SARS-CoV-2 can infect and adapt to multiple animal species, yet the host determinants that control interspecies viral adaptation remain poorly defined. Here we investigate whether interferon-induced transmembrane protein 3 (IFITM3), a key antiviral protein deficient in certain human populations, affects interspecies adaptation of SARS-CoV-2. We find that SARS-CoV-2 Beta and Omicron BA.4 variants passaged through IFITM3-deficient versus wild type mice exhibit enhanced replication and pathogenesis in this new host species. These enhancements are associated with amino acid substitutions in the viral genome, suggesting that IFITM3 limits accumulation of adaptive mutations. Mouse-adapted viruses enable comparative studies of variants in mice. Beta causes lung dysfunction and alters cilia-associated gene programs, consistent with broad viral antigen distribution in the lungs. Omicron, which shows mild pathogenicity and upper respiratory tract preference in humans, replicates to high nasal titers while exhibiting limited lung spread and reduced inflammatory responses compared to Beta. Our findings demonstrate that IFITM3 deficiency accelerates SARS-CoV-2 adaptation while preserving pre-existing variant-specific properties, highlighting that host adaptation enhances viral fitness without necessarily overriding intrinsic viral characteristics. Denz et al. show that loss of the antiviral protein IFITM3 allows human SARS-CoV-2 variants to adapt more rapidly in mice while preserving distinct, variant-specific patterns of infection and disease.

Secondhand smoke exposure (SHSe) is a public health threat for people with cystic fibrosis (CF) and other lung diseases. Primary smoking reduces CF transmembrane conductance regulator (CFTR) channel function, the causative defect in CF. We reported that SHSe worsens respiratory and nutritional outcomes in CF by disrupting immune responses and metabolic signaling. Recently, electronic cigarette (e-cigs) usage by caregivers and peers has increased rapidly, causing new secondhand e-cig vape exposures. Primary vaping is associated with immunologic deficits in healthy people, but it is unknown whether e-cigs similarly impacts CF immune function or how it differs from SHSe. Human CF and non-CF blood monocyte-derived macrophages (MDMs) and bronchial epithelial cells (HBECs) were exposed to flavored and unflavored e-cigs. The effect of e-cigs on CFTR expression and function, bacterial killing, cytokine signaling, lipid mediators, and metabolism was measured during treatment with CFTR modulators. E-cigs decreased CFTR expression and function in CF and non-CF MDMs and negated CFTR functional restoration by elexacaftor/tezacaftor/ivacaftor (ETI). E-cigs also negated the restoration of anti-inflammatory PGD2 expression in CF MDMs treated with ETI compared with controls. Flavored but not unflavored e-cigs increased proinflammatory cytokine expression in CF MDMs and e-cigs promoted glycolytic metabolism. E-cigs did not impact bacterial killing. Overall, HBECs were less impacted by e-cigs compared with MDMs. E-cigs reduced macrophage CFTR expression and hindered functional CFTR restoration by CFTR modulators, promoting a glycolytic, proinflammatory state. E-cigs are an emerging public health threat that may limit the efficacy of CFTR modulators in people with CF.NEW & NOTEWORTHY New research reveals that e-cigarettes pose a serious health risk for individuals with cystic fibrosis (CF). Exposure to electronic cigarette (e-cig) vapors decreases CF transmembrane conductance regulator (CFTR) function and undermines the effectiveness of CFTR modulators, potentially worsening inflammation and metabolic responses. This highlights an urgent need for awareness around e-cig use, especially among caregivers and peers of those with CF. E-cigarettes may further complicate the management of this chronic lung disease.

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although many people with CF (pwCF) are treated using CFTR modulators, some are non-responsive due to their genotype or other uncharacterized reasons. Autologous airway stem cell therapies, in which the CFTR cDNA has been replaced, may enable a durable therapy for all pwCF. Previously, CRISPR-Cas9 with two AAVs was used to sequentially insert two halves of the CFTR cDNA and an enrichment cassette into the CFTR locus. However, the editing efficiency was <10% and required enrichment to restore CFTR function. Further improvement in gene insertion may enhance cell therapy production. To improve CFTR cDNA insertion in human airway basal stem cells (ABCs), we evaluated the use of the small molecules AZD7648 and ART558 which inhibit non-homologous end joining (NHEJ) and micro-homology mediated end joining (MMEJ). Adding AZD7648 alone improved gene insertion by 2-3-fold. Adding both ART558 and AZD7648 improved gene insertion but induced toxicity. ABCs edited in the presence of AZD7648 produced differentiated airway epithelial sheets with restored CFTR function after enrichment. Adding AZD7648 did not increase off-target editing. Further studies are necessary to validate if AZD7648 treatment enriches cells with oncogenic mutations.

Single-stranded DNA (ssDNA) templates along with Cas9 have been used for gene insertion but suffer from low efficiency. Here, we show that ssDNA with chemical modifications in 10-17% of internal bases (eDNA) is compatible with the homologous recombination machinery. Moreover, eDNA templates improve gene insertion by 2-3 fold compared to unmodified and end-modified ssDNA in airway basal stem cells (ABCs), hematopoietic stem and progenitor cells (HSPCs), T-cells and endothelial cells. Over 50% of alleles showed gene insertion in three clinically relevant loci (CFTR, HBB, and CCR5) in ABCs using eDNA and up to 70% of alleles showed gene insertion in the HBB locus in HSPCs. This level of correction is therapeutically relevant and is comparable to adeno-associated virus-based templates. Knocking out TREX1 nuclease improved gene insertion using unmodified ssDNA but not eDNA suggesting that chemical modifications inhibit TREX1. This approach can be used for therapeutic applications and biological modeling.

Results: We demonstrated a range of CFTR function in normal and corrector-treated (VX-445 + VX-661) CF EPCAM + airway epithelial cells in whole-cell patch-clamp recording and classified them into three groups: CFTR function greater than 10 pA (CFTR function high), CFTR function between 5 pA and 10 pA, and CFTR function less than 5 pA.Post-currentrecording single cells were collected for RNA-seq.Conclusions: We detected differential single-cell CFTR function in primary airway epithelial cells derived from healthy and CF lung explant tissues.Our study could potentially identify not only ways to enrich for CFTRfunction-high populations for more-efficient therapeutic intervention for the airway cells, but could also precisely define the synergy between CFTR function and gene-level alterations in the presence of CF modulators in the CF lung.

Paneth cells are a subset of small intestinal epithelial cells specialized to maintain gastrointestinal homeostasis through production of antimicrobial products and cytokines. The fact that dysbiosis has been associated with several noninfectious pathologies, has solidified the notion that Paneth cells contribute to the general health. However, little is known about Paneth cells beyond their role as regulator of the gut microbiota. Using mice lacking Paneth cells (Sox9 ΔIECmice), we now report that Paneth cells also regulate the composition of immune cell subsets in Gut-Associated Lymphoid Tissues (GALT) and but also in sites distant from the gut. Thus, loss of Paneth cells significantly decreased the number of ILC3s and increased the number of ILC2s in the intestinal lamina propria. Paneth cell deficiency also affected Peyer’s patches. In this regard, Paneth cell deficient mice displayed an increased numbers of Peyer’s patches which were of larger size than Peyer’s patches in control wild-type mice. Furthermore, Peyer’s patches of Paneth cell deficient mice contained increase numbers of IgA +CD19 +B cells and B1a (CD19 +CD5 +) cells. Interestingly, when compared to control wild-type mice, the numbers of B1a cells were found to be also increased in mesenteric lymph nodes of Paneth cell deficient mice, but also at sites distant from the gut including the lungs, and bone marrow. Also, in the lungs there was an increase in ILC2s. Taken together, these findings indicate that Paneth cells play a key role as regulators of innate immune responses throughout the body via regulation of ILC subsets and B1 cells. NIH Grants

Respiratory viruses, such as influenza, decrease airway cilia function and expression, which leads to reduced mucociliary clearance and inhibited overall immune defense. Ubiquitination is a posttranslational modification using E3 ligases, which plays a role in the assembly and disassembly of cilia. We examined the role of membrane-associated RING-CH (MARCH) family of E3 ligases during influenza infection and determined that MARCH10, specifically expressed in ciliated epithelial cells, is significantly decreased during influenza infection in mice, human lung epithelial cells, and human lung tissue. Cellular depletion of MARCH10 in differentiated human bronchial epithelial cells (HBECs) using CRISPR/Cas9 showed a decrease in ciliary beat frequency. Furthermore, MARCH10 cellular knockdown in combination with influenza infection selectively decreased immunoreactive levels of the ciliary component, dynein axonemal intermediate chain 1. Cellular overexpression of MARCH10 significantly decreased influenza hemagglutinin protein levels in the differentiated HBECs and knockdown of MARCH10 increased IL-1β cytokine expression, whereas overexpression had the reciprocal effect. These findings suggest that MARCH10 may have a protective role in airway pulmonary host defense and innate immunity during influenza infection.

Traditionally, whooping cough or pertussis caused by the obligate human pathogen Bordetella pertussis (Bp) is described as an acute disease with severe symptoms. However, many individuals who contract pertussis are either asymptomatic or show very mild symptoms and yet can serve as carriers and sources of bacterial transmission. Biofilms are an important survival mechanism for bacteria in human infections and disease. However, bacterial determinants that drive biofilm formation in humans are ill-defined. In the current study, we show that Bp infection of well-differentiated primary human bronchial epithelial cells leads to formation of bacterial aggregates, clusters, and highly structured biofilms which are colocalized with cilia. These findings mimic observations from pathological analyses of tissues from pertussis patients. Distinct arrangements (mono-, bi-, and tri-partite) of the polysaccharide Bps, extracellular DNA, and bacterial cells were visualized, suggesting complex heterogeneity in bacteria-matrix interactions. Analyses of mutant biofilms revealed positive roles in matrix production, cell cluster formation, and biofilm maturity for three critical Bp virulence factors: Bps, filamentous hemagglutinin, and adenylate cyclase toxin. Adherence assays identified Bps as a new Bp adhesin for primary human airway cells. Taken together, our results demonstrate the multi-factorial nature of the biofilm extracellular matrix and biofilm development process under conditions mimicking the human respiratory tract and highlight the importance of model systems resembling the natural host environment to investigate pathogenesis and potential therapeutic strategies.

Mutations in the CFTR gene lead to cystic fibrosis, a genetic disease associated with chronic infection and inflammation and ultimately respiratory failure. The most common CF-causing mutation is F508del and CFTR modulators (correctors and potentiators) are being developed to rescue its trafficking and activity defects. However, there are currently no modulators that stabilize the rescued membrane F508del-CFTR which is endocytosed and quickly degraded resulting in a shorter half-life than wild-type (WT). We previously reported that the extracellular signal-regulated kinase (ERK) MAPK pathway is involved in CFTR degradation upon cigarette smoke exposure. Interestingly, we found that ERK phosphorylation was increased in CF human bronchial epithelial (HBE) cells (CF-HBE41o- and primary CF-HBE) compared to non-CF controls, and this was likely due to signaling by the epidermal growth factor receptor (EGFR). EGFR can be activated by several ligands, and we provide evidence that amphiregulin (AREG) is important for activating this signaling axis in CF. The natural osmolyte ectoine stabilizes membrane macromolecules. We show that ectoine decreases ERK phosphorylation, increases the half-life of rescued CFTR, and increases CFTR-mediated chloride transport in combination with the CFTR corrector VX-661. Additionally, ectoine reduces production of AREG and interleukin-8 by CF primary bronchial epithelial cells. In conclusion, EGFR-ERK signaling negatively regulates CFTR and is hyperactive in CF, and targeting this axis with ectoine may prove beneficial for CF patients.

Background: Elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) modulator therapy for people with cystic fibrosis (PwCF) carrying at least one copy of the F508del mutation of the CF transmembrane conductance regulator (CFTR) protein has reduced clinical exacerbations and increased forced expiratory volume in 1 second and general wellbeing.ELX/TEZ/IVA rescues the misfolded CFTR protein and traffics it to the surface membrane of airway cells, potentially restoring normal airway physiology such as airway secretions, pH balance, and cilia movement, but it is unknown whether ELX/TEZ/IVA will also help reduce pathogenic infections and prevalence in PwCF.One such deadly pathogen is Burkholderia cenocepacia, which can cause variable lung infections, ranging from asymptomatic to chronic, or 'cepacia syndrome,' characterized by a rapid decline in lung function.Because PwCF carrying B. cenocepacia are not included in ELX/TEZ/IVA clinical trials, we proposed using in vitro primary CF human bronchial epithelial (CF-HBE) 3D cultures to investigate the effects of ELX/TEZ/IVA on B. cenocepacia infections.Methods: Fully differentiated primary CF-HBE cells (3-4 donors) at the airliquid interface (ALI) were treated with ELX/TEZ/IVA before B. cenocepacia (lab strain K56-2 labeled with DsRed; MOI 0.1-1) infection on the apical surface.Response of CF-HBE cultures to ELX/TEZ/IVA was confirmed by measuring CFTR protein expression and CFTR ion channel function.Airway physiology, including ciliary beat frequency, pH of the airway-surface liquid (ASL), and expression of antimicrobial proteins such as SPLUNC1 (activity against gram-negative bacteria) were recorded after ELX/TEZ/IVA treatment.B. cenocepacia growth was measured using immunofluorescence in non-CF HBE (NHBE) and CF-HBE ± ELX/TEZ/IVA-treated cultures.Results: ELX/TEZ/IVA treatment in CF-HBE cultures significantly restored CFTR protein expression at the apical membrane and CFTR ion channel function.Downstream physiology, including ciliary beat frequency and pH of the ASL, was significantly restored to levels observed in NHBE cultures.SPLUNC1 antimicrobial expression was lower in the ASL secretions of CF-HBE than in those of NHBE cultures but increased significantly after ELX/ TEZ/IVA treatment.Furthermore, B. cenocepacia (K56-2) infections on CF-HBE cultures were significantly reduced with pre-treatment with ELX/TEZ/ IVA, despite greater burden in CF-HBE than NHBE cultures (Figure 1).B. cenocepacia infection also appeared to interfere with ELX/TEZ/IVA efficacy by reducing CFTR expression and function compared to non-infected CF-HBE+ELX/TEZ/IVA cultures, although not to the extent of non-ELX/TEZ/IVA treated CF-HBE cultures.Conclusions: The risk of B. cenocepacia infections in PwCF may be reduced with modulator therapy such as ELX/TEZ/IVA, although B. cenocepacia may also interfere with ELX/TEZ/IVA efficacy.Whether by ELX/TEZ/IVA treatment reduces B. cenocepacia infection in PwCF already colonized with B. cenocepacia remains to be determined.Starting ELX/TEZ/IVA treatment could be beneficial to PwCF to prevent infections with pathogens such as B. cenocepacia.

Additional file 1. showing the genes listed in Figure 1: “Significant DEGs were identified with low, medium and high dose of WS-CM at 4hrs (Tab 1) and 24hrs (Tab 2) exposure. Genes highlighted yellow were consistently observed in all three doses. Genes highlighted in orange were observed in both medium and high doses, but not low dose. Log2 fold change cut-off is set to ±2 and p-value ≤ 0.05. A list of genes identified across both exposure times (4hrs and 24hrs), and within each dose (low, medium and high) is provided in Tab 3.”

Significance We report the discovery of fundamental roles for the noncanonical inflammasome molecule Caspase-4/11 in promoting pathological inflammatory and prothrombotic pathways in severe acute respiratory syndrome coronavirus 2 (SARS–CoV-2) infections. Our work demonstrates that Caspase-11 has a broader role in immune responses beyond its previously appreciated effects in bacterial infections. Further, we show that Caspase-11–deficient mice infected with SARS–CoV-2 fare significantly better in terms of overall illness, lung inflammation, and thrombosis than wild-type (WT) mice, thus implicating Caspase-11 as a new therapeutic target for preventing or treating COVID-19.

AbstractBackgroundAcute exposure to cigarette smoke alters gene expression in several biological pathways such as apoptosis, immune response, tumorigenesis and stress response, among others. However, the effects of electronic nicotine delivery systems (ENDS) on early changes in gene expression is relatively unknown. The objective of this study was to evaluate the early toxicogenomic changes using a fully-differentiated primary normal human bronchial epithelial (NHBE) culture model after an acute exposure to cigarette and ENDS preparations.ResultsRNA sequencing and pathway enrichment analysis identified time and dose dependent changes in gene expression and several canonical pathways when exposed to cigarette preparations compared to vehicle control, including oxidative stress, xenobiotic metabolism, SPINK1 general cancer pathways and mucociliary clearance. No changes were observed with ENDS preparations containing up to 28 µg/mL nicotine. Full model hierarchical clustering revealed that ENDS preparations were similar to vehicle control.ConclusionThis study revealed that while an acute exposure to cigarette preparations significantly and differentially regulated many genes and canonical pathways, ENDS preparations containing the same concentration of nicotine had very little effect on gene expression in fully-differentiated primary NHBE cultures.

Cigarette smoke deregulates several biological pathways by modulating gene expression in airway epithelial cells and altering the physiology of the airway epithelium. The effects of repeated exposures of electronic cigarette delivery systems (ENDS) on gene expression in airway epithelium are relatively unknown. In order to assess the effect of repeated exposures of ENDS, primary normal human bronchial epithelial (NHBE) cells grown at air-liquid interface (ALI) were exposed to cigarette and ENDS preparations daily for 10 days. Cigarette smoke preparations significantly altered gene expression in a dose-dependent manner compared to vehicle control, including genes linked to oxidative stress, xenobiotic metabolism, cancer pathways, epithelial-mesenchymal transition, fatty acid metabolism, degradation of collagen and extracellular matrix, O-glycosylation, and chemokines/cytokines, which are known pathways found to be altered in smokers. Conversely, ENDS preparations had minimal effect on transcriptional pathways. This study revealed that a sub-chronic exposure of primary NHBE cultures to cigarette and ENDS preparations differentially regulated genes and canonical pathways, with minimal effect observed with ENDS preparations compared to cigarette preparations. This study also demonstrates the versatility of primary NHBE cultures at ALI to evaluate repeat-dose exposures of tobacco products.

Cigarette smoking is a risk factor for several lung diseases, including chronic obstructive pulmonary disease, cardiovascular disease, and lung cancer. The potential health effects of chronic use of electronic nicotine delivery systems (ENDS) is unclear. This study utilized fully differentiated primary normal human bronchial epithelial (NHBE) cultures in a repeat-dose exposure to evaluate and compare the effect of combustible cigarette and ENDS preparations. We show that 1-h daily exposure of NHBE cultures over a 10-day period to combustible cigarette whole smoke-conditioned media (WS-CM) increased expression of oxidative stress markers, cell proliferation, airway remodeling, and cellular transformation markers and decreased mucociliary function including ion channel function and airway surface liquid. Conversely, aerosol conditioned media (ACM) from ENDS with similar nicotine concentration (equivalent-nicotine units) as WS-CM and nicotine alone had no effect on those parameters. In conclusion, primary NHBE cultures in a repeat-dose exposure system represent a good model to assess the features of lung disease. This study also reveals that cigarette and ENDS preparations differentially elicit several key endpoints, some of which are potential biomarkers for lung cancer or chronic obstructive pulmonary disease (COPD).

BackgroundThe conducting airway epithelium is repaired by tissue specific stem cells (TSC). In response to mild/moderate injury, each TSC repairs a discrete area of the epithelium. In contrast, severe epithelial injury stimulates TSC migration and expands the stem cell's reparative domain. Lung transplantation (LTx) can cause a moderate/severe airway injury and the remodeled airway contains a chimeric mixture of donor and recipient cells. These studies supported the hypothesis, LTx stimulates TSC migration resulting in epithelial chimerism. We tested this hypothesis in cystic fibrosis (CF) LTx patients.MethodsAirway mucosal injury was quantified using bronchoscopic imaging and a novel grading system. Bronchial brushing was used to recover TSC from 10 sites in the recipient and allograft airways. TSC chimerism was quantified by short tandem repeat analysis. TSC self-renewal and differentiation potential were assayed using the clone forming cell frequency and air-liquid-interface methods. Electrophysiology was used to determine if TSC chimerism altered epithelial ion channel activity.ResultsLTx caused a mild to moderate airway mucosal injury. Donor and recipient TSC were identified in 91% of anastomotic sites and 93% of bronchial airways. TSC chimerism did not alter stem cell self-renewal or differentiation potential. The frequency of recipient TSC was proportional to CF Transmembrane Conductance Regulator (CFTR)-dependent ion channel activity and 33% of allograft regions were at risk for abnormal CFTR activity.ConclusionsLTx in CF patients stimulates bidirectional TSC migration across the anastomoses. TSC chimerism may alter ion homeostasis and compromise the host defense capability of the allograft airway epithelium.