Unique Transcriptional Architecture in Airway Epithelial Cells and Macrophages Shapes Distinct Responses following Influenza Virus Infection Ex Vivo

Abstract

Airway epithelial cells and macrophages differ markedly in their responses to influenza A virus (IAV) infection. To investigate transcriptional responses underlying these differences, purified subsets of type II airway epithelial cells (ATII) and alveolar macrophages (AM) recovered from the lungs of mock- or IAV-infected mice at 9 h postinfection were subjected to RNA sequencing. This time point was chosen to allow for characterization of cell types first infected with the virus inoculum, prior to multicycle virus replication and the infiltration of inflammatory cells into the airways. In the absence of infection, AM predominantly expressed genes related to immunity, whereas ATII expressed genes consistent with their physiological roles in the lung. Following IAV infection, AM almost exclusively activated cell-intrinsic antiviral pathways that were dependent on interferon (IFN) regulatory factor 3/7 (IRF3/7) and/or type I IFN signaling. In contrast, IAV-infected ATII activated a broader range of physiological responses, including cell-intrinsic antiviral pathways, which were both independent of and dependent on IRF3/7 and/or type I IFN. These data suggest that transcriptional profiles hardwired during development are a major determinant underlying the different responses of ATII and AM to IAV infection. IMPORTANCE Airway epithelial cells (AEC) and airway macrophages (AM) represent major targets of influenza A virus (IAV) infection in the lung, yet the two cell types respond very differently to IAV infection. We have used RNA sequencing to define the host transcriptional responses in each cell type under steady-state conditions as well as following IAV infection. To do this, different cell subsets isolated from the lungs of mock- and IAV-infected mice were subjected to RNA sequencing. Under steady-state conditions, AM and AEC express distinct transcriptional activities, consistent with distinct physiological roles in the airways. Not surprisingly, these cells also exhibited major differences in transcriptional responses following IAV infection. These studies shed light on how the different transcriptional architectures of airway cells from two different lineages drive transcriptional responses to IAV infection.

Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

“…During influenza A virus infection, we have previously identified interferon stimulated genes (ISGs) specifically induced in cells supporting high levels of virus replication and we have defined cell type-specific ISGs [26, 27]. Additionally, we and others have found significant heterogeneity in antiviral responses across different cell types [27, 28]. Cell type-specific responses and the degree of heterogeneity in antiviral responses can dictate the outcome of immune responses and infection.…”

Influenza A virus interactions with macrophages: Lessons from epithelial cells

“…For example, cell lineage differences in the expression of different IMP isoforms, variants of ANP32, or levels of splicing factor proline‐glutamine‐rich host factor may lead to differences in IAV replication between MΦ and epithelial cells, but this requires investigation. Genes associated with nucleocytoplasmic transport, RNA processing, ribonucleoprotein complex biogenesis, and protein serine/threonine kinase and mitogen‐activated protein kinase activities were upregulated in murine type II airway epithelial cells, but not in airway MΦ, following IAV infection (Ma et al, ).…”

“…Our recent finding that murine airway epithelial cells and MΦ exhibit major differences in transcriptional antiviral responses following IAV infection (Ma et al, 2019) infers that cell lineage-specific differences may modulate IAV replication in different cell types. For example, many antiviral genes that were upregulated in epithelial cells upon IAV infection were already constitutively expressed at high levels in MΦ.…”

“…Our prior studies, and those of others, show that infection of murine MΦ by seasonal IAV can be (a) restricted at the level of virus entry (Londrigan et al, ), (b) blocked downstream of virus internalisation but upstream of nuclear entry (Cline, Karlsson, Seufzer, & Schultz‐Cherry, ; Marvin, Russier, Huerta, Russell, & Schultz‐Cherry, ), and (c) blocked at a late stage in the viral replication cycle, such that newly‐synthesised virions are not released (Londrigan et al, ). Our recent finding that murine airway epithelial cells and MΦ exhibit major differences in transcriptional antiviral responses following IAV infection (Ma et al, ) infers that cell lineage‐specific differences may modulate IAV replication in different cell types. For example, many antiviral genes that were upregulated in epithelial cells upon IAV infection were already constitutively expressed at high levels in MΦ.…”

Cytoplasm and Beyond: Dynamic Innate Immune Sensing of Influenza A Virus by RIG-I

“…Cell type-specific difference may play a critical role in conferring these constraints. Some innate immune cells, such as macrophages, occasionally lead to abortive viral replication depending on the virus strain, yet they are the major IFN-producing cell types (65,66). Single-cell analyses further reveal stochastic IFN events among IAV-infected cell population, which partially correlates with viral genetic diversity, such as mutations and defective viral gene expression including but not limited to NS1 (55,67,68).…”