental Pulp Stem/ Stromal Cells the Vascular Endothelial Growth Factor-A and Follistatin are more evident. The distinct secretory cocktail did not result in significantly different effects on endothelial cell populations dynamics including proliferation, migration, tube formation capacity and in vivo angiogenesis, or in chemotaxis for both Mesenchymal Stem/ Stromal Cells populations.
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Affiliation(s)
- Ana Rita Caseiro
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado, Porto, Portugal
- Escola Universitária Vasco da Gama (EUVG), Lordemão, Coimbra, Portugal
| | - Sílvia Santos Pedrosa
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado, Porto, Portugal
| | - Galya Ivanova
- REQUIMTE- LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Mariana Vieira Branquinho
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado, Porto, Portugal
| | - André Almeida
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado, Porto, Portugal
- Indústria Transformadora de Subprodutos—I.T.S, SA, Grupo ETSA, Rua Padre Adriano, Olivais do Machio, Santo Antão do Tojal, Loures, Portugal
| | - Fátima Faria
- Departamento de Patologia e Imunologia Molecular, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
| | - Irina Amorim
- Departamento de Patologia e Imunologia Molecular, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
- i3S - Instituto de Investigação e Inovação da Universidade do Porto, Rua Alfredo Allen, Porto, Portugal
| | - Tiago Pereira
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado, Porto, Portugal
| | - Ana Colette Maurício
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado, Porto, Portugal
- * E-mail: ,
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Prusinkiewicz MA, Mymryk JS. Metabolic Reprogramming of the Host Cell by Human Adenovirus Infection. Viruses 2019; 11:E141. [PMID: 30744016 PMCID: PMC6409786 DOI: 10.3390/v11020141] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/02/2019] [Accepted: 02/03/2019] [Indexed: 12/19/2022] Open
Abstract
Viruses are obligate intracellular parasites that alter many cellular processes to create an environment optimal for viral replication. Reprogramming of cellular metabolism is an important, yet underappreciated feature of many viral infections, as this ensures that the energy and substrates required for viral replication are available in abundance. Human adenovirus (HAdV), which is the focus of this review, is a small DNA tumor virus that reprograms cellular metabolism in a variety of ways. It is well known that HAdV infection increases glucose uptake and fermentation to lactate in a manner resembling the Warburg effect observed in many cancer cells. However, HAdV infection induces many other metabolic changes. In this review, we integrate the findings from a variety of proteomic and transcriptomic studies to understand the subtleties of metabolite and metabolic pathway control during HAdV infection. We review how the E4ORF1 protein of HAdV enacts some of these changes and summarize evidence for reprogramming of cellular metabolism by the viral E1A protein. Therapies targeting altered metabolism are emerging as cancer treatments, and similar targeting of aberrant components of virally reprogrammed metabolism could have clinical antiviral applications.
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Affiliation(s)
- Martin A Prusinkiewicz
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada.
| | - Joe S Mymryk
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada.
- Department of Otolaryngology, Head & Neck Surgery, Western University, London, ON N6A 3K7, Canada.
- Department of Oncology, Western University, London, ON N6A 3K7, Canada.
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada.
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You R, Dai J, Zhang P, Barding GA, Raftery D. Dynamic Metabolic Response to Adriamycin-Induced Senescence in Breast Cancer Cells. Metabolites 2018; 8:metabo8040095. [PMID: 30558288 PMCID: PMC6315875 DOI: 10.3390/metabo8040095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
Cellular senescence displays a heterogeneous set of phenotypes linked to tumor suppression; however, after drug treatment, senescence may also be involved in stable or recurrent cancer. Metabolic changes during senescence can provide detailed information on cellular status and may also have implications for the development of effective treatment strategies. The metabolic response to Adriamycin (ADR) treatment, which causes senescence as well as cell death, was obtained with the aid of metabolic profiling and isotope tracing in two human breast cancer cell lines, MCF7 and MDA-MB-231. After 5 days of ADR treatment, more than 60% of remaining, intact cells entered into a senescent state, characterized by enlarged and flattened morphology and positive blue staining using SA-β-gal. Metabolic trajectory analysis showed that the two cell lines' responses were significantly different and were divided into two distinct stages. The metabolic shift from the first stage to the second was reflected by a partial recovery of the TCA cycle, as well as amino acid and lipid metabolisms. Isotope tracing analysis indicated that the higher level of glutamine metabolism helped maintain senescence. The results suggest that the dynamic changes during senescence indicate a multi-step process involving important metabolic pathways which might allow breast cancer cells to adapt to persistent ADR treatment, while the higher level of anapleurosis may be important for maintaining the senescent state. Ultimately, a better understanding of metabolic changes during senescence might provide targets for cancer therapy and tumor eradication.
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Affiliation(s)
- Rong You
- College of Life Sciences, South China Normal University, 55 Zhongshan Avenue West, Guangzhou 510631, China.
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
| | - Jin Dai
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
| | - Ping Zhang
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
- College of Plant Protection, Southwest University, 2 Tiansheng Road, Chongqing 400715, China.
| | - Gregory A Barding
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA 91768, USA.
| | - Daniel Raftery
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA.
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Yu L, Li K, Xu Z, Cui G, Zhang X. Integrated omics and gene expression analysis identifies the loss of metabolite-metabolite correlations in small cell lung cancer. Onco Targets Ther 2018; 11:3919-3929. [PMID: 30013371 PMCID: PMC6039056 DOI: 10.2147/ott.s166149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Small cell lung cancer (SCLC) is the most aggressive type of lung carcinoma with high metastatic potential and chemoresistance upon relapse. Cancer cells remodel the existing metabolic pathways for their benefits and the perturbations in cellular metabolism are the hallmark of cancer. However, the extent of these changes remains largely unknown for SCLC. MATERIALS AND METHODS We characterized the metabolic perturbations in SCLC cells (SCLCC) by metabolomics. Large-scale correlation analysis was performed between metabolites. Targeted proteomics and gene expression analysis were employed to investigate the changes of key enzymes and genes in the disturbed pathways. RESULTS We found dramatic decrease of metabolite-metabolite correlations in SCLCC compared with normal control cells and non-small cell lung cancer cells. Pathway analysis revealed that the loss of correlations was associated with the alternations of fatty acid oxidation, urea cycle, and purine salvage pathway in SCLCC. Targeted proteomics and gene expression analysis confirmed significant changes of the expression for the key enzymes and genes in the pathways in SCLCC including the upregulation of carbamoyl phosphate synthase 1 (urea cycle) and carnitine palmitoyltransferase 1A (fatty acid oxidation), and the downregulation of hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase in purine salvage pathway. CONCLUSION We demonstrated the loss of metabolite-metabolite correlations in SCLCC associated with the upregulation of fatty acid oxidation and urea cycle and the downregulation of purine salvage pathways. Our findings provide insights into the metabolic reprogramming in SCLCC and highlight the potential therapeutic targets for the treatment of SCLC.
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Affiliation(s)
- Li Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Kefeng Li
- School of Medicine, University of California-San Diego, San Diego, CA, USA
| | - Zhaoguo Xu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Guoyuan Cui
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Xiaoye Zhang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
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Madhu B, Jauhiainen A, McGuire S, Griffiths JR. Exploration of human brain tumour metabolism using pairwise metabolite-metabolite correlation analysis (MMCA) of HR-MAS 1H NMR spectra. PLoS One 2017; 12:e0185980. [PMID: 29069098 PMCID: PMC5656327 DOI: 10.1371/journal.pone.0185980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 09/23/2017] [Indexed: 01/09/2023] Open
Abstract
METHODS We quantified 378 HRMAS 1H NMR spectra of human brain tumours (132 glioblastomas, 101 astrocytomas, 75 meningiomas, 37 oligodendrogliomas and 33 metastases) from the eTumour database and looked for metabolic interactions by metabolite-metabolite correlation analysis (MMCA). RESULTS All tumour types showed remarkably similar metabolic correlations. Lactate correlated positively with alanine, glutamate with glutamine; creatine + phosphocreatine (tCr) correlated positively with lactate, alanine and choline + phosphocholine + glycerophosphocholine (tCho), and tCho correlated positively with lactate; fatty acids correlated negatively with lactate, glutamate + glutamine (tGlut), tCr and tCho. Oligodendrogliomas had fewer correlations but they still fitted that pattern. CONCLUSIONS Possible explanations include (i) glycolytic tumour cells (the Warburg effect) generating pyruvate which is converted to lactate, alanine, glutamate and then glutamine; (ii) an association between elevated glycolysis and increased choline turnover in membranes; (iii) an increase in the tCr pool to facilitate phosphocreatine-driven glutamate uptake; (iv) lipid signals come from cytosolic lipid droplets in necrotic or pre-necrotic tumour tissue that has lower concentrations of anabolic and catabolic metabolites. Additional metabolite exchanges with host cells may also be involved. If tumours co-opt a standard set of biochemical mechanisms to grow in the brain, then drugs might be developed to disrupt those mechanisms.
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Affiliation(s)
- Basetti Madhu
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, United Kingdom
| | | | - Sean McGuire
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, United Kingdom
| | - John R. Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, United Kingdom
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Bhute VJ, Bao X, Dunn KK, Knutson KR, McCurry EC, Jin G, Lee WH, Lewis S, Ikeda A, Palecek SP. Metabolomics Identifies Metabolic Markers of Maturation in Human Pluripotent Stem Cell-Derived Cardiomyocytes. Theranostics 2017; 7:2078-2091. [PMID: 28656061 PMCID: PMC5485423 DOI: 10.7150/thno.19390] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 03/22/2017] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease is a leading cause of death worldwide. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) hold immense clinical potential and recent studies have enabled generation of virtually pure hPSC-CMs with high efficiency in chemically defined and xeno-free conditions. Despite these advances, hPSC-CMs exhibit an immature phenotype and are arrhythmogenic in vivo, necessitating development of strategies to mature these cells. hPSC-CMs undergo significant metabolic alterations during differentiation and maturation. A detailed analysis of the metabolic changes accompanying maturation of hPSC-CMs may prove useful in identifying new strategies to expedite hPSC-CM maturation and also may provide biomarkers for testing or validating hPSC-CM maturation. In this study we identified global metabolic changes which take place during long-term culture and maturation of hPSC-CMs derived from three different hPSC lines. We have identified several metabolic pathways, including phospholipid metabolism and pantothenate and Coenzyme A metabolism, which showed significant enrichment upon maturation in addition to fatty acid oxidation and metabolism. We also identified increases in glycerophosphocholine and the glycerophosphocholine:phosphocholine ratio as potential metabolic biomarkers of maturation. These biomarkers were also affected in a similar manner during murine heart development in vivo. These results support that hPSC-CM maturation is associated with extensive metabolic changes in metabolic network utilization and understanding the roles of these metabolic changes has the potential to develop novel approaches to monitor and expedite hPSC-CM maturation.
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Affiliation(s)
- Vijesh J. Bhute
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaoping Bao
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kaitlin K. Dunn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kylie R. Knutson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric C. McCurry
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gyuhyung Jin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei-Hua Lee
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah Lewis
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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Saccenti E. Correlation Patterns in Experimental Data Are Affected by Normalization Procedures: Consequences for Data Analysis and Network Inference. J Proteome Res 2016; 16:619-634. [PMID: 27977202 DOI: 10.1021/acs.jproteome.6b00704] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Normalization is a fundamental step in data processing to account for the sample-to-sample variation observed in biological samples. However, data structure is affected by normalization. In this paper, we show how, and to what extent, the correlation structure is affected by the application of 11 different normalization procedures. We also discuss the consequences for data analysis and interpretation, including principal component analysis, partial least-squares discrimination, and the inference of metabolite-metabolite association networks.
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Affiliation(s)
- Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University , Stippeneng 4 6708 HB Wageningen, The Netherlands
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10
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Amabebe E, Reynolds S, Stern V, Stafford G, Paley M, Anumba DOC. Cervicovaginal Fluid Acetate: A Metabolite Marker of Preterm Birth in Symptomatic Pregnant Women. Front Med (Lausanne) 2016; 3:48. [PMID: 27777928 PMCID: PMC5056530 DOI: 10.3389/fmed.2016.00048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/28/2016] [Indexed: 11/13/2022] Open
Abstract
Changes in vaginal microbiota that is associated with preterm birth (PTB) leave specific metabolite fingerprints that can be detected in the cervicovaginal fluid (CVF) using metabolomics techniques. In this study, we characterize and validate the CVF metabolite profile of pregnant women presenting with symptoms of threatened preterm labor (PTL) by both 1H-nuclear magnetic resonance spectroscopy (NMR) and enzyme-based spectrophotometry. We also determine their predictive capacity for PTB, singly, and in combination, with current clinical screening tools – cervicovaginal fetal fibronectin (FFN) and ultrasound cervical length (CL). CVF was obtained by high-vaginal swabs from 82 pregnant women with intact fetal membranes presenting between 24 and 36 weeks gestation with symptoms of threatened, but not established, PTL. Dissolved CVF samples were scanned with a 400 MHz NMR spectrometer. Acetate and other metabolites were identified in the NMR spectrum, integrated for peak area, and normalized to the total spectrum integral. To confirm and validate our observations, acetate concentrations (AceConc) were also determined from a randomly-selected subset of the same samples (n = 57), by spectrophotometric absorption of NADH using an acetic acid assay kit. CVF FFN level, transvaginal ultrasound CL, and vaginal pH were also ascertained. Acetate normalized integral and AceConc were significantly higher in the women who delivered preterm compared to their term counterparts (P = 0.002 and P = 0.006, respectively). The 1H-NMR-derived acetate integrals were strongly correlated with the AceConc estimated by spectrophotometry (r = 0.69; P < 0.0001). Both methods were equally predictive of PTB <37 weeks (acetate integral: AUC = 0.75, 95% CI = 0.60–0.91; AceConc: AUC = 0.74, 95% CI = 0.57–0.90, optimal predictive cutoff of >0.53 g/l), and of delivery within 2 weeks of the index assessment (acetate integral: AUC = 0.77, 95% CI = 0.58–0.96; AceConc: AUC = 0.68, 95% CI = 0.5–0.9). The predictive accuracy of CVF acetate was similar to CL and FFN. The combination of CVF acetate, FFN, and ultrasound CL in a binary logistic regression model improved the prediction of PTB compared to the three markers individually, but CVF acetate offered no predictive improvement over ultrasound CL combined with CVF FFN. Elevated CVF acetate in women with symptoms of PTL appears predictive of preterm delivery, as well as delivery within 2 weeks of presentation. An assay of acetate in CVF may prove of clinical utility for predicting PTB.
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Affiliation(s)
- Emmanuel Amabebe
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield , Sheffield , UK
| | - Steven Reynolds
- Academic Unit of Radiology, University of Sheffield , Sheffield , UK
| | - Victoria Stern
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield , Sheffield , UK
| | - Graham Stafford
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield , Sheffield , UK
| | - Martyn Paley
- Academic Unit of Radiology, University of Sheffield , Sheffield , UK
| | - Dilly O C Anumba
- Academic Unit of Reproductive and Developmental Medicine, University of Sheffield , Sheffield , UK
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11
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Feng C, Zhang J, Li X, Ai B, Han J, Wang Q, Wei T, Xu Y, Li M, Li S, Song C, Li C. Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. Sci Rep 2016; 6:33262. [PMID: 27625019 PMCID: PMC5021946 DOI: 10.1038/srep33262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/24/2016] [Indexed: 12/23/2022] Open
Abstract
Metabolic pathway analysis is a popular strategy for comprehensively researching metabolites and genes of interest associated with specific diseases. However, the traditional pathway identification methods do not accurately consider the combined effect of these interesting molecules and neglects expression correlations or topological features embedded in the pathways. In this study, we propose a powerful method, Subpathway-CorSP, for identifying metabolic subpathway regions. This method improved on original pathway identification methods by using a subpathway identification strategy and emphasizing expression correlations between metabolites and genes of interest based on topological features within the metabolic pathways. We analyzed a prostate cancer data set and its metastatic sub-group data set with detailed comparison of Subpathway-CorSP with four traditional pathway identification methods. Subpathway-CorSP was able to identify multiple subpathway regions whose entire corresponding pathways were not detected by traditional pathway identification methods. Further evidences indicated that Subpathway-CorSP provided a robust and efficient way of reliably recalling cancer-related subpathways and locating novel subpathways by the combined effect of metabolites and genes. This was a novel subpathway strategy based on systematically considering expression correlations and topological features between metabolites and genes of interest within given pathways.
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Affiliation(s)
- Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081,China
| | - Qiuyu Wang
- School of Nursing, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Taiming Wei
- School of Pharmacy, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yong Xu
- The fifth Affiliated Hospital of Harbin Medical University, Daqing 163319, China
| | - Meng Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Shang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081,China
| | - Chao Song
- Department of Pharmacology, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
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