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Conventional methods to discern adeno-associated virus (AAV) vector transduction patterns are based on high, stable expression of a reporter gene. As a consequence, conventionally described tropisms omit cell types that undergo transient transduction, or have low but undetectable levels of reporter expression. This creates a blind spot for AAV-based genome editing applications because only minimal transgene expression is required for activity. Here, we use editing-reporter mice to fill this void. Our approach sensitively captures both high and low transgene expression from AAV vectors. Using AAV8 and other serotypes, we demonstrate the superiority of the approach in a side-by-side comparison with traditional methods, demonstrate numerous, previously unknown sites of AAV targeting, and better predict the gene editing footprint after AAV-CRISPR delivery. We anticipate that this system, which captures the full spectrum of transduction patterns from AAV vectors in vivo, will be foundational to current and emerging AAV technologies. Conventional methods to detect AAV vector transduction can miss transient or low levels of reporter expression. Here the authors use editing-reporter mice and discover numerous sites of AAV targeting along with better prediction of the gene editing footprint.

Type II alveolar cells (AT2s) are critical for basic respiratory homeostasis and tissue repair after lung injury. Prior studies indicate that AT2s also express major histocompatibility complex class II (MHCII) molecules, but how MHCII expression by AT2s is regulated and how it contributes to host defense remain unclear. Here we show that AT2s express high levels of MHCII independent of conventional inflammatory stimuli, and that selective loss of MHCII from AT2s in mice results in modest worsening of respiratory virus disease following influenza and Sendai virus infections. We also find that AT2s exhibit MHCII presentation capacity that is substantially limited compared to professional antigen presenting cells. The combination of constitutive MHCII expression and restrained antigen presentation may position AT2s to contribute to lung adaptive immune responses in a measured fashion, without over-amplifying damaging inflammation. Type II alveolar cells play central roles in multiple aspects of lung biology. Here the authors show that type II alveolar cells also constitutively express MHCII, exhibit limited MHCII antigen presentation capacity, and are a component of the host response to respiratory viral infection.

Alveolar epithelial regeneration is essential for recovery from devastating lung diseases. This process occurs when type II alveolar pneumocytes (AT2 cells) proliferate and transdifferentiate into type I alveolar pneumocytes (AT1 cells). We used genome-wide analysis of chromatin accessibility and gene expression following acute lung injury to elucidate repair mechanisms. AT2 chromatin accessibility changed substantially following injury to reveal STAT3 binding motifs adjacent to genes that regulate essential regenerative pathways. Single-cell transcriptome analysis identified brain-derived neurotrophic factor (Bdnf) as a STAT3 target gene with newly accessible chromatin in a unique population of regenerating AT2 cells. Furthermore, the BDNF receptor tropomyosin receptor kinase B (TrkB) was enriched on mesenchymal alveolar niche cells (MANCs). Loss or blockade of AT2-specific Stat3, Bdnf or mesenchyme-specific TrkB compromised repair and reduced Fgf7 expression by niche cells. A TrkB agonist improved outcomes in vivo following lung injury. These data highlight the biological and therapeutic importance of the STAT3–BDNF–TrkB axis in orchestrating alveolar epithelial regeneration.Paris et al. show that after injury or influenza infection alveolar type II cells signal via a STAT3–BDNF axis that activates the TrkB receptor on mesenchymal niche cells and enhances alveolar repair.

Abstract Type II alveolar cells (AT2s) are critical for basic respiratory homeostasis and tissue repair after lung injury. Prior studies indicate that AT2s also express major histocompatibility complex II (MHCII) molecules, but how MHCII expression by AT2s is regulated and how it contributes to host defense remain unclear. Here we show that AT2s express high levels of MHCII independent of conventional inflammatory stimuli, and that selective loss of MHCII from AT2s in mice results in the worsening of respiratory virus disease following influenza and Sendai virus infections. We also find that AT2s exhibit MHCII presentation capacity that is substantially limited in comparison to professional antigen presenting cells. The combination of constitutive MHCII expression and restrained presentation may position AT2s to contribute to lung adaptive immune responses in a measured fashion, without over-amplifying damaging inflammation. Competing Interest Statement The authors have declared no competing interest.

Seasonal influenza viruses are a major cause of human disease worldwide. Most neutralizing antibodies (Abs) elicited by influenza viruses target the head domain of the hemagglutinin (HA) protein. Anti-HA head Abs can be highly potent, but they have limited breadth since the HA head is variable. There is great interest in developing new universal immunization strategies that elicit broadly neutralizing Abs against conserved regions of HA, such as the stalk domain. Although HA stalk Abs can provide protection in animal models, it is unknown if they are present at sufficient levels in humans to provide protection against naturally-acquired influenza virus infections. Here, we quantified H1N1 HA head and stalk-specific Abs in 179 adults hospitalized during the 2015-2016 influenza virus season. We found that HA head Abs, as measured by hemagglutinin-inhibition (HAI) assays, were associated with protection against naturally-acquired H1N1 infection. HA stalk-specific serum total IgG titers were also associated with protection, but this association was slightly attenuated and not statistically significant after adjustment for HA head-specific Ab titers. We found higher titers of HA stalk-specific IgG1 and IgA Abs in sera from uninfected participants than from infected participants; however, we found no difference in sera in vitro antibody dependent cellular cytotoxicity activity. In passive transfer experiments, sera from participants with high HAI activity efficiently protected mice, while sera with low HAI activity protected mice to a lower extent. Our data suggest that human HA head and stalk Abs both contribute to protection against H1N1 infection.

CD4+ T cells are critical regulators of adaptive immune responses. CD4+ T cell activation is initiated and shaped by CD4+ T cell receptor (TCR) recognition of cognate peptide/major histocompatibility complex II (MHCII) complexes on the surface of antigen presenting cells (APCs). MHCII presentation of antigenic peptides has historically been viewed as a property restricted to a subset of immune cells deemed “professional” APCs–dendritic cells, macrophages, and B cells–that constitutively express MHCII. However, recently it has been demonstrated that various other immune and non-immune cell types can express MHCII, and that these “atypical” APCs make essential contributions to the regulation of CD4+ T cell responses in the periphery. In the distal lung, type II alveolar cells (AT2s), epithelial cells whose main functions are to produce surfactant and facilitate lung regeneration, have also been reported to express MHCII at homeostasis. However, the contribution of AT2 MHCII to lung adaptive immune responses, and the factors driving its expression, are unknown. Here we explore both the regulation and function of MHCII on AT2s. First, we demonstrate that AT2s constitutively express high levels of MHCII in a manner that does not require induction by inflammatory stimuli, making them unique among all other previously studied non-immune cells. Using mouse models, we also demonstrate that AT2 MHCII participates in lung immune responses in vivo. At homeostasis, aged mice lacking AT2 MHCII have lower frequencies of lung T cells with an antigen-experienced phenotype. Furthermore, following respiratory viral infection, the absence of AT2 MHCII results in increased morbidity and mortality. In both of these settings, the contribution of AT2 MHCII is moderate. Consistent with this more modest impact, we find that AT2s demonstrate a globally limited capacity to present antigen via MHCII. We propose that the combination of high MHCII expression with restrained MHCII antigen presentation enables AT2s to contribute to lung immune responses in a more measured fashion, preventing excessive inflammation that would be damaging to the delicate gas-exchange lung parenchyma.