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

Abstract

As the global COVID-19 pandemic continues to escalate, no effective treatment has yet been developed for the severe respiratory complications of this disease. This may be due in large part to the unclear immunopathological basis for the development of immune dysregulation and acute respiratory distress syndrome (ARDS) in severe and critical patients. Specifically, it remains unknown whether the immunological features of the disease that have been identified so far are compartment-specific responses or general features of COVID-19. Additionally, readily detectable biological markers correlated with strata of disease severity that could be used to triage patients and inform treatment options have not yet been identified. Here, we leveraged publicly available single-cell RNA sequencing data to elucidate the common and compartment-specific immunological features of clinically severe COVID-19. We identified a number of transcriptional programs that are altered across the spectrum of disease severity, few of which are common between the lung and peripheral immune environments. In the lung, comparing severe and moderate patients revealed severity-specific responses of enhanced interferon, A20/IκB, IL-2, and IL-6 pathway signatures along with broad signaling activity of IFNG, SPP1, CCL3, CCL8, and IL18 across cell types. These signatures contrasted with features unique to ARDS observed in the blood compartment, which included depletion of interferon and A20/IκB signatures and a lack of IL-6 response. The cell surface marker S1PR1 was strongly upregulated in patients diagnosed with ARDS compared to non-ARDS patients in γδ T cells of the blood compartment, and we nominate S1PR1 as a potential marker for immunophenotyping ARDS in COVID-19 patients using flow cytometry.HIGHLIGHTSCOVID-19 disease severity is associated with a number of compositional shifts in the cellular makeup of the blood and lung environments.Transcriptional data suggest differentially expressed cell surface proteins as markers for COVID-19 immunophenotyping from BALF and PBMC samples.Severity-specific features COVID-19 manifest at the pathway level, suggesting distinct changes to epithelia and differences between local and systemic immune dynamics.Immune-epithelial cellular communication analysis identifies ligands implicated in transcriptional regulation of proto-oncogenes in the lung epithelia of severe COVID-19 patients.Network analysis suggests broadly-acting dysregulatory ligands in the pulmonary microenvironment as candidate therapeutic targets for the treatment of severe COVID-19.

The interferon landscape along the respiratory tract impacts the severity of COVID-19

“…When we compared the protein levels in the BALF and plasma of a subset of COVID-19 patients (STAR Methods), no correlation between these levels for any protein analyzed was found (Fig- ures 6E-6J and S6I), confirming at the protein level the transcriptional differences recently highlighted between the peripheral blood and the lungs of COVID-19 patients (Overholt et al, 2021).…”

“…have opposing roles along the respiratory tract and reconcile some of the seemingly contradictory findings on IFNs in COVID-19 patients. Efficient initiation of IFN production in the upper airways can lead to a more rapid elimination of the virus and may limit viral spread to the lower airways, as suggested by studies that report defects in IFN signaling of severe COVID-19 patients (Bastard et al, 2020;Pairo-Castineira et al, 2021;Wang et al, 2021;Zhang et al, 2020). On the other hand, when the virus escapes immune control in the upper airways, the IFN production that is potently boosted in the lungs likely contributes to the cytokine storm and associated tissue damage that are typical of patients with severe-to-critical COVID-19, characterized by reduced proliferation and increased pro-apoptotic p53 transcriptional signatures.…”

“…Aside from the challenge of understanding the pattern of expression of IFNs, a major unanswered question is whether IFNs serve protective or detrimental functions in COVID-19. Recent studies show that patients with severe COVID-19 have defective IFN responses (Bastard et al, 2020;Combes et al, 2021;Laing et al, 2020;Pairo-Castineira et al, 2021;Wang et al, 2021;Zhang et al, 2020). Other studies, however, report that heightened and prolonged production of IFNs in patients infected with SARS-CoV-2 is correlated with negative clinical outcomes (Lee et al, 2020;Lucas et al, 2020).…”

Interfering with SARS-CoV-2: are interferons friends or foes in COVID-19?

“…Not only was induced the transcription of type III and type I IFNs in these patients, but a unique protein IFN signature (comprising all 3 families of IFNs) was also found to be a hallmark of the severely infected patients compared to non-microbially infected patients, and also to patients suffering from other bacterial or viral acute respiratory distress syndrome (ARDS) [ 45 •• ]. Of note, no -or very limited- correlation between the protein content of the IFNs [ 45 •• ] as well as of the transcriptional signature [ 69 ] in the lungs compared to that in the blood of the same group of patients was found. Finally, a tight correlation was found between the production of type I and type III IFNs and/or the ISGs and the levels of SARS-CoV-2 in the upper airways of COVID-19 patients: as the viral load in the upper airways increased, so did the IFN signature [ 45 •• , 70 • , 71 , 72 ].…”

Quo vadis? Central Rules of Pathogen and Disease Tropism

“…Immunomodulators are being considered to mitigate infection-induced damage, for example in COVID-19 ( Ingraham et al., 2020 ). However, local and peripheral immune responses may differ significantly; for example, different patterns of interferon expression were observed in peripheral blood mononuclear cells vs. lung cells in bronchoalveolar lavage fluid of COVID-19 patients ( Overholt et al., 2020 ), and in upper vs. lower airways ( Broggi et al., 2020 ). Regulatory T cell depletion also had opposite effects on murine cytomegalovirus (MCMV) reactivation in the spleen and salivary gland ( Almanan et al., 2017 ).…”