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Gainullina A, Mogilenko DA, Huang LH, Todorov H, Narang V, Kim KW, Yng LS, Kent A, Jia B, Seddu K, Krchma K, Wu J, Crozat K, Tomasello E, Dress R, See P, Scott C, Gibbings S, Bajpai G, Desai JV, Maier B, This S, Wang P, Aguilar SV, Poupel L, Dussaud S, Zhou TA, Angeli V, Blander JM, Choi K, Dalod M, Dzhagalov I, Gautier EL, Jakubzick C, Lavine K, Lionakis MS, Paidassi H, Sieweke MH, Ginhoux F, Guilliams M, Benoist C, Merad M, Randolph GJ, Sergushichev A, Artyomov MN. Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes. Cell Rep 2023; 42:112046. [PMID: 36708514 PMCID: PMC10372199 DOI: 10.1016/j.celrep.2023.112046] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/06/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
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.
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Affiliation(s)
- Anastasiia Gainullina
- Department 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, Russia
| | - Denis A Mogilenko
- Department 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, USA
| | - Li-Hao Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Helena Todorov
- Laboratory of Immunoregulation, Inflammation Research Centre, VIB Ghent University, 9052 Ghent, Belgium
| | - Vipin Narang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Ki-Wook Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lim Sheau Yng
- Immunology 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, Singapore
| | - Andrew Kent
- The 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, USA
| | - Baosen Jia
- The 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, USA
| | - Kumba Seddu
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Karine Crozat
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, France
| | - Elena Tomasello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, France
| | - Regine Dress
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Peter See
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Charlotte Scott
- Laboratory of Immunoregulation, Inflammation Research Centre, VIB Ghent University, 9052 Ghent, Belgium
| | - Sophie Gibbings
- Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Geetika Bajpai
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jigar V Desai
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara Maier
- Immunology Institute and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sébastien This
- Centre International de Recherche en Infectiologie (CIRI), University Lyon, Inserm, U1111, Université Claude Bernard Lyon ,1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Peter Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie Vargas Aguilar
- Aix 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, Germany
| | - Lucie Poupel
- INSERM UMR-S 1166, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France
| | - Sébastien Dussaud
- INSERM UMR-S 1166, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France
| | - Tyng-An Zhou
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan
| | - Veronique Angeli
- Immunology 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, Singapore
| | - J Magarian Blander
- The 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, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marc Dalod
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13288 Marseille, France
| | - Ivan Dzhagalov
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan
| | - Emmanuel L Gautier
- INSERM UMR-S 1166, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France
| | - Claudia Jakubzick
- Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Kory Lavine
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helena Paidassi
- Centre International de Recherche en Infectiologie (CIRI), University Lyon, Inserm, U1111, Université Claude Bernard Lyon ,1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Michael H Sieweke
- Aix 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, Germany
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Martin Guilliams
- Laboratory of Immunoregulation, Inflammation Research Centre, VIB Ghent University, 9052 Ghent, Belgium
| | | | - Miriam Merad
- Immunology Institute and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gwendalyn J Randolph
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexey Sergushichev
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Computer Technologies Department, ITMO University, St. Petersburg 197101, Russia.
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Tsai TL, Zhou TA, Hsieh YT, Wang JC, Cheng HK, Huang CH, Tsai PY, Fan HH, Feng HK, Huang YC, Lin CC, Lin CH, Lin CY, Dzhagalov IL, Hsu CL. Multiomics reveal the central role of pentose phosphate pathway in resident thymic macrophages to cope with efferocytosis-associated stress. Cell Rep 2022; 40:111065. [PMID: 35830797 DOI: 10.1016/j.celrep.2022.111065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/07/2022] [Accepted: 06/16/2022] [Indexed: 11/29/2022] Open
Abstract
Tissue-resident macrophages (TRMs) are heterogeneous cell populations found throughout the body. Depending on their location, they perform diverse functions maintaining tissue homeostasis and providing immune surveillance. To survive and function within, TRMs adapt metabolically to the distinct microenvironments. However, little is known about the metabolic signatures of TRMs. The thymus provides a nurturing milieu for developing thymocytes yet efficiently removes those that fail the selection, relying on the resident thymic macrophages (TMφs). This study harnesses multiomics analyses to characterize TMφs and unveils their metabolic features. We find that the pentose phosphate pathway (PPP) is preferentially activated in TMφs, responding to the reduction-oxidation demands associated with the efferocytosis of dying thymocytes. The blockade of PPP in Mφs leads to decreased efferocytosis, which can be rescued by reactive oxygen species (ROS) scavengers. Our study reveals the key role of the PPP in TMφs and underscores the importance of metabolic adaptation in supporting Mφ efferocytosis.
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Affiliation(s)
- Tsung-Lin Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Tyng-An Zhou
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Ting Hsieh
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ju-Chu Wang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hui-Kuei Cheng
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chen-Hua Huang
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Pei-Yuan Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hsiu-Han Fan
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hsing-Kai Feng
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Chia Huang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chih-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 112, Taiwan
| | - Ivan L Dzhagalov
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chia-Lin Hsu
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan.
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Zhou TA, Hsu HP, Tu YH, Cheng HK, Lin CY, Chen NJ, Tsai JW, Robey EA, Huang HC, Hsu CL, Dzhagalov IL. Thymic macrophages consist of two populations with distinct localization and origin. eLife 2022; 11:75148. [PMID: 36449334 PMCID: PMC9754631 DOI: 10.7554/elife.75148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Tissue-resident macrophages are essential to protect from pathogen invasion and maintain organ homeostasis. The ability of thymic macrophages to engulf apoptotic thymocytes is well appreciated, but little is known about their ontogeny, maintenance, and diversity. Here, we characterized the surface phenotype and transcriptional profile of these cells and defined their expression signature. Thymic macrophages were most closely related to spleen red pulp macrophages and Kupffer cells and shared the expression of the transcription factor (TF) SpiC with these cells. Single-cell RNA sequencing (scRNA-Seq) showed that the macrophages in the adult thymus are composed of two populations distinguished by the expression of Timd4 and Cx3cr1. Remarkably, Timd4+ cells were located in the cortex, while Cx3cr1+ macrophages were restricted to the medulla and the cortico-medullary junction. Using shield chimeras, transplantation of embryonic thymuses, and genetic fate mapping, we found that the two populations have distinct origins. Timd4+ thymic macrophages are of embryonic origin, while Cx3cr1+ macrophages are derived from adult hematopoietic stem cells. Aging has a profound effect on the macrophages in the thymus. Timd4+ cells underwent gradual attrition, while Cx3cr1+ cells slowly accumulated with age and, in older mice, were the dominant macrophage population in the thymus. Altogether, our work defines the phenotype, origin, and diversity of thymic macrophages.
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Affiliation(s)
- Tyng-An Zhou
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Hsuan-Po Hsu
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yueh-Hua Tu
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia SinicaTaipeiTaiwan,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan UniversityTaipeiTaiwan
| | - Hui-Kuei Cheng
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Chih-Yu Lin
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Nien-Jung Chen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Jin-Wu Tsai
- Brain Research Center, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Hsuan-Cheng Huang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia SinicaTaipeiTaiwan,Institute of Biomedical Informatics, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Chia-Lin Hsu
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ivan L Dzhagalov
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
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Chang PC, Wang TY, Chang YT, Chu CY, Lee CL, Hsu HW, Zhou TA, Wu Z, Kim RH, Desai SJ, Liu S, Kung HJ. Autophagy pathway is required for IL-6 induced neuroendocrine differentiation and chemoresistance of prostate cancer LNCaP cells. PLoS One 2014; 9:e88556. [PMID: 24551118 PMCID: PMC3925144 DOI: 10.1371/journal.pone.0088556] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/07/2014] [Indexed: 12/29/2022] Open
Abstract
Prostate cancer (PCa) cells undergoing neuroendocrine differentiation (NED) are clinically relevant to the development of relapsed castration-resistant PCa. Increasing evidences show that autophagy involves in the development of neuroendocrine (NE) tumors, including PCa. To clarify the effect of autophagy on NED, androgen-sensitive PCa LNCaP cells were examined. Treatment of LNCaP cells with IL-6 resulted in an induction of autophagy. In the absence of androgen, IL-6 caused an even stronger activation of autophagy. Similar result was identified in NED induction. Inhibition of autophagy with chloroquine (CQ) markedly decreased NED. This observation was confirmed by beclin1 and Atg5 silencing experiments. Further supporting the role of autophagy in NED, we found that LC3 was up-regulated in PCa tissue that had relapsed after androgen-deprivation therapy when compared with their primary tumor counterpart. LC3 staining in relapsed PCa tissue showed punctate pattern similar to the staining of chromogranin A (CgA), a marker for NED cells. Moreover, autophagy inhibition induced the apoptosis of IL-6 induced NE differentiated PCa cells. Consistently, inhibition of autophagy by knockdown of beclin1 or Atg5 sensitized NE differentiated LNCaP cells to etoposide, a chemotherapy drug. To identify the mechanisms, phosphorylation of IL-6 downstream targets was analyzed. An increase in phospho-AMPK and a decrease in phospho-mTOR were found, which implies that IL-6 regulates autophagy through the AMPK/mTOR pathway. Most important to this study is the discovery of REST, a neuronal gene-specific transcriptional repressor that is involved in autophagy activation. REST was down-regulated in IL-6 treatment. Knockdown experiments suggest that REST is critical to NED and autophagy activation by IL-6. Together, our studies imply that autophagy is involved in PCa progression and plays a cytoprotective role when NED is induced in PCa cells by IL-6 treatment. These results reveal the potential of targeting autophagy as part of a combined therapeutic regime for NE tumors.
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Affiliation(s)
- Pei-Ching Chang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, R.O.C
- * E-mail: (PCC); (HJK)
| | - Tao-Yeuan Wang
- Department of Pathology, Mackay Medical College and Mackay Memorial Hospital, New Taipei City, Taiwan, R.O.C
- Mackay Junior College of Medicine, Nursing, and Management, New Taipei City, Taiwan, R.O.C
| | - Yi-Ting Chang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Cheng-Ying Chu
- Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Chin-Ling Lee
- Department of Pathology, Mackay Medical College and Mackay Memorial Hospital, New Taipei City, Taiwan, R.O.C
- Mackay Junior College of Medicine, Nursing, and Management, New Taipei City, Taiwan, R.O.C
| | - Hung-Wei Hsu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Tyng-An Zhou
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Zhaoju Wu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
- UC Davis Cancer Center, University of California Davis, Davis, California, United States of America
| | - Randie H. Kim
- Department of Dermatology, New York University School of Medicine, New York, New York, United States of America
| | - Sonal J. Desai
- UC Davis Cancer Center, University of California Davis, Davis, California, United States of America
| | - Shangqin Liu
- Department of Hematlogy, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hsing-Jien Kung
- Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, R.O.C
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, R.O.C
- * E-mail: (PCC); (HJK)
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