1
|
Rizzo G, Gropper J, Piollet M, Vafadarnejad E, Rizakou A, Bandi SR, Arampatzi P, Krammer T, DiFabion N, Dietrich O, Arias-Loza AP, Prinz M, Mack M, Schlepckow K, Haass C, Silvestre JS, Zernecke A, Saliba AE, Cochain C. Dynamics of monocyte-derived macrophage diversity in experimental myocardial infarction. Cardiovasc Res 2023; 119:772-785. [PMID: 35950218 PMCID: PMC10153424 DOI: 10.1093/cvr/cvac113] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/07/2022] [Accepted: 06/26/2022] [Indexed: 05/03/2023] Open
Abstract
AIMS Macrophages have a critical and dual role in post-ischaemic cardiac repair, as they can foster both tissue healing and damage. Multiple subsets of tissue resident and monocyte-derived macrophages coexist in the infarcted heart, but their precise identity, temporal dynamics, and the mechanisms regulating their acquisition of discrete states are not fully understood. To address this, we used multi-modal single-cell immune profiling, combined with targeted cell depletion and macrophage fate mapping, to precisely map monocyte/macrophage transitions after experimental myocardial infarction. METHODS AND RESULTS We performed single-cell transcriptomic and cell-surface marker profiling of circulating and cardiac immune cells in mice challenged with acute myocardial infarction, and integrated single-cell transcriptomes obtained before and at 1, 3, 5, 7, and 11 days after infarction. Using complementary strategies of CCR2+ monocyte depletion and fate mapping of tissue resident macrophages, we determined the origin of cardiac macrophage populations. The macrophage landscape of the infarcted heart was dominated by monocyte-derived cells comprising two pro-inflammatory populations defined as Isg15hi and MHCII+Il1b+, alongside non-inflammatory Trem2hi cells. Trem2hi macrophages were observed in the ischaemic area, but not in the remote viable myocardium, and comprised two subpopulations sequentially populating the heart defined as Trem2hiSpp1hi monocyte-to-macrophage intermediates, and fully differentiated Trem2hiGdf15hi macrophages. Cardiac Trem2hi macrophages showed similarities to 'lipid-associated macrophages' found in mouse models of metabolic diseases and were observed in the human heart, indicating conserved features of this macrophage state across diseases and species. Ischaemic injury induced a shift of circulating Ly6Chi monocytes towards a Chil3hi state with granulocyte-like features, but the acquisition of the Trem2hi macrophage signature occurred in the ischaemic tissue. In vitro, macrophages acquired features of the Trem2hi signature following apoptotic-cell efferocytosis. CONCLUSION Our work provides a comprehensive map of monocyte/macrophage transitions in the ischaemic heart, constituting a valuable resource for further investigating how these cells may be harnessed and modulated to promote post-ischaemic heart repair.
Collapse
Affiliation(s)
- Giuseppe Rizzo
- Comprehensive Heart Failure Center, University Hospital Würzburg, Am Schwarzenberg 15, A15, 97078 Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| | - Julius Gropper
- Comprehensive Heart Failure Center, University Hospital Würzburg, Am Schwarzenberg 15, A15, 97078 Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| | - Marie Piollet
- Comprehensive Heart Failure Center, University Hospital Würzburg, Am Schwarzenberg 15, A15, 97078 Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Str. 2, D15, 97080 Würzburg, Germany
| | - Anna Rizakou
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| | - Sourish Reddy Bandi
- Comprehensive Heart Failure Center, University Hospital Würzburg, Am Schwarzenberg 15, A15, 97078 Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| | - Panagiota Arampatzi
- Core Unit Systems Medicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D15, 97080 Würzburg, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Str. 2, D15, 97080 Würzburg, Germany
| | - Nina DiFabion
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Str. 2, D15, 97080 Würzburg, Germany
| | - Oliver Dietrich
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Str. 2, D15, 97080 Würzburg, Germany
| | - Anahi-Paula Arias-Loza
- Comprehensive Heart Failure Center, University Hospital Würzburg, Am Schwarzenberg 15, A15, 97078 Würzburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Mack
- Department of Internal Medicine II, Nephrology, Franz-Josef-Strauss Allee 11, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Kai Schlepckow
- German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | | | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Str. 2, D15, 97080 Würzburg, Germany
| | - Clément Cochain
- Comprehensive Heart Failure Center, University Hospital Würzburg, Am Schwarzenberg 15, A15, 97078 Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Josef-Schneider-Str. 2, D16, 97080 Würzburg, Germany
| |
Collapse
|
2
|
Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T. Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information. Front Med (Lausanne) 2022; 9:1008527. [PMID: 36405591 PMCID: PMC9669072 DOI: 10.3389/fmed.2022.1008527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2023] Open
Abstract
Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.
Collapse
Affiliation(s)
- Shishir K. Gupta
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Özge Osmanoglu
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Rashmi Minocha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sourish Reddy Bandi
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- BioComputing Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| |
Collapse
|
3
|
Vafadarnejad E, Rizzo G, Krampert L, Arampatzi P, Arias-Loza AP, Nazzal Y, Rizakou A, Knochenhauer T, Bandi SR, Nugroho VA, Schulz DJJ, Roesch M, Alayrac P, Vilar J, Silvestre JS, Zernecke A, Saliba AE, Cochain C. Dynamics of Cardiac Neutrophil Diversity in Murine Myocardial Infarction. Circ Res 2020; 127:e232-e249. [PMID: 32811295 DOI: 10.1161/circresaha.120.317200] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RATIONALE After myocardial infarction, neutrophils rapidly and massively infiltrate the heart, where they promote both tissue healing and damage. OBJECTIVE To characterize the dynamics of circulating and cardiac neutrophil diversity after infarction. METHODS AND RESULTS We employed single-cell transcriptomics combined with cell surface epitope detection by sequencing to investigate temporal neutrophil diversity in the blood and heart after murine myocardial infarction. At day 1, 3, and 5 after infarction, cardiac Ly6G+ (lymphocyte antigen 6G) neutrophils could be delineated into 6 distinct clusters with specific time-dependent patterning and proportions. At day 1, neutrophils were characterized by a gene expression profile proximal to bone marrow neutrophils (Cd177, Lcn2, Fpr1), and putative activity of transcriptional regulators involved in hypoxic response (Hif1a) and emergency granulopoiesis (Cebpb). At 3 and 5 days, 2 major subsets of Siglecfhi (enriched for eg, Icam1 and Tnf) and Siglecflow (Slpi, Ifitm1) neutrophils were found. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) analysis in blood and heart revealed that while circulating neutrophils undergo a process of aging characterized by loss of surface CD62L and upregulation of Cxcr4, heart infiltrating neutrophils acquired a unique SiglecFhi signature. SiglecFhi neutrophils were absent from the bone marrow and spleen, indicating local acquisition of the SiglecFhi signature. Reducing the influx of blood neutrophils by anti-Ly6G treatment increased proportions of cardiac SiglecFhi neutrophils, suggesting accumulation of locally aged neutrophils. Computational analysis of ligand/receptor interactions revealed putative pathways mediating neutrophil to macrophage communication in the myocardium. Finally, SiglecFhi neutrophils were also found in atherosclerotic vessels, revealing that they arise across distinct contexts of cardiovascular inflammation. CONCLUSIONS Altogether, our data provide a time-resolved census of neutrophil diversity and gene expression dynamics in the mouse blood and ischemic heart at the single-cell level, and reveal a process of local tissue specification of neutrophils in the ischemic heart characterized by the acquisition of a SiglecFhi signature.
Collapse
Affiliation(s)
- Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany (E.V., A.-E.S.)
| | - Giuseppe Rizzo
- Comprehensive Heart Failure Center Wuerzburg (G.R., L.K., A.-P.A.-L., V.A.N., D.J.J.S., C.C.), University Hospital Wuerzburg, Germany.,Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Laura Krampert
- Comprehensive Heart Failure Center Wuerzburg (G.R., L.K., A.-P.A.-L., V.A.N., D.J.J.S., C.C.), University Hospital Wuerzburg, Germany.,Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | | | - Anahi-Paula Arias-Loza
- Comprehensive Heart Failure Center Wuerzburg (G.R., L.K., A.-P.A.-L., V.A.N., D.J.J.S., C.C.), University Hospital Wuerzburg, Germany
| | - Yara Nazzal
- Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Anna Rizakou
- Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Tim Knochenhauer
- Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Sourish Reddy Bandi
- Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Vallery Audy Nugroho
- Comprehensive Heart Failure Center Wuerzburg (G.R., L.K., A.-P.A.-L., V.A.N., D.J.J.S., C.C.), University Hospital Wuerzburg, Germany.,Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Dirk J J Schulz
- Comprehensive Heart Failure Center Wuerzburg (G.R., L.K., A.-P.A.-L., V.A.N., D.J.J.S., C.C.), University Hospital Wuerzburg, Germany.,Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Melanie Roesch
- Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Paul Alayrac
- Université de Paris, PARCC, INSERM, F-75015 Paris, France (P. Alayrac, J.V., J.-S.S.)
| | - Jose Vilar
- Université de Paris, PARCC, INSERM, F-75015 Paris, France (P. Alayrac, J.V., J.-S.S.)
| | | | - Alma Zernecke
- Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany (E.V., A.-E.S.)
| | - Clément Cochain
- Comprehensive Heart Failure Center Wuerzburg (G.R., L.K., A.-P.A.-L., V.A.N., D.J.J.S., C.C.), University Hospital Wuerzburg, Germany.,Institute of Experimental Biomedicine (G.R., L.K.,Y.N., A.R., T.K., S.R.B., V.A.N., D.J.J.S., M.R., A.Z., C.C.), University Hospital Wuerzburg, Germany
| |
Collapse
|