Efferocytosis of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory functions and clearance of apoptotic cells
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
- Hospital Israelita Albert Einstein, Brazil
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Farmacologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
- Center of Research in Inflammatory Diseases (CRID), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
- Divisão de Imunologia Clinica, Emergência, Doenças Infecciosas e Unidade de Terapia Intensiva, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
- Departamento de Patologia e Medicina Legal, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
- Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Brazil
Figures
Figure 1 with 1 supplement
Macrophages engulf apoptotic cells (AC) carrying viable SARS-CoV-2.
(A) Immunoblot of caspase-8 and caspase-3 cleavage in Calu-3 and Vero CCL81 cells in response to infection with SARS-CoV-2 for 48 hr (CoV2, detected with rabbit anti-Spike), UV irradiation (UV), or …
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Figure 1—source data 1
Source data for Figure 1.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig1-data1-v2.xlsx
Figure 1—figure supplement 1
Support data for Figure 1.
(A) Immunofluorescence images of tissue samples immunolabeled with secondary antibodies only used for detection of anti-cleaved caspase-3 (red, anti-rabbit IgG conjugated to Alexa 594), anti-dsRNA …
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Figure 1—figure supplement 1—source data 1
Source data for Figure 1—figure supplement 1.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig1-figsupp1-data1-v2.xlsx
Figure 2 with 1 supplement
Engulfment of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory functions.
Macrophages were unstimulated (Cntrl), co-incubated with apoptotic Vero CCL81 cells (AC) isolated from UV-irradiated (UV-AC) or SARS-CoV-2-infected (CoV2-AC) cultures, stimulated with the …
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Figure 2—source data 1
Source data for Figure 2.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Support data for Figure 2.
(A) Representative gating strategy used to determine the CD206 expression on the surface of macrophages in response to the different stimuli by flow cytometry (backgating corresponds to FMO control …
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Figure 2—figure supplement 1—source data 1
Source data for Figure 2—figure supplement 1.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig2-figsupp1-data1-v2.xlsx
Figure 3 with 1 supplement
Engulfment of SARS-CoV-2-infected dying cells causes inflammatory cytokine production.
Macrophages were left unstimulated (Cntrl), co-incubated with apoptotic Vero CCL81 cells (AC) isolated from UV-irradiated (UV-AC) or SARS-CoV-2-infected (CoV2-AC) cultures, stimulated with the …
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Figure 3—source data 1
Source data for Figure 3.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig3-data1-v2.xlsx
Figure 3—figure supplement 1
Support data for Figure 3.
(A) THP-1-derived macrophages were incubated with UV-AC, Cov2-AC, or CoV2-Sup obtained from infected Vero CCL81 cells or infected with CoV2. Expression of IL6 in macrophages showed as fold change …
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Figure 3—figure supplement 1—source data 1
Source data for Figure 3—figure supplement 1.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig3-figsupp1-data1-v2.xlsx
Figure 4 with 1 supplement
Engulfment of SARS-CoV-2-infected dying cells suppresses continual efferocytosis by macrophages.
(A) Expression of efferocytic receptors in human primary monocyte-derived macrophages. Macrophages were left unstimulated (Cntrl), co-incubated for 24 hr with apoptotic Vero CCL81 cells (AC) …
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Figure 4—source data 1
Source data for Figure 4.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig4-data1-v2.xlsx
Figure 4—figure supplement 1
Support data for Figure 4.
(A) THP-1-derived macrophages were incubated with UV-AC or CoV2-AC obtained from infected Vero CCL81 cells or infected with CoV2. Expression of the efferocytic receptors CD36, SRA-I, ITGB5, TIMD4, …
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Figure 4—figure supplement 1—source data 1
Source data for Figure 4—figure supplement 1.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig4-figsupp1-data1-v2.xlsx
Figure 5
Lung monocytes and macrophages of severe COVID-19 patients express reduced levels of efferocytic receptors.
(A–B) Representative histological findings in post-mortem lung tissue from control patients (Cntrl) and COVID-19 patients, obtained by ultrasound-guided minimally invasive autopsy. Tissue samples …
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Figure 5—source data 1
Source data for Figure 5.
- https://cdn.elifesciences.org/articles/74443/elife-74443-fig5-data1-v2.xlsx
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | anti-Sars-CoV-2 Spike (rabbit polyclonal) | Abcam | Cat: #ab272504 RRID: AB_2847845 | WB and FACS (1:1000); Immunofluorescence (1:1000) |
| Antibody | anti-CD11b+CD11 c (mouse monoclonal) | Abcam | Cat: #ab1211 RRID: AB_442947 | Immunofluorescence (1:300) |
| Antibody | anti-human CD68 (mouse monoclonal) | Abcam | Cat: #ab955 RRID: AB_307338 | Immunofluorescence (1:100) |
| Antibody | anti-CD206-FITC (mouse monoclonal) | BD Biosciences | Cat: #551135 RRID: AB_394065 | FACS (1:200) |
| Antibody | anti-caspase-3 (rabbit polyclonal) | Cell Signaling | Cat: #9662 RRID: AB_331439 | WB (1:1000) |
| Antibody | anti-cleaved caspase-3 (rabbit monoclonal) | Cell Signaling | Cat: #9664 RRID: AB_10694088 | WB and Immunofluorescence (1:1000); FACS (1:200) |
| Antibody | anti-caspase-8 (rabbit monoclonal) | Cell Signaling | Cat: #4790 RRID: AB_10545768 | WB (1:1000) |
| Antibody | anti-cleaved caspase-8 (rabbit monoclonal) | Cell Signaling | Cat: #9496 RRID: AB_561381 | WB (1:1000) |
| Antibody | anti-βactin HRP conjugate (mouse monoclonal) | Cell Signaling | Cat: #12262 RRID: AB_2566811 | WB (1:5000) |
| Antibody | anti-human CD36 (rabbit polyclonal) | Thermo Fisher Scientific | Cat: # PA5-81996 RRID: AB_2789157 | Immunofluorescence (1:100) |
| Antibody | anti-human Mertk (rabbit monoclonal) | Thermo Fisher Scientific | Cat: # MA5-31991 RRID: AB_2809285 | Immunofluorescence (1:150) |
| Antibody | anti-human cytokeratin 18 (rabbit polyconal) | GeneTex | Cat: #GTX112977 RRID: AB_10719880 | Immunofluorescence (1:500) |
| Antibody | anti-dsRNA J2 (mouse monoclonal) | SCICONS English & Scientific Consulting Kft | Cat: #10010200 RRID: AB_2651015 | Immunofluorescence (1:1000) |
| Antibody | donkey anti-rabbit IgG HRP (donkey polyclonal) | Jackson ImmunoResearch | Cat: #711-036-152 RRID: AB_2340590 | WB (1:5000) |
| Antibody | Alexa-594 goat-anti mouse IgG (goat polyclonal) | Thermo Fisher Scientific | Cat: #A11005 RRID: AB_2534073 | Immunofluorescence (1:500) |
| Antibody | Alexa-488 donkey-anti rabbit IgG (donkey polyclonal) | Thermo Fisher Scientific | Cat: #A21206 RRID: AB_2535792 | FACS (1:2500) and Immunofluorescence (1:500) |
| Antibody | Alexa-594 goat-anti rabbit IgG (goat polyclonal) | Thermo Fisher Scientific | Cat: #A11012 RRID: AB_141359 | Immunofluorescence (1:500 or 1:1000) |
| Antibody | Alexa-488 F(ab)'2 goat-anti mouse IgG (goat polyclonal) | Thermo Fisher Scientific | Cat: #A11017 RRID: AB_2534084 | Immunofluorescence (1:500) |
| Antibody | Alexa-647 donkey-anti mouse IgG (donkey polyclonal) | Thermo Fisher Scientific | Cat: #A31571 RRID: AB_162542 | Immunofluorescence (1:500 or 1:1000) |
| Antibody | Alexa-647 goat anti-rabbit IgG (goat polyclonal) | Thermo Fisher Scientific | Cat: #A21244 RRID: AB_2535812 | Immunofluorescence (1:500) |
| Cell line (Homo sapiens) | Calu-3 | BCRJ #0264 | ATCC #HTB-55 | |
| Cell line (H. sapiens) | Jurkat E6-1 | BCRJ #0125 | ATCC #TIB-152 | |
| Cell line (H. sapiens) | THP-1 | Dario Zamboni’s lab | ATCC: #TIB-202 | |
| Cell line (Cercopithecus aethiops) | Vero CCL81 | Dario Zamboni’s lab | ATCC: #CCL-81 | |
| Strain, strain background (human) | SARS-CoV-2 | Brazil/SPBR-02/2020 | ||
| Strain, strain background (human) | Coxsackievirus B5 | Roger M. Loria’s lab | ||
| Chemical compound, drug | FITC Annexin V | BD Biosciences | Cat: #556,420 | FACS (1:200) |
| Chemical compound, drug | Purified Recombinant Annexin V | BD Biosciences | Cat: #556,416 | |
| Chemical compound, drug | Zombie NIR Fixable Viability | Biolegend | Cat: #423,106 | FACS (1:400) |
| Chemical compound, drug | Zombie Violet Fixable Viability Kit | Biolegend | Cat: #423,114 | FACS (1:400) |
| Chemical compound, drug | Remdesivir | BOC Sciences | Cat: #1809249-37-3 | |
| Chemical compound, drug | phorbol 12-myristate 13-acetate (PMA) | InvivoGen | Cat: #Tlrl-pma | |
| Chemical compound, drug | Annexin V MicroBeads | Miltenyi Biotec | Cat: #130-090-201 | |
| Chemical compound, drug | Z-VAD-FMK | Selleckchem | Cat: #S7023 | |
| Chemical compound, drug | Glycine | Sigma | Cat: #G7126 | |
| Chemical compound, drug | complete, Mini Protease Inhibitor Cocktail | Sigma | Cat: #11836153001 | |
| Chemical compound, drug | Cytochalasin D | Sigma | Cat: #C8273 | |
| Chemical compound, drug | CellTrace CFSE Cell Proliferation Kit | Thermo Fisher Scientific | Cat: #C34554 | |
| Chemical compound, drug | CellTrace Far Red Cell Proliferation Kit | Thermo Fisher Scientific | Cat: #C34564 | |
| Chemical compound, drug | CellTrace Violet Cell Proliferation Kit | Thermo Fisher Scientific | Cat: #C34557 | |
| Chemical compound, drug | pHrodo Red AM Intracellular pH Indicator | Thermo Fisher Scientific | Cat: #P35372 | |
| Chemical compound, drug | Hoechst 33,342 | Thermo Fisher Scientific | Cat: #H3570 | |
| Commercial assay or kit | BD Cytofix/Cytoperm Fixation/Permeabilization Kit | BD Biosciences | Cat: #554,715 | |
| Commercial assay or kit | CytoTox 96 Non-Radioactive Cytotoxicity Assay | BD Biosciences | Cat: #G1780 | |
| Commercial assay or kit | Human Inflammatory Cytokine Cytometric Bead Array (CBA) | BD Biosciences | Cat: #551,811 | |
| Commercial assay or kit | Human IL-6 DuoSet ELISA | R&D Systems | Cat: #DY206-05 | |
| Commercial assay or kit | PowerUp SYBR Green Master Mix | Thermo Fisher Scientific | Cat: #A25742 | |
| Commercial assay or kit | Zenon Rabbit IgG Labeling Kits | Thermo Fisher Scientific | Cat: #Z25306 | |
| Commercial assay or kit | Direct-zol RNA Miniprep Kits | Zymo Research | Cat: #R2052 | |
| Software, algorithm | Adobe Photoshop | Adobe Inc | ||
| Software, algorithm | FlowJo v10.8.0 | FlowJo, LLC | ||
| Software, algorithm | Graphpad PRISM 8.0 | GraphPad Software, Inc | ||
| Software, algorithm | ImageJ (Fiji) | National Institutes of Health | ||
| Software, algorithm | NIS Elements | Nikon Instruments Inc. | ||
| Software, algorithm | ClusterProfiler | Wu et al., 2021 | ||
| Software, algorithm | fgsea R | Korotkevich et al., 2016 | ||
| Software, algorithm | R v4.0.4 | |||
| Software, algorithm | Seurat v4.1.0 | Stuart et al., 2019 | ||
| Software, algorithm | Enrichr | Chen et al., 2013 |
Additional files
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Supplementary file 1
Custom gene sets incorporating associated to efferocytic pathway and related to human diseases (related to Figure 5C).
- https://cdn.elifesciences.org/articles/74443/elife-74443-supp1-v2.docx
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Supplementary file 2
Medical characteristics of COVID-19 patients.
- https://cdn.elifesciences.org/articles/74443/elife-74443-supp2-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/74443/elife-74443-transrepform1-v2.pdf
