COVID-19 single cells studies in BAL.
The majority of single-cell studies to date were performed on peripheral
blood mononuclear cells (PBMC), a minority on NP swabs and BAL. Few
studies have dissected the epithelial and immune profiles of BAL derived
from severe COVID-19 patients at a single-cell level. Wauters et al
revealed infected lung epithelial cells, a significant proportion of
neutrophils and macrophages involved in viral
clearance.50 They performed single-cell deep-immune
profiling BAL from 5 patients with mild and 26 with critical COVID-19
(compared to non-COVID-19 pneumonia and normal lung) showing divergent
immunologic profiles. In mild COVID-19, CD8+ resident-memory (TRM) and
CD4+ T-helper-17 (TH17) cells undergo active expansion with good
effector functions, while in critical cases they remain more naïve. Vice
versa, CD4+ T-cells with T-helper-1 characteristics (TH1-like) and CD8+
T-cells expressing exhaustion markers (TEX-like) are enriched halfway
their trajectories in mild COVID-19, where they also exhibit good
effector functions, while in critical COVID-19 they show evidence of
inflammation-associated stress. Monocyte-to-macrophage trajectories show
that chronic hyperinflammatory monocytes are enriched in critical
COVID-19, while alveolar macrophages, otherwise characterized by
anti-inflammatory and antigen-presenting characteristics, are depleted.
Moreover, in critical COVID-19, monocytes contribute to an ATP-
purinergic signaling-inflammasome footprint that could enable COVID-19
associated fibrosis and worsen disease-severity.50Liao et al evaluated BAL from 3 moderate and 6 severe COVID-19 and found
abundant pro-inflammatory monocytes derived macrophages in patients with
severe COVID-19, whereas highly clonally expanded CD8+ T cells
characterized moderate COVID-19 cases.51 Patients with
severe/critical infection had much higher levels of inflammatory
cytokines, particularly interleukin (IL)-8, IL-6 and IL-1β, expressed by
macrophages that in severe patients may contribute to local inflammation
by recruiting monocytic cells and neutrophils thought CCR1 and CXCR2,
while in moderate cases can produce more T cell attracting chemokines
through CXCR3 and CXCR6.51 He et al performed
single-cell RNA sequencing (sc-RNA-seq) in the leukocytes and epithelial
cells of 3 SARS-Cov-2 induced ARDS.52 They detected 23
cells with viral mRNA reads, but minimal number of expressed genes, thus
indicating that SARS-Cov-2 suppresses host gene expression. These cells
were identified as monocytes/neutrophils and club cells. Compared to
healthy controls club cells showed a significantly elevated mucins genes
expression (MUC5AC, MUC5BMUC4, MUC16 and MUC20). The mucin secretion
seems stimulated through the innate immune regulators IL-1β and TNF-α
(were found 6 transcription factors involved in IL-1β and TNF- α induced
MUC5B promoter activation). Four critical surfactant proteins (SPs)—
SP-A, SP-B, SP-C, and SP-D, known to maintain the structural integrity
of alveoli, were down-regulated in COVID-19 disease and the level of
NKX2-1, the transcription factor required for surfactant synthesis was
also reduced, thus indicating the loss of alveoli integrity and the
possible pathogenesis of ARDS in COVID-19.52 The
transcriptomic signature of major regulators of innate immunity
(monocytes, neutrophils and macrophages) in severe COVID-19 indicates
different immune profiles among COVID-19 patients: Liao et al. showed
abundant macrophages expressing FCN1 in BAL of COVID-19 patients,
whereas He et al. noticed only a minor increase in FCN1+ macrophages,
with a significant decrease in FCN1+
monocytes/neutrophils.51,52 By analyzing scRNA-seq
data of BAL from 6 severe COVID-19, 3 recovered COVID-19 with mild
symptoms and 10 heathy controls, Chen et al. showed high expression of
SARS-Cov-2 receptor ACE2 and TMPRSS2 in club and ciliated cells of
patients.53 In severe COVID-19 high neutrophils with
excessive expression of cytokines were noted and the dysregulated
cytokines/receptors interplay among lung epithelial cells and immune
cells correlated with disease severity (ANXA1/FPR2 and TNFSF13/TNFRSF1A
interactions between club and macrophage or neutrophils, CXCL2/DPP4
interaction between club and T/NK cells, and ANXA1, C3, CXCL2, SAA1,
TNFSF13 expressions in lung epithelial cells).53 In
conclusion scRNA-seq studies can reveal information of critical
importance in the understanding of COVID-19 pathogenesis. However,
current data on BAL are limited, mostly derived from small sample sizes
studies and with large difficulties in validating most conclusions
across datasets, possibly due to inconsistent mapping between different
diseases stages and different protocols used. Therefore, conclusions
from these early scRNA-seq studies of COVID-19 patients may not always
be robust and need to be validated before fully relied
upon.54