Integrated single-cell analysis unveils diverging immune features of COVID-19, influenza, and other community-acquired pneumonia
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Netherlands
Figures
Figure 1 with 2 supplements
The immune response in COVID-19 is characterized by an expansion of CD8 EMRA-like T cells and type I interferon-stimulated NK cells, both demonstrating high cytotoxic potential.
(a) Experimental overview: PBMCs from a matched cohort of hospitalized patients with CAP caused by SARS-CoV-2 (COVID-19), CAP caused by Influenza A or other pathogens, and non-infectious controls, …
Figure 1—figure supplement 1
mRNA, surface protein expression, and cell cluster distribution of patients with COVID-19 and non-infectious controls.
(a) Heatmap depicting mRNA expression of genes identified via differential expression analysis comparing the clusters identified by the single-cell transcriptomic analysis of PBMCs from control …
Figure 1—figure supplement 2
Comprehensive gene expression profile of T and NK cells in patients with COVID-19 compared with non-infectious controls.
(a) Heatmap depicting normalized mRNA expression of genes identified via differential expression analysis comparing CD8 EM and EMRA-like T cells (adjusted p<0.05) as depicted in Figure 1E. The …
Figure 2 with 2 supplements
The peripheral immune features of T cells, NK cells, and monocytes vary between CAP-flu and CAP-other.
(a, b) UMAPs depicting the clusters identified by the single-cell transcriptomic analysis of PBMCs from controls, CAP-flu, and CAP-other patients, where each dot represents a single cell. In the …
Figure 2—figure supplement 1
mRNA, surface protein expression, and cell cluster distribution of controls, patients with CAP-flu, and patients with CAP-other.
(a) Heatmap depicting mRNA expression of genes identified via differential expression analysis comparing the clusters identified by the single-cell transcriptomic analysis of PBMCs from control …
Figure 2—figure supplement 2
Differentially expressed genes of T cell, NK cell, and monocyte clusters between patients with CAP-flu, CAP-other, and control subjects.
(a, b) Dot plot depicting the differentially expressed genes (adjusted p<0.05) between PBMCs from CAP-flu patients and control subjects present in the CD8 EMRA-like cell cluster (a) or NK cell …
Figure 3 with 2 supplements
Divergent composition of major immune cell types in patients with COVID-19, CAP-flu, and CAP-other.
(a, b) UMAPs depicting the metaclusters identified by the single-cell transcriptomic analysis of PBMCs from controls, COVID-19, CAP-flu, and CAP-other patients, where each dot represents a single …
Figure 3—figure supplement 1
Cell clusters in individual samples from COVID-19, CAP-flu, and CAP-other.
(a) UMAP depicting all 15 clusters identified by the single-cell transcriptomic analysis of PBMCs from COVID-19, CAP-flu, and CAP-other patients, where each dot represents a single cell with each …
Figure 3—figure supplement 2
Differential mRNA and surface protein expression between COVID-19, CAP-flu, and CAP-other patients.
(a) Heatmap depicting normalized mRNA expression of genes identified via differential expression analysis comparing all 15 cell clusters identified by the single-cell transcriptomic analysis of …
Figure 4
CAP-flu is characterized by expansion of T cells and NK cells expressing granulysin, while COVID-19 T and NK cells exhibit a clear type I interferon signature.
(a) UMAP depicting the T and NK cell clusters identified by the single-cell transcriptomic analysis of PBMCs from COVID-19, CAP-flu, and CAP-other patients, where each dot represents a single cell …
Figure 5
Distinctive subset compositions and transcriptional profiles in monocytes from patients with COVID-19, CAP-flu, and CAP-other.
(a) UMAP depicting the monocyte cell clusters identified by the single-cell transcriptomic analysis of PBMCs from COVID-19, CAP-flu, and CAP-other patients, where each dot represents a single cell …
Tables
Table 1
Clinical characteristics and disease course.
ACE = angiotensin-converting enzyme; AT-II = angiotensin II; CAP = community-acquired pneumonia; CURB-65 = confusion, blood urea nitrogen, respiratory rate, blood pressure, age 65 or older; COPD = …
| COVID-19 (n=8) | CAP* (n=8) | Controls (n=4) | |
|---|---|---|---|
| Demographics | |||
| Age (years) | 66.9 (9.4) | 70.9 (14.3) | 72.2 (1.7) |
| Sex (male) | 5 | 5 | 2 |
| Body mass index | 32.8 (6.5) | 23.8 (7.6) | 25.7 (4.9) |
| Race (white/black) | 4/4 | 7/1 | 4/0 |
| Chronic comorbidities | |||
| COPD | 0 | 3 | 0 |
| Asthma | 0 | 2 | 0 |
| Hypertension | 4 | 3 | 1 |
| History of myocardial infarction | 0 | 2 | 0 |
| History of stroke | 1 | 0 | 1 |
| Diabetes mellitus, type 2 | 3 | 1 | 1 |
| Chronic kidney disease | 0 | 1 | 1 |
| Chronic medications | |||
| Inhaled corticosteroids | 0 | 2 | 0 |
| Low-dose oral corticosteroids† | 0 | 1 | 0 |
| ACE-inhibitor/AT-II antagonist | 4 | 3 | 1 |
| Statins | 3 | 1 | 3 |
| Platelet aggregation inhibitors | 2 | 1 | 2 |
| Laboratory tests | |||
| Platelets (×109/L) | 284 (112) | 294 (85) | |
| Leukocytes (×109/L) | 5.7 [2.6, 7.2] | 13.9 [6.0, 19.5] | |
| Neutrophils (×109/L) | 4.4 [1.5, 5.8] | 11.7 [5.3, 17.9] | |
| Lymphocytes (×109/L) | 0.8 [0.4, 1.5] | 1.1 [0.5, 3.1] | |
| Severity scores‡ | |||
| Modified Early Warning Score | 3.5 [1.0, 5.0] | 3.5 [2.0, 6.0] | |
| Pneumonia Severity Index | 3.0 [2.0, 4.0] | 3.5 [1.0, 5.0] | |
| CURB-65 | 1.0 [0.0, 2.0] | 1.0 [0.0, 3.0] | |
| qSOFA | 1.0 [0.0, 1.0] | 1.0 [0.0, 1.0] | |
| Disease course | |||
| Symptoms to admission (days) | 10.0 [2.0, 14.0] | 3.5 [2.0, 9.0] | |
| Hospital length of stay (days) | 3.5 [1.0, 6.0] | 3.0 [2.0, 8.0] | |
| 28 day mortality | 1 | 0 |
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Continuous data are presented as mean (standard deviation) or median (range). Categorical data are presented as counts.
* Caused by either Influenza A, bacterial, or unknown pathogens.
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† Corticosteroids<7.5mg prednisolone/day.
‡ Measured upon presentation to the emergency department.
Table 2
Overview of proportionally increased cell clusters and transcriptional characteristics in the direct comparison between COVID-19, CAP-flu, and CAP-other.
| COVID-19 | CAP-flu | CAP-other | |
|---|---|---|---|
| NK cells | Granulysin+ NK cells ↑ higher type I interferon response than CAP-flu NK cells high IFITM3 expression | Granulysin+ NK cells ↑↑ higher AREG expression than COVID-19 | Low numbers of NK cells |
| T cells | CD8 EMRA-like 2 ↑ cytotoxicity, activation and inflammation | CD8 EMRA-like 2 ↑↑ cytotoxicity, activation and inflammation | Naive CD4/CD8 not activated CD8 EM less activated than EMRA-like 1 and 2 clusters |
| Monocytes | Intermediate monocytes high type I interferon response, increased antiviral potential | Classical monocytes ribosomal and viral transcription genes | Non-classical monocytes heterogenous gene expression |
Additional files
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Supplementary file 1
Overview of clinical data per individual subject.
- https://cdn.elifesciences.org/articles/69661/elife-69661-supp1-v1.xlsx
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Supplementary file 2
Overview of all antibodies that were used in this study.
- https://cdn.elifesciences.org/articles/69661/elife-69661-supp2-v1.xlsx
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Supplementary file 3
Overview of technical information per sample.
- https://cdn.elifesciences.org/articles/69661/elife-69661-supp3-v1.csv
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Transparent reporting form
- https://cdn.elifesciences.org/articles/69661/elife-69661-transrepform-v1.pdf
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Reporting standard 1
Strobe checklist.
- https://cdn.elifesciences.org/articles/69661/elife-69661-repstand1-v1.pdf
