Single-Cell Analysis Reveals Macrophage-Driven T Cell Dysfunction in Severe COVID-19 Patients

Abstract

The vastly spreading COVID-19 pneumonia is caused by SARS-CoV-2. Lymphopenia and cytokine levels are tightly associated with disease severity. However, virus-induced immune dysregulation at cellular and molecular levels remains largely undefined. Here, the leukocytes in the pleural effusion, sputum, and peripheral blood biopsies from severe and mild patients were analyzed at single-cell resolution. Drastic T cell hyperactivation accompanying elevated T cell exhaustion was observed, predominantly in pleural effusion. The mechanistic investigation identified a group of CD14+ monocytes and macrophages highly expressing CD163 and MRC1 in the biopsies from severe patients, suggesting M2 macrophage polarization. These M2-like cells exhibited up-regulated IL10, CCL18, APOE, CSF1 (M-CSF), and CCL2 signaling pathways. Further, SARS-CoV-2-specific T cells were observed in pleural effusion earlier than in peripheral blood. Together, our results suggest that severe SARS-CoV-2 infection causes immune dysregulation by inducing M2 polarization and subsequent T cell exhaustion. This study improves our understanding of COVID-19 pathogenesis.

Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution

“…All of the pan-ligands we report have been previously implicated in SARSr-CoV infection, with IL-18, CCL8, and IFN-γ having been detected in serum from COVID-19 patients [9,13,14], SPP1 upregulation measured in microarrays from SARS-CoV-infected nonhuman primates, and CCL3, CCL8, IL18, and IFNG upregulation detected in single-cell or bulk RNA-seq from the lungs of COVID-19 patients [21,22,27,28]. Importantly, our data supports accumulating evidence for a nuanced interferon response in severe disease depending on cell type and local versus systemic immune environment, as discussed above [25,26,28,33,34,36,55]. We suspect that treatment strategies consisting of a direct type II interferon blockade (NIH clinical trial NCT04324021) [62,63] would exert different effects systemically and locally.…”

“…Cell type-specific immunopathological responses in severe COVID-19 have been investigated at both local and systemic levels in recent studies comparing severe patients to healthy controls [21,22,23,24,25,26,32,53,54,55]. We sought to build on this knowledge by determining the cell-type specific biological responses that differentiate mild and severe disease courses in the lung and systemic circulation.…”

“…A number of recent studies have compared severe patients to healthy control subjects in an effort to define immunological hallmarks of disease severity in both the lung and peripheral circulation using scRNA-seq. These studies have identified that severe disease in the lung compartment is associated with lymphopenia, T cell hyperactivation, and inflammatory macrophage polarization, while severe disease in the blood is associated with lymphopenia, suppression of type I and type II interferon activity, and decreased monocyte HLA class II expression [23,24,25,26]. Although these studies describe immunological dysregulation in severe COVID-19 patients requiring intensive care, they do not explore immunological features distinguishing these patients from those who experience a mild to moderate symptomatic disease course that does not become life-threatening.…”

Teaching Old Dogs New Tricks? The Plasticity of Lung Alveolar Macrophage Subsets

“…Infiltration of inflammatory monocytes and macrophages (IMMs) has been previously reported in fatal cases of SARS [ 84 ] and IMMs were shown to be responsible for the increased expression of proinflammatory cytokines, including IL-6 and IL-1β, in the SARS mouse model [ 85 , 86 ]. Single-cell RNA-seq (scRNA-seq) has revealed an altered macrophage composition in the lungs of patients with moderate or severe COVID-19, with a drastically reduced resident AM population and emerging populations expressing monocyte-like markers, but also AMs with a reparative but potentially profibrotic phenotype [ 77 , 87 ]. Also, peripheral blood classical monocytes can express increased amounts of IL-6 and IL-1β [ 80 , 88 , 89 ].…”

Immunopathology of galectin-3: an increasingly promising target in COVID-19

“…Patients suffering from severe coronavirus disease 2019 (COVID-19) show highly elevated levels of Gal-3, TNFα, IL-1β, and IL-6, as compared to those with moderate disease ( De Biasi et al, 2020 ; Wang et al, 2020a ). Inhibition of Gal-3 significantly reduces the levels of these cytokines, and so may show promise in reducing inflammatory sequelae associated with COVID-19 ( De Biasi et al, 2020 ; Kalfaoglu et al, 2020 ; Liu et al, 2020 ).…”