SARS-CoV-2 activates lung epithelia cell proinflammatory signaling and leads to immune dysregulation in COVID-19 patients by single-cell sequencing

Abstract

Objective: The outbreak of Coronavirus disease 2019 caused by SARS-CoV-2 infection has become a global health emergency. We aim to decipher SARS-CoV-2 infected cell types, the consequent host immune response and their interplay in the lung of COVID-19 patients. Design:We analyzed single-cell RNA sequencing (scRNA-seq) data of lung samples from 17 subjects (6 severe COVID-19 patients, 3 mild patients who recovered and 8 healthy controls). The expression of SARS-CoV-2 receptors (ACE2 and TMPRSS2) was examined among different cell types in the lung. The immune cells infiltration patterns, their gene expression profiles, and the interplay of immune cells and SARS-CoV-2 target cells were further investigated. Results: Compared to healthy controls, the overall ACE2 (receptor of SARS-CoV-2) expression was significantly higher in lung epithelial cells of COVID-19 patients, in particular in ciliated cell, club cell and basal cell. Comparative transcriptome analysis of these lung epithelial cells of COVID-19 patients and healthy controls identified that SARS-CoV-2 infection activated pro-inflammatory signaling including interferon pathway and cytokine signaling. Moreover, we identified dysregulation of immune response in patients with COVID-19. In severe COVID-19 patients, significantly higher neutrophil, but lower T and NK cells in lung were observed along with markedly increased cytokines (CCL2, CCL3, CCL4, CCL7, CCL3L1 and CCL4L2) compared with healthy controls as well as mild patients who recovered. The cytotoxic phenotypes were shown in lung T and NK cells of severe patients as evidenced by enhanced IFNγ, Granulysin, Granzyme B and Perforin expression. Moreover, SARS-CoV-2 infection altered the community interplay of lung epithelial cells and immune cells: the interaction between epithelial cells with macrophage, T and NK cell was stronger, but their interaction with neutrophils was lost in COVID-19 patients compared to healthy controls. : medRxiv preprint Conclusions: SARS-CoV-2 infection activates pro-inflammatory signaling in lung epithelial cells expressing ACE2 and causes dysregulation of immune response to release more pro-inflammatory cytokines. Moreover, SARS-CoV-2 infection breaks the interplay of lung epithelial cells and immune cells.

Multifunctional angiotensin converting enzyme 2, the SARS-CoV-2 entry receptor, and critical appraisal of its role in acute lung injury

“…However, the opposite is also conceivable: upregulation of ACE2 as an IFN-stimulated gene may counteract viral infection, which is in line with the anti-inflammatory and protective functions of ACE2 in ARDS [ 210 ]. In agreement with these findings, upregulation of ACE2 expression after rhinovirus [ 219 ], human respiratory viruses [ 212 ], upper respiratory tract infections [ 220 ], and SARS-CoV-2 infections has been reported in vivo , in vitro and post mortem in pulmonary [ 210 , [221] , [222] , [223] ] and renal tubular [ 37 ] epithelial cells. Upregulation could also be demonstrated in broncho-alveolar lavage samples [ 224 ] and peripheral blood monocytes [ 225 ] of COVID-19 patients [ 226 ] as well as in lung tissue of SARS-CoV-2-infected mice [ 227 ].…”

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

“…Due to the involvement of these genes in oncogenic programs, we further investigated pathway-level alterations in epithelial cells and detected the enrichment of epithelial-to-mesenchymal transition, K-Ras, PI3K/AKT and p53 pathways. We note that a separate analysis of epithelial cells from the same BALF dataset failed to detect differential enrichment of these pathways through GSEA when comparing control samples to pooled mild and severe samples [21,53], likely as a result of this pooling and using a much shorter list of statistically tested genes (a single set of 118 genes common to all epithelial cells compared to sets of 1,561 genes for ciliated cells and 1,092 genes for club cells). Our results may be cautiously interpreted as providing evidence for the molecular underpinnings of the morphological changes known to occur in the severely damaged lung epithelia of severe COVID-19 patients, previously described as cellular proliferation resembling atypical adenomatous hyperplasia, in situ adenocarcinoma, or even invasive adenocarcinoma [15].…”

“…Exploring the expression of these 16 ligands across the diversity of BALF cell types indicates that MPs and neutrophils may act as "sender cells" signaling to the epithelium, as suggested in recent reports [21,28,53]. In particular, aberrant neutrophil responses have been implicated in severe COVID-19 through a number of studies focusing on either the lung or the blood [21,28,34,35,36,53].…”

“…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.…”

SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease

“…The inflammatory signals observed in the DKD PTECs, expected based on prior studies in this and other cohorts, 50,51 could be maladaptive for viral infection. Recent results from COVID-19 pulmonary samples described impaired immune responses, 52,53 and work on SARS-CoV-2-infected cultured lung epithelial cells specifically showed a blunted interferon response despite robust cytokine production. 40 Thus, there may be immune hallmarks associated with SARS-CoV-2 pathology.…”