Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes
Summary: The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through metabolic network analysis applied to three large-scale transcriptional...
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Elsevier
2023-02-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124723000578 |
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| author | Anastasiia Gainullina Denis A. Mogilenko Li-Hao Huang Helena Todorov Vipin Narang Ki-Wook Kim Lim Sheau Yng Andrew Kent Baosen Jia Kumba Seddu Karen Krchma Jun Wu Karine Crozat Elena Tomasello Regine Dress Peter See Charlotte Scott Sophie Gibbings Geetika Bajpai Jigar V. Desai Barbara Maier Sébastien This Peter Wang Stephanie Vargas Aguilar Lucie Poupel Sébastien Dussaud Tyng-An Zhou Veronique Angeli J. Magarian Blander Kyunghee Choi Marc Dalod Ivan Dzhagalov Emmanuel L. Gautier Claudia Jakubzick Kory Lavine Michail S. Lionakis Helena Paidassi Michael H. Sieweke Florent Ginhoux Martin Guilliams Christophe Benoist Miriam Merad Gwendalyn J. Randolph Alexey Sergushichev Maxim N. Artyomov |
| author_facet | Anastasiia Gainullina Denis A. Mogilenko Li-Hao Huang Helena Todorov Vipin Narang Ki-Wook Kim Lim Sheau Yng Andrew Kent Baosen Jia Kumba Seddu Karen Krchma Jun Wu Karine Crozat Elena Tomasello Regine Dress Peter See Charlotte Scott Sophie Gibbings Geetika Bajpai Jigar V. Desai Barbara Maier Sébastien This Peter Wang Stephanie Vargas Aguilar Lucie Poupel Sébastien Dussaud Tyng-An Zhou Veronique Angeli J. Magarian Blander Kyunghee Choi Marc Dalod Ivan Dzhagalov Emmanuel L. Gautier Claudia Jakubzick Kory Lavine Michail S. Lionakis Helena Paidassi Michael H. Sieweke Florent Ginhoux Martin Guilliams Christophe Benoist Miriam Merad Gwendalyn J. Randolph Alexey Sergushichev Maxim N. Artyomov |
| author_sort | Anastasiia Gainullina |
| collection | DOAJ |
| description | Summary: The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through metabolic network analysis applied to three large-scale transcriptional datasets: we introduce (1) an ImmGen MNP open-source dataset of 337 samples across 26 tissues; (2) a myeloid subset of ImmGen Phase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) dataset (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we develop a network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identification of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworks that encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules reveal that cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages. |
| first_indexed | 2024-04-10T19:51:51Z |
| format | Article |
| id | doaj.art-8a6a390493e44f40a7321fccee2cd51c |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-04-10T19:51:51Z |
| publishDate | 2023-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-8a6a390493e44f40a7321fccee2cd51c2023-01-28T04:07:41ZengElsevierCell Reports2211-12472023-02-01422112046Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytesAnastasiia Gainullina0Denis A. Mogilenko1Li-Hao Huang2Helena Todorov3Vipin Narang4Ki-Wook Kim5Lim Sheau Yng6Andrew Kent7Baosen Jia8Kumba Seddu9Karen Krchma10Jun Wu11Karine Crozat12Elena Tomasello13Regine Dress14Peter See15Charlotte Scott16Sophie Gibbings17Geetika Bajpai18Jigar V. Desai19Barbara Maier20Sébastien This21Peter Wang22Stephanie Vargas Aguilar23Lucie Poupel24Sébastien Dussaud25Tyng-An Zhou26Veronique Angeli27J. Magarian Blander28Kyunghee Choi29Marc Dalod30Ivan Dzhagalov31Emmanuel L. Gautier32Claudia Jakubzick33Kory Lavine34Michail S. Lionakis35Helena Paidassi36Michael H. Sieweke37Florent Ginhoux38Martin Guilliams39Christophe Benoist40Miriam Merad41Gwendalyn J. Randolph42Alexey Sergushichev43Maxim N. Artyomov44Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Computer Technologies Department, ITMO University, St. Petersburg 197101, Russia; Laboratory of Bioinformatics and Molecular Genetics, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow 119334, RussiaDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USADepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USALaboratory of Immunoregulation, Inflammation Research Centre, VIB Ghent University, 9052 Ghent, BelgiumSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, SingaporeDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USAImmunology Translational Research Programme, Yong Loo Lin School of Medicine, Department of Microbiology and Immunology, National University of Singapore, Singapore 117545, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117545, SingaporeThe Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USAThe Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USADepartment of Immunology, Harvard Medical School, Boston, MA 02115, USADepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USADepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USAAix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, FranceAix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, FranceSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, SingaporeSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, SingaporeLaboratory of Immunoregulation, Inflammation Research Centre, VIB Ghent University, 9052 Ghent, BelgiumDepartment of Pediatrics, National Jewish Health, Denver, CO 80206, USACenter for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USAFungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USAImmunology Institute and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USACentre International de Recherche en Infectiologie (CIRI), University Lyon, Inserm, U1111, Université Claude Bernard Lyon ,1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, FranceDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USAAix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, France; Center for Regenerative Therapies (CRTD), TU Dresden, 01307 Dresden, Germany; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, GermanyINSERM UMR-S 1166, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, 75013 Paris, FranceINSERM UMR-S 1166, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, 75013 Paris, FranceInstitute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, TaiwanImmunology Translational Research Programme, Yong Loo Lin School of Medicine, Department of Microbiology and Immunology, National University of Singapore, Singapore 117545, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117545, SingaporeThe Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USADepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USAAix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, FranceInstitute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, TaiwanINSERM UMR-S 1166, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, 75013 Paris, FranceDepartment of Pediatrics, National Jewish Health, Denver, CO 80206, USACenter for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USAFungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USACentre International de Recherche en Infectiologie (CIRI), University Lyon, Inserm, U1111, Université Claude Bernard Lyon ,1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, FranceAix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, France; Center for Regenerative Therapies (CRTD), TU Dresden, 01307 Dresden, Germany; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, GermanySingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, SingaporeLaboratory of Immunoregulation, Inflammation Research Centre, VIB Ghent University, 9052 Ghent, BelgiumDepartment of Immunology, Harvard Medical School, Boston, MA 02115, USAImmunology Institute and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USADepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USADepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Computer Technologies Department, ITMO University, St. Petersburg 197101, Russia; Corresponding authorDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Corresponding authorSummary: The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through metabolic network analysis applied to three large-scale transcriptional datasets: we introduce (1) an ImmGen MNP open-source dataset of 337 samples across 26 tissues; (2) a myeloid subset of ImmGen Phase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) dataset (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we develop a network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identification of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworks that encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules reveal that cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.http://www.sciencedirect.com/science/article/pii/S2211124723000578CP: ImmunologyCP: Metabolism |
| spellingShingle | Anastasiia Gainullina Denis A. Mogilenko Li-Hao Huang Helena Todorov Vipin Narang Ki-Wook Kim Lim Sheau Yng Andrew Kent Baosen Jia Kumba Seddu Karen Krchma Jun Wu Karine Crozat Elena Tomasello Regine Dress Peter See Charlotte Scott Sophie Gibbings Geetika Bajpai Jigar V. Desai Barbara Maier Sébastien This Peter Wang Stephanie Vargas Aguilar Lucie Poupel Sébastien Dussaud Tyng-An Zhou Veronique Angeli J. Magarian Blander Kyunghee Choi Marc Dalod Ivan Dzhagalov Emmanuel L. Gautier Claudia Jakubzick Kory Lavine Michail S. Lionakis Helena Paidassi Michael H. Sieweke Florent Ginhoux Martin Guilliams Christophe Benoist Miriam Merad Gwendalyn J. Randolph Alexey Sergushichev Maxim N. Artyomov Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes Cell Reports CP: Immunology CP: Metabolism |
| title | Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes |
| title_full | Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes |
| title_fullStr | Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes |
| title_full_unstemmed | Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes |
| title_short | Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes |
| title_sort | network analysis of large scale immgen and tabula muris datasets highlights metabolic diversity of tissue mononuclear phagocytes |
| topic | CP: Immunology CP: Metabolism |
| url | http://www.sciencedirect.com/science/article/pii/S2211124723000578 |
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