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Hamley M, Leyk S, Casar C, Liebold I, Jawazneh AA, Lanzloth C, Böttcher M, Haas H, Richardt U, Rothlin CV, Jacobs T, Huber S, Adlung L, Pelczar P, Henao-Mejia J, Bosurgi L. Nmes1 is a novel regulator of mucosal response influencing intestinal healing potential. Eur J Immunol 2024; 54:e2350434. [PMID: 37971166 DOI: 10.1002/eji.202350434] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
The initiation of tissue remodeling following damage is a critical step in preventing the development of immune-mediated diseases. Several factors contribute to mucosal healing, leading to innovative therapeutic approaches for managing intestinal disorders. However, uncovering alternative targets and gaining mechanistic insights are imperative to enhance therapy efficacy and broaden its applicability across different intestinal diseases. Here we demonstrate that Nmes1, encoding for Normal Mucosa of Esophagus-Specific gene 1, also known as Aa467197, is a novel regulator of mucosal healing. Nmes1 influences the macrophage response to the tissue remodeling cytokine IL-4 in vitro. In addition, using two murine models of intestinal damage, each characterized by a type 2-dominated environment with contrasting functions, the ablation of Nmes1 results in decreased intestinal regeneration during the recovery phase of colitis, while enhancing parasitic egg clearance and reducing fibrosis during the advanced stages of Schistosoma mansoni infection. These outcomes are associated with alterations in CX3CR1+ macrophages, cells known for their wound-healing potential in the inflamed colon, hence promising candidates for cell therapies. All in all, our data indicate Nmes1 as a novel contributor to mucosal healing, setting the basis for further investigation into its potential as a new target for the treatment of colon-associated inflammation.
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Affiliation(s)
- Madeleine Hamley
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephanie Leyk
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christian Casar
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Bioinformatics Core, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Imke Liebold
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Amirah Al Jawazneh
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Clarissa Lanzloth
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Marius Böttcher
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Ulricke Richardt
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Carla V Rothlin
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thomas Jacobs
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lorenz Adlung
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Penelope Pelczar
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jorge Henao-Mejia
- The Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lidia Bosurgi
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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2
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Oubounyt M, Adlung L, Patroni F, Wenke NK, Maier A, Hartung M, Baumbach J, Elkjaer ML. Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet. Bioinformatics 2023; 39:btad644. [PMID: 37862243 PMCID: PMC10628438 DOI: 10.1093/bioinformatics/btad644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/07/2023] [Accepted: 10/19/2023] [Indexed: 10/22/2023] Open
Abstract
MOTIVATION The reconstruction of small key regulatory networks that explain the differences in the development of cell (sub)types from single-cell RNA sequencing is a yet unresolved computational problem. RESULTS To this end, we have developed SCANet, an all-in-one package for single-cell profiling that covers the whole differential mechanotyping workflow, from inference of trait/cell-type-specific gene co-expression modules, driver gene detection, and transcriptional gene regulatory network reconstruction to mechanistic drug repurposing candidate prediction. To illustrate the power of SCANet, we examined data from two studies. First, we identify the drivers of the mechanotype of a cytokine storm associated with increased mortality in patients with acute respiratory illness. Secondly, we find 20 drugs for eight potential pharmacological targets in cellular driver mechanisms in the intestinal stem cells of obese mice. AVAILABILITY AND IMPLEMENTATION SCANet is a free, open-source, and user-friendly Python package that can be seamlessly integrated into single-cell-based systems medicine research and mechanistic drug discovery.
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Affiliation(s)
- Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Lorenz Adlung
- Department of Medicine, Hamburg Center for Translational Immunology (HCTI) and Center for Biomedical AI (bAIome), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20246, Germany
| | - Fabio Patroni
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Campinas, SP 13083-875, Brazil
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense 5000, Denmark
| | - Maria L Elkjaer
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
- Department of Neurology, Odense University Hospital, Odense 5000, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense 5000, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense 5000, Denmark
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3
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Chakraborty S, Andrieux G, Kastl P, Adlung L, Altamura S, Boehm ME, Schwarzmüller LE, Abdullah Y, Wagner MC, Helm B, Gröne HJ, Lehmann WD, Boerries M, Busch H, Muckenthaler MU, Schilling M, Klingmüller U. Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo. Cell Rep 2022; 40:111360. [PMID: 36130519 DOI: 10.1016/j.celrep.2022.111360] [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: 03/14/2022] [Revised: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
Erythropoietin (Epo) ensures survival and proliferation of colony-forming unit erythroid (CFU-E) progenitor cells and their differentiation to hemoglobin-containing mature erythrocytes. A lack of Epo-induced responses causes embryonic lethality, but mechanisms regulating the dynamic communication of cellular alterations to the organismal level remain unresolved. By time-resolved transcriptomics and proteomics, we show that Epo induces in CFU-E cells a gradual transition from proliferation signature proteins to proteins indicative for differentiation, including heme-synthesis enzymes. In the absence of the Epo receptor (EpoR) in embryos, we observe a lack of hemoglobin in CFU-E cells and massive iron overload of the fetal liver pointing to a miscommunication between liver and placenta. A reduction of iron-sulfur cluster-containing proteins involved in oxidative phosphorylation in these embryos leads to a metabolic shift toward glycolysis. This link connecting erythropoiesis with the regulation of iron homeostasis and metabolic reprogramming suggests that balancing these interactions is crucial for protection from iron intoxication and for survival.
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Affiliation(s)
- Sajib Chakraborty
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Systems Cell-Signalling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Philipp Kastl
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lorenz Adlung
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine & Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sandro Altamura
- Center for Translational Biomedical Iron Research (CeTBI), Department of Pediatric Hematology, Oncology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin E Boehm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Luisa E Schwarzmüller
- Division Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yomn Abdullah
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marie-Christine Wagner
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Barbara Helm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hermann-Josef Gröne
- Division Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Wolf D Lehmann
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Comprehensive Cancer Center Freiburg (CCCF), Medical Center-University of Freiburg, University of Freiburg, 79106 Freiburg im Breisgau, Germany.
| | - Hauke Busch
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany.
| | - Martina U Muckenthaler
- Center for Translational Biomedical Iron Research (CeTBI), Department of Pediatric Hematology, Oncology and Immunology, Heidelberg University, 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany; German Center for Cardiovascular Research, Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
| | - Marcel Schilling
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
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4
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Adlung L, Stapor P, Tönsing C, Schmiester L, Schwarzmüller LE, Postawa L, Wang D, Timmer J, Klingmüller U, Hasenauer J, Schilling M. Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells. Cell Rep 2021; 36:109507. [PMID: 34380040 DOI: 10.1016/j.celrep.2021.109507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/01/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Survival or apoptosis is a binary decision in individual cells. However, at the cell-population level, a graded increase in survival of colony-forming unit-erythroid (CFU-E) cells is observed upon stimulation with erythropoietin (Epo). To identify components of Janus kinase 2/signal transducer and activator of transcription 5 (JAK2/STAT5) signal transduction that contribute to the graded population response, we extended a cell-population-level model calibrated with experimental data to study the behavior in single cells. The single-cell model shows that the high cell-to-cell variability in nuclear phosphorylated STAT5 is caused by variability in the amount of Epo receptor (EpoR):JAK2 complexes and of SHP1, as well as the extent of nuclear import because of the large variance in the cytoplasmic volume of CFU-E cells. 24-118 pSTAT5 molecules in the nucleus for 120 min are sufficient to ensure cell survival. Thus, variability in membrane-associated processes is sufficient to convert a switch-like behavior at the single-cell level to a graded population-level response.
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Affiliation(s)
- Lorenz Adlung
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Paul Stapor
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany; Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Garching, Germany
| | - Christian Tönsing
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Leonard Schmiester
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany; Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Garching, Germany
| | - Luisa E Schwarzmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lena Postawa
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dantong Wang
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany; Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Garching, Germany
| | - Jens Timmer
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
| | - Jan Hasenauer
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany; Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, 85748 Garching, Germany; Faculty of Mathematics and Natural Sciences, University of Bonn, 53113 Bonn, Germany.
| | - Marcel Schilling
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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5
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Adlung L, Cohen Y, Mor U, Elinav E. Machine learning in clinical decision making. Med 2021; 2:642-665. [DOI: 10.1016/j.medj.2021.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/24/2022]
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6
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Tuganbaev T, Mor U, Bashiardes S, Liwinski T, Nobs SP, Leshem A, Dori-Bachash M, Thaiss CA, Pinker EY, Ratiner K, Adlung L, Federici S, Kleimeyer C, Moresi C, Yamada T, Cohen Y, Zhang X, Massalha H, Massasa E, Kuperman Y, Koni PA, Harmelin A, Gao N, Itzkovitz S, Honda K, Shapiro H, Elinav E. Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. Cell 2020; 182:1441-1459.e21. [DOI: 10.1016/j.cell.2020.08.027] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/27/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023]
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7
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8
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Matos ÂP, Kauffman A, Vickery C, Naegeli K, Strittmatter L, Sybirna A, van Blijswijk J, Adlung L, Berbasova T, Enterina J, Eismann L, Tierney B, Jordi J, Zhu L, Verkuijl S, Tallorin L, Wehling A, Ogden M, Lammel S, Hasslacher MK, Wuelfroth P, Neumann S, Tidona C, Betz UA. Synthetic Biology Category Wins the 350th Anniversary Merck Innovation Cup. Trends Biotechnol 2020; 38:1-4. [DOI: 10.1016/j.tibtech.2019.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/18/2022]
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Affiliation(s)
- Lorenz Adlung
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Amit
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany
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10
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Jaitin DA, Adlung L, Thaiss CA, Weiner A, Li B, Descamps H, Lundgren P, Bleriot C, Liu Z, Deczkowska A, Keren-Shaul H, David E, Zmora N, Eldar SM, Lubezky N, Shibolet O, Hill DA, Lazar MA, Colonna M, Ginhoux F, Shapiro H, Elinav E, Amit I. Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner. Cell 2019; 178:686-698.e14. [PMID: 31257031 PMCID: PMC7068689 DOI: 10.1016/j.cell.2019.05.054] [Citation(s) in RCA: 597] [Impact Index Per Article: 119.4] [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: 02/25/2019] [Revised: 04/18/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
Immune cells residing in white adipose tissue have been highlighted as important factors contributing to the pathogenesis of metabolic diseases, but the molecular regulators that drive adipose tissue immune cell remodeling during obesity remain largely unknown. Using index and transcriptional single-cell sorting, we comprehensively map all adipose tissue immune populations in both mice and humans during obesity. We describe a novel and conserved Trem2+ lipid-associated macrophage (LAM) subset and identify markers, spatial localization, origin, and functional pathways associated with these cells. Genetic ablation of Trem2 in mice globally inhibits the downstream molecular LAM program, leading to adipocyte hypertrophy as well as systemic hypercholesterolemia, body fat accumulation, and glucose intolerance. These findings identify Trem2 signaling as a major pathway by which macrophages respond to loss of tissue-level lipid homeostasis, highlighting Trem2 as a key sensor of metabolic pathologies across multiple tissues and a potential therapeutic target in metabolic diseases.
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Affiliation(s)
- Diego Adhemar Jaitin
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lorenz Adlung
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Christoph A Thaiss
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Baoguo Li
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hélène Descamps
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Lundgren
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Camille Bleriot
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Biopolis, Singapore 138648, Singapore
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | | | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Zmora
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shai Meron Eldar
- Division of Surgery, Tel-Aviv Medical Center and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Nir Lubezky
- Division of Surgery, Tel-Aviv Medical Center and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oren Shibolet
- Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - David A Hill
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Biopolis, Singapore 138648, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Hagit Shapiro
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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11
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Adlung L, Kar S, Wagner MC, She B, Chakraborty S, Bao J, Lattermann S, Boerries M, Busch H, Wuchter P, Ho AD, Timmer J, Schilling M, Höfer T, Klingmüller U. Protein abundance of AKT and ERK pathway components governs cell type-specific regulation of proliferation. Mol Syst Biol 2017; 13:904. [PMID: 28123004 PMCID: PMC5293153 DOI: 10.15252/msb.20167258] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell cycle progression, is poorly understood. Here, we study different hematopoietic cell types, in which AKT and ERK signaling is triggered by erythropoietin (Epo). Although these cell types share the molecular network topology for pro‐proliferative Epo signaling, they exhibit distinct proliferative responses. Iterating quantitative experiments and mathematical modeling, we identify two molecular sources for cell type‐specific proliferation. First, cell type‐specific protein abundance patterns cause differential signal flow along the AKT and ERK pathways. Second, downstream regulators of both pathways have differential effects on proliferation, suggesting that protein synthesis is rate‐limiting for faster cycling cells while slower cell cycles are controlled at the G1‐S progression. The integrated mathematical model of Epo‐driven proliferation explains cell type‐specific effects of targeted AKT and ERK inhibitors and faithfully predicts, based on the protein abundance, anti‐proliferative effects of inhibitors in primary human erythroid progenitor cells. Our findings suggest that the effectiveness of targeted cancer therapy might become predictable from protein abundance.
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Affiliation(s)
- Lorenz Adlung
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandip Kar
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany.,Department of Chemistry, Indian Institute of Technology, Mumbai, India
| | - Marie-Christine Wagner
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bin She
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sajib Chakraborty
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Bao
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany
| | - Susen Lattermann
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Wuchter
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany.,Institute for Transfusion Medicine and Immunology, University of Heidelberg, Mannheim, Germany
| | - Anthony D Ho
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Jens Timmer
- Center for Biological Signaling Studies (BIOSS), Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Marcel Schilling
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany .,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany .,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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12
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Wolf D, Rippa V, Mobarec JC, Sauer P, Adlung L, Kolb P, Bischofs IB. The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs. Nucleic Acids Res 2015; 44:2160-72. [PMID: 26582911 PMCID: PMC4797271 DOI: 10.1093/nar/gkv1242] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/30/2015] [Indexed: 11/27/2022] Open
Abstract
ComA-like transcription factors regulate the quorum response in numerous Gram-positive bacteria. ComA proteins belong to the tetrahelical helix-turn-helix superfamily of transcriptional activators, which bind as homodimers to inverted sequence repeats in the DNA. Here, we report that ComA from Bacillus subtilis recognizes a topologically distinct motif, in which the binding elements form a direct repeat. We provide in vitro and in vivo evidence that the canonical and non-canonical site play an important role in facilitating type I and type II promoter activation, respectively, by interacting with different subunits of RNA polymerase. We furthermore show that there is a variety of contexts in which the non-canonical site can occur and identify new direct target genes that are located within the integrative and conjugative element ICEBs1. We therefore suggest that ComA acts as a multifunctional transcriptional activator and provides a striking example for complexity in protein–DNA interactions that evolved in the context of quorum sensing.
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Affiliation(s)
- Diana Wolf
- Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Valentina Rippa
- Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Juan Carlos Mobarec
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Patricia Sauer
- Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Lorenz Adlung
- Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Ilka B Bischofs
- Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
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13
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Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, Tönsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, Höfer T, Klipp E, Theis F, Klingmüller U, Schöberl B, Timmer J. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 2015; 31:3558-60. [PMID: 26142188 DOI: 10.1093/bioinformatics/btv405] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/28/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions and to perform efficient and reliable parameter estimation for model fitting. We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such as the solving of the differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient C code. A variety of parameter estimation algorithms as well as frequentist and Bayesian methods for uncertainty analysis have been implemented and used on a range of applications that lead to publications. AVAILABILITY AND IMPLEMENTATION The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org. CONTACT andreas.raue@fdm.uni-freiburg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A Raue
- Merrimack Pharmaceuticals Inc., Discovery Devision, Cambridge, MA 02139, USA
| | - B Steiert
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - M Schelker
- Humboldt-Universität zu Berlin, Theoretical Biophysics, 10115 Berlin, Germany
| | - C Kreutz
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - T Maiwald
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - H Hass
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - J Vanlier
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - C Tönsing
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - L Adlung
- Systems Biology of Signal Transduction and
| | - R Engesser
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - W Mader
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - T Heinemann
- Divison of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - J Hasenauer
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany, Technische Universität München, Department of Mathematics, 85748 Garching, Germany and
| | | | - T Höfer
- Divison of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - E Klipp
- Humboldt-Universität zu Berlin, Theoretical Biophysics, 10115 Berlin, Germany
| | - F Theis
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany, Technische Universität München, Department of Mathematics, 85748 Garching, Germany and
| | | | - B Schöberl
- Merrimack Pharmaceuticals Inc., Discovery Devision, Cambridge, MA 02139, USA
| | - J Timmer
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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14
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Boehm ME, Adlung L, Schilling M, Roth S, Klingmüller U, Lehmann WD. Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent STAT5 Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling. J Proteome Res 2014; 13:5685-94. [DOI: 10.1021/pr5006923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | | | | | - Susanne Roth
- Systems
Bioinformatics, Netherlands Institute for Systems Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, Netherlands
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15
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Beer R, Herbst K, Ignatiadis N, Kats I, Adlung L, Meyer H, Niopek D, Christiansen T, Georgi F, Kurzawa N, Meichsner J, Rabe S, Riedel A, Sachs J, Schessner J, Schmidt F, Walch P, Niopek K, Heinemann T, Eils R, Di Ventura B. Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange. ACTA ACUST UNITED AC 2014; 10:1709-18. [DOI: 10.1039/c3mb70594c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Production of indigoidine can be enhanced by swapping a synthetic T domain into the NRPS IndC.
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