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Despite much concerted effort to better understand SARS-CoV-2 viral infection, relatively little is known about the dynamics of early viral entry and infection in the airway. Here we analyzed a single-cell RNA sequencing dataset of early SARS-CoV-2 infection in a humanized in vitro model, to elucidate key mechanisms by which the virus triggers a cell-systems-level response in the bronchial epithelium. We find that SARS-CoV-2 virus preferentially enters the tissue via ciliated cell precursors, giving rise to a population of infected mature ciliated cells, which signal to basal cells, inducing further rapid differentiation. This feed-forward loop of infection is mitigated by further cell-cell communication, before interferon signaling begins at three days post-infection. These findings suggest hijacking by the virus of potentially beneficial tissue repair mechanisms, possibly exacerbating the outcome. This work both elucidates the interplay between barrier tissues and viral infections, and may suggest alternative therapeutic approaches targeting non- immune response mechanisms.
Strikingly, we observed a distinct, acute depletion of basal cells at 1dpi, which recovered to near-control (Mock) levels by 3dpi (Fig. 1E). More broadly, at 1dpi, there was a profound depletion of all less-mature cells in the model, as identified by pseudotime (Cao et al., 2019), across all cell types at 1dpi (Fig. 1F). This indicated a transient depletion of all population-specific resident progenitors, suggesting a phenotypic switch from renewal to differentiation, and an increased phenotypic flux toward mature cell types in the infected conditions. Like the basal cell cluster, population-specific resident progenitor cells also recovered their numbers by 3dpi. Using viral transcripts to indicate SARS-CoV-2 infection (consistent with prior methods(Ravindra et al., 2021)), we ascertained that viral load initiates and concentrates in the ciliated cell cluster, but, interestingly, primarily in a subset of cells in one region of the ciliated cluster that express markers of immaturity (Fig. 1G,H). Longitudinal analysis of data on subsequent post-infection days suggests that the viral infection then spreads from this somewhat immature cell type to more mature cells, either by maturation of these infected cells or by viral replication and re-infection of more mature cells. By 3dpi, nearly 25% of ciliated cells in the culture system are infected (Fig. 1I). Overall, our initial observations using dynamic scRNAseq demonstrate a transient depletion of basal and other progenitor cells upon infection, as well as greater SARS-CoV-2 tropism toward an immature subset of ciliated cells.Viral load is concentrated first in Novel Infected cells at 1dpi, followed by Ciliated Progenitor cells as their numbers are replenished (Fig. 2F,G). By 3dpi, nearly 25% of Ciliated Progenitor cells are infected, as well as nearly 100% of Novel Infected Ciliated cells (Fig. 2H). By 2dpi and 3dpi, when the cell populations begin to re-stabilize, Ciliated Progenitor cells account for 60% of all infected ciliated cells, with Novel Infected Ciliated cells accounting for 28% at 3dpi ..this method further suggested that Ciliated Progenitors are the main hub of viral entry and transcription among ciliated cells. GO analysis also confirmed functional roles of the other ciliated subtypes, including antigen presentation in Mature Ciliated 1 cells, cilia function in Mature Ciliated 2 cells, and interferon production in Novel Infected Ciliated cells. By pulling the genes categorized in the “viral entry into host cell” GO category, as well as known and putative genes associated with specific entry of SARS-CoV-2, such as ACE2, TMPRSS2 (Hoffmann et al., 2020), Cathepsin L (CTSL), HMGB1 (Wei et al., 2020), neuropilin-1 (NRP1) (Cantuti-Castelvetri et al., 2020), BSG (Matusiak and Schurch, 2020), and FURIN (Walls et al., 2020), we observed that most of these genes are preferentially expressed in the Ciliated Progenitor population (Fig. 2K). In addition, TMPRSS2, BSG, HMGB1, and CTSL also showed high expression in Mature Ciliated 1 cells. Interestingly, the Novel Infected Ciliated cells, which are nearly ubiquitously infected with SARS-CoV-2, did not significantly express any genes associated with viral entry, suggesting these cells arise from already infected ciliated cells. At 3dpi, genes associated with interferon production and response are uniquely upregulated over all other time points (Fig. 3A). Comparison of genes associated with interferon-related gene ontology (GO) categories demonstrates that expression of most of these genes increases over time following infection, peaking around 3dpi (Fig. 3B). Specifically, IFIT1, IFIT2, IFIT3, and IFIT5 appear most strongly at 3dpi. is worth noting that these viral response signals appear as part of the innate immune response and are mounted by epithelium in the absence of immune cells (Shenoy et al., 2021)... interferon secretion is not the immediate response of epithelial cells to infection with SARS-CoV-2 virus, leaving the possibility that the epithelium may undergo another defensive response first. Interestingly, we found that Novel Infected Ciliated cells, which harbor the greatest viral load, rapidly increased expression of TGFβ2 and BMP4, which can exert pro-differentiation and anti-proliferation effects on pulmonary basal cells. However, by 3dpi, there was an increase of expression of a potent inhibitor of BMP and TGFβ signaling, follistatatin (FST), as well as a strong increase of expression of EGFR ligands AREG and EREG (Fig. 4G-I). AREG has been shown to promote basal cell self-renewal at the expense of differentiation (Zuo et al., 2017), suggesting that these signals can curtail pro-differentiation signaling. By shutting off pro-differentiation cues and encouraging self-renewal, the system can prevent total exhaustion of the basal cell pool, and support replenishment of basal and progenitor cells. Taken together, these data suggest that basal cells are initially being induced to differentiate by TGFβ and BMP signals arising from Novel Infected Ciliated cells, potentially aided by antagonism of pro-renewal WNT signaling. By 3dpi, these prodifferentiation signals are halted by inhibition of TGFβ and BMP signaling by FST, and pro-renewal of basal cells is restored by expression of AREG and EREG.These observations raised the question of how the pro-differentiation, and later proproliferation, signals were induced. Both TGFβ2 and BMP4 can be induced in response to tissue damage from acute or chronic injury (Aschner and Downey, 2016; Bartram and Speer, 2004; Saito et al., 2018; Tadokoro et al., 2016). However, importantly, TGFβ signaling can also be induced by various viral infections (Mirzaei and Faghihloo, 2018). This could occur, for example, due to an increase of intracellular reactive oxygen species (ROS) triggered following viral entry, which has been observed in SARS-CoV-2 infection (Delgado-Roche and Mesta, 2020).Interestingly, TXN underwent rapid downregulation, specifically in Novel Infected Ciliated cells, suggesting a virus-mediated repression of the anti-oxidative stress mechanisms in these cells, consistent with prior results showing suppressive effects of various viral infections, including SARS-CoV-2, on Nrf2-mediated anti-oxidative stress responses (Olagnier et al., 2020). This view was corroborated by the surprising decrease of ACE2 in the Novel Infected Ciliated cells. Overall, these data suggest that a particularly high level of oxidative stress in Novel Infected Ciliated cells, not mitigated by the Nrf2-mediated response, may have led to enhanced TFGβ signaling from Novel Infected Ciliated cells to other cell targets, including basal cells. By deriving the source of this pro-differentiation signaling, we can complete the picture of the communication network that drives a brief period of rapid basal cell differentiation following viral infection.Metabolic dynamics may also be a possible mechanism of viral tropism to progenitor cells subpopulations. The respiratory pathways in the lung tissue are thought to be primarily glycolytic,... Consistent with this assumption, analysis of the Mock control displayed greater expression of genes involved in glycolysis than oxidative phosphorylation (Supp. Fig. 2A). However, subsets of cells undergoing differentiation displayed an increase in gene expression that was specific to oxidative phosphorylation, consistent with observations suggesting that oxidative phosphorylation may accompany epithelial cell differentiation (Zheng et al., 2016). Surprisingly, upon infection with SARS-CoV-2, most cells underwent a rapid switch from glycolysis to oxidative phosphorylation. This was revealed by a sustained down-regulation of glycolytic genes at 1dpi, and a corresponding up-regulation of genes associated with oxidative phosphorylation Furthermore, the cell sub-populations showing higher and increasing viral load were also the sub-populations with a particularly high oxidative phosphorylation gene expression signature (Fig. 1H). This relationship may not be coincidental, since differentiation, even under homeostatic conditions, is frequently associated with increasing oxidative phosphorylation and oxidative stress (Drehmer et al., 2016; Shyh-Chang and Daley, 2015; Tatapudy et al., 2017; Zheng et al., 2016). Oxidative stress, in turn, may promote expression of ACE2, thereby biasing viral tropism towards progenitor cells. This putative mechanism remains to be further validated experimentally, but it may help explain the apparent predilection of the virus for progenitor cells in SARS-CoV-2 infection.

The results presented here suggest that SARS-CoV-2 infection can trigger a rapid and transient increase in basal and progeni
tor cell differentiation, enabled by expression of pro-differentiation signaling cues by virally infected cells
(Fig. 4). The cues are secreted by a newly described subset of infected ciliated cells (Novel Infected Ciliated cells, or NICs), that cluster separately from other mature and progenitor ciliated cells and display a virtually 100% infection rate. The prodifferentiation cues, particularly TGFβ, may be produced as a result of the increased oxidative stress precipitated by viral infection. The process of differentiation transiently depletes basal cells, a key airway epithelial stem cell reservoir, while supporting the proportion of ciliated cells. As cellular proportions stabilize by 3dpi, up-regulation of new anti-differentiation, pro-renewal cues, particularly those of the EGF receptor family, restores the renewal of basal and progenitor cells. Although this process can serve as a typical strategy to repair the bronchial tissue damage inflicted by the initial viral infection, it may also be compromised by the apparent tropism of the virus toward active progenitor cells rather than to stable mature cells. As a result, the tissue repair process itself may open the door wider to infection by exposing increased progenitors for viral entry, and subsequent progressive infection of mature epithelial cells. A similar viral entry and infection strategy by targeting progenitor cells has been previously observed in placental infection by Zika virus and human cytomegalovirus (Tabata et al., 2016; Tabata et al., 2015). Another interesting finding is the rapid down-regulation of ACE2 receptor in NICs. This down-regulation was correlated with suppression of other oxidative stress response genes, likely as part of the viral effect on cells. This effect may be coupled with the potential reduction in ACE2 protein content in SARS-CoV-2 infected cells (Blume et al., 2021; Glowacka et al., 2010; Verdecchia et al., 2020). A decrease of ACE2 expression may help limit the multiplicity of single cell infection by the virus, thereby increasing viral yield by the cell due to an increased cell survival by avoidance of high multiplicity of infection. This effect is observed and exploited in viral vaccine production (Aggarwal et al., 2011), and is supported by mathematical modeling (Rudiger et al., 2019). An increased viral yield, on a per-cell basis, may help spread the infection within the epithelial layers, increasing the overall pathogenicity of the virus. These results add a new dimension to the discussion of age and gender dependence of COVID-19 progression. Indeed, children and young people may experience reduced SARS-CoV-2 infection rates due to naturally higher epithelial regenerative capacities. Homeostatic airway epithelial turnover and progenitor cell function decreases with age (Watson et al., 2020). In young people, rapid epithelial turnover in response to sensing inhaled SARS-CoV-2 particles, as observed in our study, may be adequate to successfully block viral entry or shed and replace infected cells before systemic transmission, except in cases of exposure to sufficiently high viral loads. This protective mechanism would be greatly reduced in older populations. Furthermore, it has been suggested that reduction of ACE2 expression with age (less pronounced in females) in animal models (Xie et al., 2006), and possibly in humans may be, somewhat paradoxically, related to a lower incidence but higher severity of the disease in older patients, possibly due to an amplified inflammatory reaction (AlGhatrif et al., 2020). Our data suggest that these results may need to be viewed in a boarder context of a decrease of Nrf2 expression with aging (Zhou et al., 2018), particularly in the context of the respiratory pathways and the related increase in the oxidative stress. Enhanced oxidative stress in older individuals may lead to an enhanced expression of TGFβ and, possibly other pro-differentiation ligands (Lehmann et al., 2016; Tominaga and Suzuki, 2019), prompting differentiation of precursor cells and contributing to depletion of the progenitor cell pools. Thus, the reparative capacity of the aged bronchial and lung tissues can be compromised in the elderly. As suggested above, lower ACE2 expression in aged individuals, or in patients where ACE2 expression may be altered as a side effect of pre-existing conditions, may limit the per-cell MOI and increase the yield of viral replication and the infection spread to adjacent cells. Taken together, these effects of aging, coupled with potential age-related alterations in the immune response, may provide a wider framework in which to understand and address the age- and gender-related differences in COVID-19 severity and morbidity. The COVID-19 pandemic is not yet beaten, and the infection dynamics of the virus must be elucidated in order to treat remaining cases and fully vanquish this disease. By identifying systemic vulnerabilities and modeling offensive viral strategies, this work may open the door to potential points of intervention for the prevention and/or treatment of SARS-CoV-2 infection.

Date: 2022-02-01 12:15 pm (UTC)
juan_gandhi: (Default)
From: [personal profile] juan_gandhi

Ого какая сложность. Сложнее, чем в программировании. И я и не подозревал, что клетки бывают mature и immature.

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