A Single-Cell Atlas of the Human Healthy Airways

Epithelial cell dynamics: Key drivers of type 2 inflammation in eosinophilic chronic rhinosinusitis

Sinonasal mucosal epithelial cells act not only as a physical barrier, but also as dynamic regulators of immune responses through innate and acquired immunity. These cells play a key role in detecting environmental stimuli, such as pathogens, allergens, and pollutants, and in initiating the inflammatory cascade that shapes the overall immune response. By releasing cytokines, such as interleukin (IL)-25 and IL-33, and thymic stromal lymphopoietin, epithelial cells interact with immune cells and promote type 2 inflammation. The pathogenesis of eosinophilic chronic rhinosinusitis (ECRS), which is driven by type 2 inflammation, is heterogeneous. While immune cells have traditionally been considered to be central to the disease pathogenesis, emerging evidence has indicated the critical role of epithelial cells. Furthermore, novel biologics targeting the IL-4/IL-13 signaling pathway have shown potential in alleviating epithelial dysfunction and inflammation. Eosinophilic mucins that accumulate in the sinuses impair mucociliary function, and especially eosinophil extracellular trap cell death (EETosis) stimulate epithelial cells and amplify eosinophilic inflammation. Eosinophilic mucin formation has been shown to significantly increase viscosity through EETosis, and novel biologics targeting the IL-5 signaling pathway hold promise for effectively mitigating this process. To develop targeted interventions, it is important to explore the role of epithelial subpopulations, such as basal cells and tuft cells, in maintaining the balance between tissue repair and chronic inflammation. Single-cell transcriptomics and spatial transcriptomics technologies have provided significant insights into the complexity of epithelial cell-derived inflammation in ECRS. The heterogeneity of the pathogenesis of CRS with nasal polyps and ECRS across patient populations complicates the development of universal therapies, underscoring the need for stratified medicine approaches. Potential future therapeutic strategies include the restoration of epithelial integrity and immune balance by disrupting aberrant crosstalk between epithelial and immune cells, particularly in patients unresponsive to current treatments.

Single-cell profiling demonstrates the combined effect of wheeze phenotype and infant viral infection on airway epithelial development

The development of the airway epithelium in asthma is unclear. We characterized nasal airway epithelial cell (NAEC) developmental phenotypes from children aged 2 to 3 years in an a priori designed nested birth cohort from four mutually exclusive groups of wheezers/nonwheezers and respiratory syncytial virus (RSV)-infected/uninfected in the first year of life. NAECs were differentiated, followed by single-cell RNA sequencing analysis and in vitro RSV infection. Gene expression of NAECs from children with a wheeze phenotype indicated abnormal differentiation and basal cell activation of developmental pathways, plasticity in precursor differentiation, delayed onset of maturation, increased diversity of RSV receptors, and blunted antiviral immune responses to in vitro RSV infection. The most marked changes in differentiation were observed in NAECs from children with both wheeze and RSV in the first year of life. Together, this suggests that airway epithelium in children with wheeze is developmentally reprogrammed and characterized by increased barrier permeability, decreased antiviral response, and altered RSV receptor expression.

Metabolic modeling elucidates phenformin and atpenin A5 as broad-spectrum antiviral drugs against RNA viruses

The SARS-CoV-2 pandemic has reemphasized the urgent need for broad-spectrum antiviral therapies. We developed a computational workflow using scRNA-Seq data to assess cellular metabolism during viral infection. With this workflow we predicted the capacity of cells to sustain SARS-CoV-2 virion production in patients and found a tissue-wide induction of metabolic pathways that support viral replication. Expanding our analysis to influenza A and dengue viruses, we identified metabolic targets and inhibitors for potential broad-spectrum antiviral treatment. These targets were highly enriched for known interaction partners of all analyzed viruses. Indeed, phenformin, an NADH:ubiquinone oxidoreductase inhibitor, suppressed SARS-CoV-2 and dengue virus replication. Atpenin A5, blocking succinate dehydrogenase, inhibited SARS-CoV-2, dengue virus, respiratory syncytial virus, and influenza A virus with high selectivity indices. In vivo, phenformin showed antiviral activity against SARS-CoV-2 in a Syrian hamster model. Our work establishes host metabolism as druggable for broad-spectrum antiviral strategies, providing invaluable tools for pandemic preparedness.

Bat organoids reveal antiviral responses at epithelial surfaces

Bats can host viruses of pandemic concern without developing disease. The mechanisms underlying their exceptional resilience to viral infections are largely unresolved, necessitating the development of physiologically relevant and genetically tractable research models. Here, we developed respiratory and intestinal organoids that recapitulated the cellular diversity of the in vivo epithelium present in Rousettus aegyptiacus, the natural reservoir for the highly pathogenic Marburg virus (MARV). In contrast to human counterparts, bat organoids and mucosal tissue exhibited elevated constitutive expression of innate immune effectors, including type I interferon-ε (IFNε) and IFN-stimulated genes (ISGs). Upon infection with diverse zoonotic viruses, including MARV, bat organoids strongly induced type I and III IFN responses, which conferred robust antiviral protection. Type III IFNλ3 additionally displayed virus-independent self-amplification, acting as an ISG to enhance antiviral immunity. Our organoid platform reveals key features of bat epithelial antiviral immunity that may inform therapeutic strategies for viral disease resilience.

Optimization of seeding cell density for differentiation of adipose-derived stem cells into epithelial-like cells on bioengineered composite scaffolds

This study investigates the biological factors influencing the epithelial differentiation of adipose-derived stem cells (ASC) to develop an engineered upper airway construct. One fraction of ASC was seeded onto a fibrin sealant (Tisseel) matrix encompassing an additional equal fraction of ASC that has been integrated into a porous polyethylene scaffold (Medpor®). Constructs with ASC seeded at total densities of 5 × 105, 1 × 106, 2.5 × 106, and 5 × 106 cells cm-2 were cultured under submerged conditions for 11 days to achieve partial epithelial differentiation (PD). To simulate post-transplantation exposure to air and interaction with host epithelial cells, PD constructs with ASC at 5 × 106 cells cm-2 were transitioned to air-liquid interface (ALI) conditions for additional 10 days (PD/ALI-21d) or 21 days (PD/ALI-32d). The latter cultures were either maintained alone or co-cultured with bronchial epithelial cells (PD/ALI-32d + BEAS). Gene expressions of mesenchymal and epithelial basal, secretory, and ciliated cell markers were assessed and validated via immunohistochemistry. ASC seeded at 5 × 106 cells cm-2 achieved the highest partial epithelial differentiation, supporting the use of this density for further experiments. In PD/ALI-21d, basal and secretory epithelial marker gene expression significantly increased, while ciliated cell markers remained unchanged. In PD/ALI-32d, expression of basal and goblet cell markers and several mesenchymal stem cell markers decreased, but co-culturing with BEAS maintained the levels of their expression. These results indicate that long-term ALI cultures cannot sustain terminal differentiation of ASC into secretory phenotypes without co-culture with primary epithelial cells. In conclusion, partially differentiated ASC on constructs maintain a stem cell phenotype and may promote differentiation into basal/secretory phenotypes, but not ciliated cells. Enhancing ciliogenesis and ensuring ASC commitment to the epithelial lineage, require modifications to the study design.

Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics

Automatic cell-type annotation methods assign cell-type labels to new, unlabeled datasets by leveraging relationships from a reference RNA-seq atlas. However, new datasets may include labels absent from the reference dataset or exhibit feature distributions that diverge from it. These scenarios can significantly affect the reliability of cell type predictions, a factor often overlooked in current automatic annotation methods. The field of out-of-distribution detection (OOD), primarily focused on computer vision, addresses the identification of instances that differ from the training distribution. Therefore, the implementation of OOD methods in the context of novel cell type annotation and data shift detection for single-cell transcriptomics may enhance annotation accuracy and trustworthiness. We evaluate six OOD detection methods: LogitNorm, MC dropout, Deep Ensembles, Energy-based OOD, Deep NN, and Posterior networks, for their annotation and OOD detection performance in both synthetical and real-life application settings. We show that OOD detection methods can accurately identify novel cell types and demonstrate potential to detect significant data shifts in non-integrated datasets. Moreover, we find that integration of the OOD datasets does not interfere with OOD detection of novel cell types.

Functional Microendoscopy Reveals Calcium Responses of Single Cells in Tracheal Tuft Cells and Kidney Podocytes

Microendoscopy, a crucial technology for minimally invasive investigations of organs, facilitates studies within confined cavities. However, conventional microendoscopy is often limited by probe size and the constraint of using a single excitation wavelength. In response to these constraints, a multichannel microendoscope with a slender profile of only 360 µm is engineered. Functional signals both in situ and in vivo are successfully captured from individual single cells, employing a specially developed software suite for image processing, and exhibiting an effective resolution of 4.6 µm, allowing for the resolution of subcellular neuronal structures. This system enabled the first examination of calcium dynamics in vivo in murine tracheal tuft cells (formerly named brush cells) and in situ in kidney podocytes. Additionally, it recorded ratiometric redox reactions in various biological settings, including intact explanted organs and pancreatic islet cultures. The flexibility and streamlined operation of the microendoscopic technique open new avenues for conducting in vivo research, allowing for studies of tissue and organ function at cellular resolution.

Aberrant basal cell clonal dynamics shape early lung carcinogenesis

Preinvasive squamous lung lesions are precursors of lung squamous cell carcinoma (LUSC). The cellular events underlying lesion formation are unknown. Using a carcinogen-induced model of LUSC with no added genetic hits or cell type bias, we find that carcinogen exposure leads to non-neutral competition among basal cells, aberrant clonal expansions, and basal cell mobilization along the airways. Ultimately, preinvasive lesions develop from a few highly mutated clones that dominate most of the bronchial tree. Multi-site sequencing in human patients confirms the presence of clonally related preinvasive lesions across distinct airway regions. Our work identifies a transition in basal cell clonal dynamics, and an associated shift in basal cell fate, as drivers of field cancerization in the lung.

Beyond circulating B cells: Characteristics and role of tissue-infiltrating B cells in systemic sclerosis

B cells play a key role in the pathophysiology of systemic sclerosis (SSc). While they are less characterized than their circulating counterparts, tissue-infiltrating B cells may have a more direct pathological role in tissues. In this review, we decipher the multiple evidence of B cells infiltration in the skin and lungs of SSc patients and animal models of SSc but also of other chronic fibrotic diseases with similar pathological mechanisms such as chronic graft versus host disease, idiopathic pulmonary fibrosis or morphea. We also recapitulate the current knowledge about mechanisms of B cells infiltration and their functions in tissues. Finally, we discuss B cell targeted therapies, and their specific impact on infiltrated B cells. Understanding the local consequences of infiltrating B cells is an important step for a better management of patients and the improvement of therapies in SSc.

Somatic Miwi2 modulates mitochondrial function in airway multiciliated cells and exacerbates influenza pathogenesis

MIWI2, a P element-induced wimpy testes (PIWI) argonaute protein known for suppressing retrotransposons during male gonadogenesis, has an unexplored role in mammalian somatic cells. We identify MIWI2 multiciliated (M2MC) cells as a rare subset of airway multiciliated cells and investigate MIWI2's function in antiviral host defense. We analyzed transcriptomes from Miwi2 heterozygous (Miwi2 +/tom) and deficient (Miwi2 tom/tom) mice following influenza A infection. During infection, Miwi2 deficiency was associated with reduced mitochondrial and ribosomal gene expression in M2MC cells, increased mitochondrial reactive oxygen species (ROS) production and ADP/ATP ratios in multiciliated cells, and enhanced viral clearance and recovery. Additionally, Miwi2-expressing cells exhibited reduced levels of small RNAs derived from nuclear mitochondrial DNA. These findings reveal a previously unrecognized role for Miwi2 in regulating small non-coding RNAs and mitochondrial oxidant production in somatic cells, indicating a function beyond its established germline activities. Our study identifies Miwi2/Piwil4 as a potential factor influencing susceptibility to severe respiratory infections.

Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery

Disease-specific subtype identification can deepen our understanding of disease progression and pave the way for personalized therapies, given the complexity of disease heterogeneity. Large-scale transcriptomic, proteomic, and imaging datasets create opportunities for discovering subtypes but also pose challenges due to their high dimensionality. To mitigate this, many feature selection methods focus on selecting features that distinguish known diseases or cell states, yet often miss features that preserve heterogeneity and reveal new subtypes. To overcome this gap, we develop Preserving Heterogeneity (PHet), a statistical methodology that employs iterative subsampling and differential analysis of interquartile range, in conjunction with Fisher's method, to identify a small set of features that enhance subtype clustering quality. Here, we show that this method can maintain sample heterogeneity while distinguishing known disease/cell states, with a tendency to outperform previous differential expression and outlier-based methods, indicating its potential to advance our understanding of disease mechanisms and cell differentiation.

Innate immunity of the lungs in homeostasis and disease

Humans breathe thousands of litres of non-sterile air each day containing bacteria, viruses, and fungi, as well as pollutants, allergens, and other particles. The continual exposure to foreign particles is juxtaposed with the vast surface area of the blood-air-barrier which becomes extremely thin to allow for efficient gas exchange. To prevent infection and injury, the healthy lung relies on a robust innate immune system to protect itself. Critically, this innate immune system must clear insults while maintaining immune tolerance and minimizing inflammation to avoid disrupting the lung's vital gas exchange function. In this review, we discuss how the innate immune system protects the lung from its environment.

Transmembrane Serine Protease TMPRSS11B promotes an acidified tumor microenvironment and immune suppression in lung squamous cell carcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide. Existing therapeutic options have limited efficacy, particularly for lung squamous cell carcinoma (LUSC), underscoring the critical need for the identification of new therapeutic targets. We previously demonstrated that the Transmembrane Serine Protease TMPRSS11B promotes transformation of human bronchial epithelial cells and enhances lactate export from LUSC cells. To determine the impact of TMPRSS11B activity on the host immune system and the tumor microenvironment (TME), we evaluated the effect of Tmprss11b depletion in a syngeneic mouse model. Tmprss11b depletion significantly reduced tumor burden in immunocompetent mice and triggered an infiltration of immune cells. RNA FISH analysis and spatial transcriptomics in the autochthonous Rosa26-Sox2-Ires-Gfp LSL/LSL ; Nkx2-1 fl/fl ; Lkb 1 fl/fl (SNL) model revealed an enrichment of Tmprss11b expression in LUSC tumors, specifically in Krt13 + hillock-like cells. Ultra-pH sensitive nanoparticle imaging and metabolite analysis identified regions of acidification, elevated lactate, and enrichment of M2-like macrophages in LUSC tumors. These results demonstrate that TMPRSS11B promotes an acidified and immunosuppressive TME and nominate this enzyme as a therapeutic target in LUSC.

Airway Spatial Transcriptomics in Smoking

Background

Cigarette smoking has a significant impact on global health. Although cessation has positive health benefits, some molecular changes to intercellular communications may persist in the lung. In this study we created a framework to generate hypotheses by predicting altered cell-cell communication in smoker lungs using single-cell and spatial transcriptomic data.

Methods

We integrated publicly available lung single-cell transcriptomic data with spatial transcriptomic data from never-smoker and current-smoker lung tissue samples to create spatial transcriptomic data at virtual single-cell resolution by mapping individual cells from our lung scRNA-seq atlas to spots in the spatial transcriptomic data. Cell-cell communications altered in smoking were identified using the virtual single-cell transcriptomic data.

Results

We identified pathways altered in the three current-smoker samples compared with the three never-smoker samples, including the up-regulated collagen pathway. We observed increased collagen pathway activity involving the ligands COL1A1 and COL1A2 in adventitial fibroblasts and decreased activity involving COL1A2 and COL6A3 in pericytes and myofibroblasts, respectively. We also identified other pathways with structural (e.g. Fibronectin-1), immune-related (e.g. MHC-II), growth factor (e.g. Pleiotrophin) and immunophilin (e.g. Cyclophilin A) roles.

Conclusions

In this study we inferred spatially proximal cell-cell communication between interacting cell types from spatial transcriptomics at virtual single-cell resolution to identify lung intercellular signaling altered in smoking. Our findings further implicate several pathways previously identified, and provide additional molecular context to inform future functional experiments and therapeutic avenues to mitigate pathogenic effects of smoking.

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics

The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.

Human Pulmonary Neuroendocrine Cells Respond to House Dust Mite Extract With PAR-1 Dependent Release of CGRP

BACKGROUND

Pulmonary neuroendocrine cells (PNEC) are rare airway epithelial cells that have recently gained attention as potential amplifiers of allergic asthma. However, studying PNEC function in humans has been challenging due to a lack of cell isolation methods, and little is known about human PNEC function in response to asthma-relevant stimuli. Here we developed and characterized an in vitro human PNEC model and investigated the neuroendocrine response to extracts of the common aeroallergen house dust mite (HDM).

METHODS

PNEC-enriched cultures were generated from human induced pluripotent stem cells (iPNEC) and primary bronchial epithelial cells (ePNEC). Characterized PNEC cultures were exposed to HDM extract, a volatile chemical odorant (Bergamot oil), or the bacterial membrane component, lipopolysaccharide (LPS), and neuroendocrine gene expression and neuropeptide release determined.

RESULTS

Both iPNEC and ePNEC models demonstrated similar baseline neuroendocrine characteristics and a stimuli-specific modulation of gene expression. Most notably, exposure to HDM but not Bergamot oil or LPS, leads to dose-dependent induction of the CGRP encoding gene, CALCB, and corresponding release of the neuropeptide. HDM-induced CALCB expression and CGRP release could be inhibited by a protease-activated receptor 1 (PAR1) antagonist or protease inhibitors and was mimicked by a PAR1 agonist.

CONCLUSIONS

We have characterized a novel model of PNEC-enriched human airway epithelium and utilized this model to demonstrate a previously unrecognized role for human PNEC in mediating a direct neuroendocrine response to aeroallergen exposure.

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization

SUMMARY

In single-cell transcriptomics, inconsistent cell type annotations due to varied naming conventions and hierarchical granularity impede data integration, machine learning applications, and meaningful evaluations. To address this challenge, we developed the unified Hierarchical Annotation Framework (uHAF), which includes organ-specific hierarchical cell type trees (uHAF-T) and a mapping tool (uHAF-Agent) based on large language models. uHAF-T provides standardized hierarchical references for 38 organs, allowing for consistent label unification and analysis at different levels of granularity. uHAF-Agent leverages GPT-4 to accurately map diverse and informal cell type labels onto uHAF-T nodes, streamlining the harmonization process. By simplifying label unification, uHAF enhances data integration, supports machine learning applications, and enables biologically meaningful evaluations of annotation methods. Our framework serves as an essential resource for standardizing cell type annotations and fostering collaborative refinement in the single-cell research community.

AVAILABILITY AND IMPLEMENTATION

uHAF is publicly available at: https://uhaf.unifiedcellatlas.org and https://github.com/SuperBianC/uhaf.

Variable DPP4 expression in multiciliated cells of the human nasal epithelium as a determinant for MERS-CoV tropism

Transmissibility of respiratory viruses is a complex viral trait that is intricately linked to tropism. Several highly transmissible viruses, including severe acute respiratory syndrome coronavirus 2 and Influenza viruses, specifically target multiciliated cells in the upper respiratory tract to facilitate efficient human-to-human transmission. In contrast, the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) generally transmits poorly between humans, which is largely attributed to the absence of its receptor dipeptidyl peptidase 4 (DPP4) in the upper respiratory tract. At the same time, MERS-CoV epidemiology is characterized by occasional superspreading events, suggesting that some individuals can disseminate this virus effectively. Here, we utilized well-differentiated human pulmonary and nasal airway organoid-derived cultures to further delineate the respiratory tropism of MERS-CoV. We find that MERS-CoV replicated to high titers in both pulmonary and nasal airway cultures. Using single-cell messenger-RNA sequencing, immunofluorescence, and immunohistochemistry, we show that MERS-CoV preferentially targeted multiciliated cells, leading to loss of ciliary coverage. MERS-CoV cellular tropism was dependent on the differentiation of the organoid-derived cultures, and replication efficiency varied considerably between donors. Similarly, variable and focal expression of DPP4 was revealed in human nose tissues. This study indicates that the upper respiratory tract tropism of MERS-CoV may vary between individuals due to differences in DPP4 expression, providing an explanation for the unpredictable transmission pattern of MERS-CoV.

Intrinsic OASL expression licenses interferon induction during influenza A virus infection

Effective control of viral infection requires rapid induction of the innate immune response, especially the type I and type III interferon (IFN) systems. Despite the critical role of IFN induction in host defense, numerous studies have established that most cells fail to produce IFNs in response to viral stimuli. The specific factors that govern cellular heterogeneity in IFN induction potential during infection are not understood. To identify specific host factors that license some cells but not others to mount an IFN response to viral infection, we developed an approach for analyzing temporal scRNA-seq data of influenza A virus (IAV)-infected cells. This approach identified the expression of several interferon stimulated genes (ISGs) within pre-infection cells as correlates of IFN induction potential of those cells, post-infection. Validation experiments confirmed that intrinsic expression of the ISG OASL is essential for robust IFNL induction during IAV infection. Altogether, our findings reveal an important role for IFN-independent, intrinsic expression of ISGs in promoting IFN induction and provide new insights into the mechanisms that regulate cell-to-cell heterogeneity in innate immune activation.

Structure and function relationships of mucociliary clearance in human and rat airways

Mucociliary clearance is a vital defense mechanism of the human airways, protecting against harmful particles and infections. When this process fails, it contributes to respiratory diseases like chronic obstructive pulmonary disease (COPD) and asthma. While advances in single-cell transcriptomics have revealed the complexity of airway composition, much of what we know about how airway structure impacts clearance relies on animal studies. This limits our ability to create accurate human-based models of airway diseases. Here we show that the airways in female rats and in humans exhibit species-specific differences in the distribution of ciliated and secretory cells as well as in ciliary beat, resulting in significantly higher clearance effectiveness in humans. We further reveal that standard lab-grown cultures exhibit lower clearance effectiveness compared to human airways, and we identify the underlying structural differences. By combining diverse experiments and physics-based modeling, we establish universal benchmarks to assess human airway function, interpret preclinical models, and better understand disease-specific impairments in mucociliary clearance.

Nutrition, Lifestyle, and Environmental Factors in Lung Homeostasis and Respiratory Health

The lungs play a vital role in maintaining homeostasis by facilitating gas exchange and serving as a structural and immune barrier. External factors, including nutrition, lifestyle, and environmental exposures, profoundly influence normal lung function and contribute to the development, progression, and prognosis of various respiratory diseases. Deficiencies in key micronutrients, such as vitamins A, D, and C, as well as omega-3 fatty acids, can impair the integrity of the epithelial lining, compromising the lungs' defense mechanisms and increasing susceptibility to injury and disease. Obesity and physical inactivity further disrupt respiratory function by inducing structural changes in the chest wall and promoting a pro-inflammatory state. Environmental pollutants further worsen oxidative damage and activate inflammatory pathways. Addressing these modifiable factors through interventions such as dietary optimization, physical activity programs, and strategies to reduce environmental exposure offers promising avenues for preserving lung function and preventing disease progression. This review examines the molecular pathways through which nutrition, lifestyle, and environmental influences impact lung homeostasis.

Heterogeneity-Preserving Discriminative Feature Selection for Disease-Specific Subtype Discovery

The identification of disease-specific subtypes can provide valuable insights into disease progression and potential individualized therapies, important aspects of precision medicine given the complex nature of disease heterogeneity. The advent of high-throughput technologies has enabled the generation and analysis of various molecular data types, such as single-cell RNA-seq, proteomic, and imaging datasets, on a large scale. While these datasets offer opportunities for subtype discovery, they also pose challenges in finding subtype signatures due to their high dimensionality. Feature selection, a key step in the machine learning pipeline, involves selecting signatures that reduce feature size for more efficient downstream computational analysis. Although many existing methods focus on selecting features that differentiate known diseases or cell states, they often struggle to identify features that both preserve heterogeneity and reveal subtypes. To address this, we utilized deep metric learning-based feature embedding to explore the statistical properties of features crucial for preserving heterogeneity. Our analysis indicated that features with a notable difference in interquartile range (IQR) between classes hold important subtype information. Guided by this insight, we developed a statistical method called PHet (Preserving Heterogeneity), which employs iterative subsampling and differential analysis of IQR combined with Fisher's method to identify a small set of features that preserve heterogeneity and enhance subtype clustering quality. Validation on public single-cell RNA-seq and microarray datasets demonstrated PHet's ability to maintain sample heterogeneity while distinguishing known disease/cell states, with a tendency to outperform previous differential expression and outlier-based methods. Furthermore, an analysis of a single-cell RNA-seq dataset from mouse tracheal epithelial cells identified two distinct basal cell subtypes differentiating towards a luminal secretory phenotype using PHet-based features, demonstrating promising results in a real-data application. These results highlight PHet's potential to enhance our understanding of disease mechanisms and cell differentiation, contributing significantly to the field of personalized medicine.

Location, Location, Location: Spatial Immune-Stroma Crosstalk Drives Pathogenesis in Asthma

Chronic lung diseases including asthma are characterized by an abnormal immune response and active tissue remodeling. These changes in the architecture of the tissue are a fundamental part of the pathology across the life course of patients suffering from asthma. Current treatments aim at dampening the immune system hyperactivation, but effective drugs targeting stromal or acellular structures are still lacking. This is mainly due to the lack of a detailed understanding of the composition of the large airways and the cellular interactions taking place in this niche. We and others have revealed multiple aspects of the spatial architecture of the airway wall in response to airborne insults. In this review, we discuss four elements that we believe should be the focus of future asthma research across the life course, to increase understanding and improve therapies: (i) specialized lung niches, (ii) the 3D architecture of the epithelium, (iii) the extracellular matrix, and (iv) the vasculature. These components comprise the main stromal structures at the airway wall, each playing a key role in the development of asthma and directing the immune response. We summarize promising future directions that will enhance lung research, ultimately benefiting patients with asthma.

Cystic fibrosis alters the structure of the olfactory epithelium and the expression of olfactory receptors affecting odor perception

A reduced sense of smell is a common condition in people with cystic fibrosis (CF) that negatively affects their quality of life. While often attributed to nasal mucosa inflammation, the underlying causes of the olfactory loss remain unknown. Here, we characterized gene expression in olfactory epithelium cells from patients with CF using single-nuclei RNA sequencing and found altered expression of olfactory receptors (ORs) and genes related to progenitor cell proliferation. We confirmed these findings in newborn, inflammation-free samples of a CF animal model and further identified ultrastructural alterations in the olfactory epithelium and bulbs of these animals. We established that CFTR, the anion channel whose dysfunction causes CF, is dispensable for odor-evoked signaling in sensory neurons, yet CF animals displayed defective odor-guided behaviors consistent with the morphological and molecular alterations. Our study highlights CF's major role in modulating epithelial structure and OR expression, shedding light on the mechanisms contributing to olfactory loss in CF.

Lung immune challenge study protocol: controlled exposure to inhaled resiquimod (R848) to study mechanisms of inflammation

This study aims to develop a human lung immune challenge model using inhaled Resiquimod (R848), a Toll-like receptor 7/8 agonist, to investigate inflammatory mechanisms involved in the human respiratory mucosa in health and disease. This approach seeks to induce innate immune anti-viral responses in the lungs and blood, with a suitable dose of inhaled R848 that is clinically tolerable. The study will include healthy volunteers and individuals with asthma. The primary outcome is a change in CXCL10, a biomarker representative of anti-viral responses, at 24 hours post-exposure. Secondary outcomes include changes in lung function, physiological parameters, and inflammatory markers, including C-reactive protein and eosinophil counts. This trial involves a single ascending dose, randomized, single-blind, placebo-controlled design. Participants will receive R848 via nebulization in escalating doses from 0.1 to 100 µg/ml or saline placebo. Safety assessments include spirometry, vital signs, and blood samples to monitor systemic and lung-specific immune responses. The study will contribute to understanding immune pathways in asthma and provide a platform for testing novel anti-inflammatory therapeutics. The protocol has been approved by relevant ethics committees and will be disseminated via peer-reviewed publications and open-access data repositories.

Structure and Function Relationships of Mucociliary Clearance in Human and Rat Airways

Mucociliary clearance is a vital defense mechanism of the human airways, protecting against harmful particles and infections. When this process fails, it contributes to respiratory diseases like chronic obstructive pulmonary disease (COPD) and asthma. While advances in single-cell transcriptomics have revealed the complexity of airway composition, much of what we know about how airway structure impacts clearance relies on animal studies. This limits our ability to create accurate human-based models of airway diseases. Here we show that the airways in female rats and in humans exhibit species-specific differences in the distribution of ciliated and secretory cells as well as in ciliary beat, resulting in significantly higher clearance effectiveness in humans. We further reveal that standard lab-grown cultures exhibit lower clearance effectiveness compared to human airways, and we identify the underlying structural differences. By combining diverse experiments and physics-based modeling, we establish universal benchmarks to assess human airway function, interpret preclinical models, and better understand disease-specific impairments in mucociliary clearance.

Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics

The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.

Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2

Viral variant and host vaccination status impact infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet how these factors shift cellular responses in the human nasal mucosa remains uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on nasopharyngeal swabs from vaccinated and unvaccinated adults with acute Delta and Omicron SARS-CoV-2 infections and integrated with data from acute infections with ancestral SARS-CoV-2. Patients with Delta and Omicron exhibited greater similarity in nasal cell composition driven by myeloid, T cell and SARS-CoV-2hi cell subsets, which was distinct from that of ancestral cases. Delta-infected samples had a marked increase in viral RNA, and a subset of PER2+EGR1+GDF15+ epithelial cells was enriched in SARS-CoV-2 RNA+ cells in all variants. Prior vaccination was associated with increased frequency and activation of nasal macrophages. Expression of interferon-stimulated genes negatively correlated with coronavirus disease 2019 (COVID-19) severity in patients with ancestral and Delta but not Omicron variants. Our study defines nasal cell responses and signatures of disease severity across SARS-CoV-2 variants and vaccination.

A Single-Cell Atlas of the Upper Respiratory Epithelium Reveals Heterogeneity in Cell Types and Patterning Strategies

The upper respiratory tract, organized along the pharyngolaryngeal-to-tracheobronchial axis, is essential for homeostatic functions such as breathing and vocalization. The upper respiratory epithelium is frequently exposed to pollutants and pathogens, making this an area of first-line defense against respiratory injury and infection. The respiratory epithelium is composed of a rich array of specialized cell types, each with unique capabilities in immune defense and injury repair. However, the precise transcriptomic signature and spatial distribution of these cell populations, as well as potential cell subpopulations, have not been well defined. Here, using single cell RNAseq combined with spatial validation, we present a comprehensive atlas of the mouse upper respiratory epithelium. We systematically analyzed our rich RNAseq dataset of the upper respiratory epithelium to reveal 17 cell types, which we further organized into three spatially distinct compartments: the Tmprss11a + pharyngolaryngeal, the Nkx2-1 + tracheobronchial, and the Dmbt1 + submucosal gland epithelium. We profiled/analyzed the pharyngolaryngeal epithelium, composed of stratified squamous epithelium, and identified distinct regional signatures, including a Keratin gene expression code. In profiling the tracheobronchial epithelium, which is composed of a pseudostratified epithelium-with the exception of the hillock structure-we identified that regional luminal cells, such as club cells and basal cells, show varying gradients of marker expression along the proximal-distal and/or dorsal-ventral axis. Lastly, our analysis of the submucosal gland epithelium, composed of an array of cell types, such as the unique myoepithelial cells, revealed the colorful diversity of between and within cell populations. Our single-cell atlas with spatial validation highlights the distinct transcriptional programs of the upper respiratory epithelium and serves as a valuable resource for future investigations to address how cells behave in homeostasis and pathogenesis.

Highlights

- Defined three spatially distinct epithelial compartments, Tmprss11a + pharyngolaryngeal, Nkx2-1 + tracheobronchial, and Dmbt1 + submucosal gland, comprising 17 total cell types - Profiled Keratin gene expression code along proximal-distal and basal-luminal axes and highlighted "stress-induced" Keratins KRT6A and KRT17 at homeostasis - Demarcated expression gradients of Scgb1a1 + and Scgb3a2+ club cells along the proximal-distal axes - Specified submucosal gland cell heterogeneity including Nkx3-1+ mucin-producing cells, with ACTA2+ basal myoepithelial cells exhibiting gene profile for neuroimmune mediated signaling.

Advances in the Development and Application of Human Organoids: Techniques, Applications, and Future Perspectives

Organoids are three-dimensional (3D) cell cultures derived from human pluripotent stem cells or adult stem cells that recapitulate the cellular heterogeneity, structure, and function of human organs. These microstructures are invaluable for biomedical research due to their ability to closely mimic the complexity of native tissues while retaining human genetic material. This fidelity to native organ systems positions organoids as a powerful tool for advancing our understanding of human biology and for enhancing preclinical drug testing. Recent advancements have led to the successful development of a variety of organoid types, reflecting a broad range of human organs and tissues. This progress has expanded their application across several domains, including regenerative medicine, where organoids offer potential for tissue replacement and repair; disease modeling, which allows for the study of disease mechanisms and progression in a controlled environment; drug discovery and evaluation, where organoids provide a more accurate platform for testing drug efficacy and safety; and microecological research, where they contribute to understanding the interactions between microbes and host tissues. This review provides a comprehensive overview of the historical development of organoid technology, highlights the key achievements and ongoing challenges in the field, and discusses the current and emerging applications of organoids in both laboratory research and clinical practice.

Lung stem cells and respiratory epithelial chimerism in transplantation

Stem cells are capable of self-renewal and differentiation into specialised types. They range from totipotent cells to multipotent or somatic stem cells and ultimately to unipotent cells. Some adult multipotent stem cells can have the potential to regenerate and colonise diverse tissues. The respiratory airways and lung mucosa, exposed to ambient air, perform vital roles for all human tissues and organs. They serve as barriers against airborne threats and are essential for tissue oxygenation. Despite low steady-state turnover, lungs are vulnerable to injuries and diseases from environmental exposure. Lung stem cells are crucial due to their regenerative potential and ability to replace damaged cells. Lung repair with extrapulmonary stem cells can occur, leading to the coexistence of respiratory cells with different genetic origins, a phenomenon known as airway epithelial chimerism. The impact of such chimerism in lung repair and disease is actively studied. This review explores different stem cell types, focusing on pulmonary stem cells. It discusses airway epithelium models derived from stem cells for studying lung diseases and examines lung chimerism, particularly in lung transplantation and haematopoietic stem cell transplantation, highlighting its significance in understanding tissue repair and chimerism-mediated repair processes in lung pathology.

Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma

Two APOBEC DNA cytosine deaminase enzymes, APOBEC3A and APOBEC3B, generate somatic mutations in cancer, thereby driving tumour development and drug resistance. Here, we used single-cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell-cycle stage associated with APOBEC-mediated mutagenesis. In contrast, in squamous cell carcinoma we find that, there is expansion of GRHL3expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings suggest that APOBEC3A may play a functional role during keratinocyte differentiation, and offer a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.

Methods and Models for Studying Mycobacterium tuberculosis in Respiratory Infections

Respiratory infections, including tuberculosis, constitute a major global health challenge. Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the leading causes of mortality worldwide. The disease's complexity is attributed to Mtb's capacity to persist in latent states, evade host immune defenses, and develop resistance to antimicrobial treatments, posing significant challenges for diagnosis and therapy. Traditional models, such as animal studies and two-dimensional (2D) in vitro systems, often fail to accurately recapitulate human-specific immune processes, particularly the formation of granulomas-a defining feature of tubercular infection. These limitations underscore the need for more physiologically relevant models to study TB pathogenesis. Emerging three-dimensional (3D) in vitro systems, including organoids and lung-on-chip platforms, offer innovative approaches to mimic the structural and functional complexity of the human lung. These models enable the recreation of key aspects of the tubercular granulomas, such as cellular interactions, oxygen gradients, and nutrient limitations, thereby providing deeper insights into Mtb pathogenesis. This review aims to elucidate the advantages of 3D in vitro systems in bridging the translational gap between traditional experimental approaches and clinical applications. Particular emphasis is placed on their potential to address challenges related to genetic variability in both the host and pathogen, thereby advancing tubercular research and therapeutic development.

An atlas of the shared genetic architecture between atopic and gastrointestinal diseases

Comorbidity among atopic diseases (ADs) and gastrointestinal diseases (GIDs) has been repeatedly demonstrated by epidemiological studies, whereas the shared genetic liability remains largely unknown. Here we establish an atlas of the shared genetic architecture between 10 ADs or related traits and 11 GIDs, comprehensively investigating the comorbidity-associated genomic regions, cell types, genes and genetically predicted causality. Although distinct genetic correlations between AD-GID are observed, including 14 genome-wide and 28 regional correlations, genetic factors of Crohn's disease (CD), ulcerative colitis (UC), celiac disease and asthma subtypes are converged on CD4+ T cells consistently across relevant tissues. Fourteen genes are associated with comorbidities, with three genes are known treatment targets, showing probabilities for drug repurposing. Lower expressions of WDR18 and GPX4 in PBMC CD4+ T cells predict decreased risk of CD and asthma, which could be novel drug targets. MR unveils certain ADs led to higher risk of GIDs or vice versa. Taken together, here we show distinct genetic correlations between AD-GID pairs, but the correlated genomic loci converge on the dysregulation of CD4+ T cells. Inhibiting WDR18 and GPX4 expressions might be candidate therapeutic strategies for CD and asthma. Estimated causality indicates potential guidance for preventing comorbidity.

Increased Levels of hsa-miR-199a-3p and hsa-miR-382-5p in Maternal and Neonatal Blood Plasma in the Case of Placenta Accreta Spectrum

Despite the increasing number of placenta accreta spectrum (PAS) cases in recent years, its impact on neonatal outcomes and respiratory morbidity, as well as the underlying pathogenetic mechanism, has not yet been extensively studied. Moreover, no study has yet demonstrated the effectiveness of antenatal corticosteroid therapy (CT) for the prevention of respiratory distress syndrome (RDS) in newborns of mothers with PAS at the molecular level. In this regard, microRNA (miRNA) profiling by small RNA deep sequencing and quantitative real-time PCR was performed on 160 blood plasma samples from preterm infants (gestational age: 33-36 weeks) and their mothers who had been diagnosed with or without PAS depending on the timing of the antenatal RDS prophylaxis. A significant increase in hsa-miR-199a-3p and hsa-miR-382-5p levels was observed in the blood plasma of the newborns from mothers with PAS compared to the control group. A clear trend toward the normalization of hsa-miR-199a-3p and hsa-miR-382-5p levels in the neonatal blood plasma of the PAS groups was observed when CT was administered within 14 days before delivery, but not beyond 14 days. Direct correlations were found among the hsa-miR-382-5p level in neonatal blood plasma and the hsa-miR-199a-3p level in the same sample (r = 0.49; p < 0.001), the oxygen requirements in the NICU (r = 0.41; p = 0.001), the duration of the NICU stay (r = 0.31; p = 0.019), and the severity of the newborn's condition based on the NEOMOD scale (r = 0.36; p = 0.005). Logistic regression models based on the maternal plasma levels of hsa-miR-199a-3p and hsa-miR-382-5p predicted the need for cardiotonic therapy, invasive mechanical ventilation, or high-frequency oscillatory ventilation in newborns during the early neonatal period, with a sensitivity of 95-100%. According to the literary data, these miRNAs regulate fetal organogenesis via IGF-1, the formation of proper lung tissue architecture, surfactant synthesis in alveolar cells, and vascular tone.

Airway-derived emphysema-specific alveolar type II cells exhibit impaired regenerative potential in COPD

Emphysema, the progressive destruction of gas exchange surfaces in the lungs, is a hallmark of COPD that is presently incurable. This therapeutic gap is largely due to a poor understanding of potential drivers of impaired tissue regeneration, such as abnormal lung epithelial progenitor cells, including alveolar type II (ATII) and airway club cells. We discovered an emphysema-specific subpopulation of ATII cells located in enlarged distal alveolar sacs, termed asATII cells. Single-cell RNA sequencing and in situ localisation revealed that asATII cells co-express the alveolar marker surfactant protein C and the club cell marker secretaglobin-3A2 (SCGB3A2). A similar ATII subpopulation derived from club cells was also identified in mouse COPD models using lineage labelling. Human and mouse ATII subpopulations formed 80-90% fewer alveolar organoids than healthy controls, indicating reduced progenitor function. Targeting asATII cells or their progenitor club cells could reveal novel COPD treatment strategies.

Cellular Mechanisms of Lung Injury: Current Perspectives

The alveolar-capillary barrier includes microvascular endothelial and alveolar epithelial cells and their matrices, and its disruption is a critical driver of lung injury during development of acute respiratory distress syndrome. In this review, we provide an overview of the structure and function of the alveolar-capillary barrier during health and highlight several important signaling mechanisms that underlie endothelial and epithelial injury during critical illness, emphasizing areas with potential for development of therapeutic strategies targeting alveolar-capillary leak. We also emphasize the importance of biomarker and preclinical studies in developing novel therapies and highlight important areas warranting future investigation.

Single-cell atlas of healthy vocal folds and cellular function in the endothelial-to-mesenchymal transition

The vocal fold is an architecturally complex organ comprising a heterogeneous mixture of various layers of individual epithelial and mesenchymal cell lineages. Here we performed single-cell RNA sequencing profiling of 5836 cells from the vocal folds of adult Sprague-Dawley rats. Combined with immunostaining, we generated a spatial and transcriptional map of the vocal fold cells and characterized the subpopulations of epithelial cells, mesenchymal cells, endothelial cells, and immune cells. We also identified a novel epithelial-to-mesenchymal transition-associated epithelial cell subset that was mainly found in the basal epithelial layers. We further confirmed that this subset acts as intermediate cells with similar genetic features to epithelial-to-mesenchymal transition in head and neck squamous cell carcinoma. Finally, we present the complex intracellular communication network involved homeostasis using CellChat analysis. These studies define the cellular and molecular framework of the biology and pathology of the VF mucosa and reveal the functional importance of developmental pathways in pathological states in cancer.

Recent advances and applications of human lung alveolar organoids

The human lung alveolus is a well-structured and coordinated pulmonary unit, allowing them to perform diverse functions. While there has been significant progress in understanding the molecular and cellular mechanisms behind human alveolar development and pulmonary diseases, the underlying mechanisms of alveolar differentiation and disease development are still unclear, mainly due to the limited availability of human tissues and a lack of proper in vitro lung model systems mimicking human lung physiology. In this review, we summarize recent advances in creating human lung organoid models that mimic alveolar epithelial cell types. Moreover, we discuss how lung alveolar organoid systems are being applied to recent cutting-edge research on lung development, regeneration, and diseases.

Airway ciliary microenvironment responses in mice with primary ciliary dyskinesia and central pair apparatus defects

Dysfunction of motile cilia can impair mucociliary clearance in the airway and result in primary ciliary dyskinesia (PCD). We previously showed that mutations in central pair apparatus (CPA) genes perturb ciliary motility and result in PCD in mouse models. However, little is known about how epithelial cell types in the ciliary microenvironment of the upper airway respond to defects in ciliary motility and mucociliary clearance. Here, we have used single-cell RNA sequencing to investigate responses in tracheal epithelial cells from mice with mutations in CPA genes Cfap221/ Pcdp1, Cfap54, and Spef2. Expected cell types were identified, along with an unidentified cell type not expressing markers of typical airway cells. Deuterosomal cells were found to exist in two states that differ largely in expression of genes involved in differentiation into ciliated cells. Functional enrichment analysis of differentially expressed genes (DEGs) revealed important cellular functions and molecular pathways for each cell type that are altered in mutant mice. Overlapping DEGs shed light on general responses to cilia dysfunction, while unique DEGs indicate that some responses may be specific to the individual mutation and ciliary defect.

scDOT: optimal transport for mapping senescent cells in spatial transcriptomics

The low resolution of spatial transcriptomics data necessitates additional information for optimal use. We developed scDOT, which combines spatial transcriptomics and single cell RNA sequencing to improve the ability to reconstruct single cell resolved spatial maps and identify senescent cells. scDOT integrates optimal transport and expression deconvolution to learn non-linear couplings between cells and spots and to infer cell placements. Application of scDOT to lung spatial transcriptomics data improves on prior methods and allows the identification of the spatial organization of senescent cells, their neighboring cells and novel genes involved in cell-cell interactions that may be driving senescence.

Profibrotic monocyte-derived alveolar macrophages are expanded in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19

Monocyte-derived alveolar macrophages drive lung injury and fibrosis in murine models and are associated with pulmonary fibrosis in humans. Monocyte-derived alveolar macrophages have been suggested to develop a phenotype that promotes lung repair as injury resolves. We compared single-cell and cytokine profiling of the alveolar space in a cohort of 35 patients with post-acute sequelae of COVID-19 who had persistent respiratory symptoms and abnormalities on a computed tomography scan of the chest that subsequently improved or progressed. The abundance of monocyte-derived alveolar macrophages, their gene expression programs, and the level of the monocyte chemokine CCL2 in bronchoalveolar lavage fluid positively associated with the severity of radiographic fibrosis. Monocyte-derived alveolar macrophages from patients with resolving or progressive fibrosis expressed the same set of profibrotic genes. Our findings argue against a distinct reparative phenotype in monocyte-derived alveolar macrophages, highlighting their utility as a biomarker of failed lung repair and a potential target for therapy.

Single-cell analysis of nasal epithelial cell development in domestic pigs

The nasal mucosa forms a critical barrier against the invasion of respiratory pathogens. Composed of a heterogeneous assortment of cell types, the nasal mucosa relies on the unique characteristics and complex intercellular dynamics of these cells to maintain their structural integrity and functional efficacy. In this study, single-cell RNA sequencing (scRNA-seq) of porcine nasal mucosa was performed, and nineteen distinct nasal cell types, including nine epithelial cell types, five stromal cell types, and five immune cell types, were identified. The distribution patterns of three representative types of epithelial cells (basal cells, goblet cells, and ciliated cells) were subsequently detected by immunofluorescence. We conducted a comparative analysis of these data with published human single-cell data, revealing consistent differentiation trajectories among porcine and human nasal epithelial cells. Specifically, basal cells serve as the initial stage in the differentiation process of nasal epithelial cells, which then epithelial cells. This research not only enhances our understanding of the composition and transcriptional signature of porcine nasal mucosal cells but also offers a theoretical foundation for developing alternative models for human respiratory diseases.

FORMATION OF MALIGNANT, METASTATIC SMALL CELL LUNG CANCERS THROUGH OVERPRODUCTION OF cMYC PROTEIN IN TP53 AND RB1 DEPLETED PULMONARY NEUROENDOCRINE CELLS DERIVED FROM HUMAN EMBRYONIC STEM CELLS

We recently described our initial efforts to develop a model for small cell lung cancer (SCLC) derived from human embryonic stem cells (hESCs) that were differentiated to form pulmonary neuroendocrine cells (PNECs), a putative cell of origin for neuroendocrine-positive SCLC. Although reduced expression of the tumor suppressor genes TP53 and RB1 allowed the induced PNECs to form subcutaneous growths in immune-deficient mice, the tumors did not display the aggressive characteristics of SCLC seen in human patients. Here we report that the additional, doxycycline-regulated expression of a transgene encoding wild-type or mutant cMYC protein promotes rapid growth, invasion, and metastasis of these hESC-derived cells after injection into the renal capsule. Similar to others, we find that the addition of cMYC encourages the formation of the SCLC-N subtype, marked by high levels of NEUROD1 RNA. Using paired primary and metastatic samples for RNA sequencing, we observe that the subtype of SCLC does not change upon metastatic spread and that production of NEUROD1 is maintained. We also describe histological features of these malignant, SCLC-like tumors derived from hESCs and discuss potential uses of this model in efforts to control and better understand this recalcitrant neoplasm.

IL-1β-induced epithelial cell and fibroblast transdifferentiation promotes neutrophil recruitment in chronic rhinosinusitis with nasal polyps

Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases, including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated with an unfavorable prognosis. Here, using single-cell RNA sequencing (scRNA-seq) to profile human nasal mucosa obtained from the inferior turbinates, middle turbinates, and nasal polyps of CRSwNP patients, we identify two IL-1 signaling-induced cell subsets-LY6D+ club cells and IDO1+ fibroblasts-that promote neutrophil recruitment by respectively releasing S100A8/A9 and CXCL1/2/3/5/6/8 into inflammatory regions. IL-1β, a pro-inflammatory cytokine involved in IL-1 signaling, induces the transdifferentiation of LY6D+ club cells and IDO1+ fibroblasts from primary epithelial cells and fibroblasts, respectively. In an LPS-induced neutrophilic CRSwNP mouse model, blocking IL-1β activity with a receptor antagonist significantly reduces the numbers of LY6D+ club cells and IDO1+ fibroblasts and mitigates nasal inflammation. This study implicates the function of two cell subsets in neutrophil recruitment and demonstrates an IL-1-based intervention for mitigating neutrophilic inflammation in CRSwNP.

Single cell transcriptional analysis of human adenoids identifies molecular features of airway microfold cells

The nasal, oropharyngeal, and bronchial mucosa are primary contact points for airborne pathogens like Mycobacterium tuberculosis (Mtb), SARS-CoV-2, and influenza virus. While mucosal surfaces can function as both entry points and barriers to infection, mucosa-associated lymphoid tissues (MALT) facilitate early immune responses to mucosal antigens. MALT contains a variety of specialized epithelial cells, including a rare cell type called a microfold cell (M cell) that functions to transport apical antigens to basolateral antigen-presenting cells, a crucial step in the initiation of mucosal immunity. M cells have been extensively characterized in the gastrointestinal (GI) tract in murine and human models. However, the precise development and functions of human airway M cells is unknown. Here, using single-nucleus RNA sequencing (snRNA-seq), we generated an atlas of cells from the human adenoid and identified 16 unique cell types representing basal, club, hillock, and hematopoietic lineages, defined their developmental trajectories, and determined cell-cell relationships. Using trajectory analysis, we found that human airway M cells develop from progenitor club cells and express a gene signature distinct from intestinal M cells. Surprisingly, we also identified a heretofore unknown epithelial cell type demonstrating a robust interferon-stimulated gene signature. Our analysis of human adenoid cells enhances our understanding of mucosal immune responses and the role of M cells in airway immunity. This work also provides a resource for understanding early interactions of pathogens with airway mucosa and a platform for development of mucosal vaccines.

Multifaceted roles of mitochondria in asthma

Mitochondria are essential organelles within cells, playing various roles in numerous cellular processes, including differentiation, growth, apoptosis, energy conversion, metabolism, and cellular immunity. The phenotypic variation of mitochondria is specific to different tissues and cell types, resulting in significant differences in their function, morphology, and molecular characteristics. Asthma is a chronic, complex, and heterogeneous airway disease influenced by external factors such as environmental pollutants and allergen exposure, as well as internal factors at the tissue, cellular, and genetic levels, including lung and airway structural cells, immune cells, granulocytes, and mast cells. Therefore, a comprehensive understanding of the specific responses of mitochondria to various external environmental stimuli and internal changes are crucial for elucidating the pathogenesis of asthma. Previous research on mitochondrial-targeted therapy for asthma has primarily focused on antioxidants. Consequently, it is necessary to summarize the multifaceted roles of mitochondria in the pathogenesis of asthma to discover additional strategies targeting mitochondria in this context. In this review, our goal is to describe the changes in mitochondrial function in response to various exposure factors across different cell types and other relevant factors in the context of asthma, utilizing a new mitochondrial terminology framework that encompasses cell-dependent mitochondrial characteristics, molecular features, mitochondrial activity, function, and behavior.

Studying the Pulmonary Endothelium in Health and Disease: An Official American Thoracic Society Workshop Report

Lung endothelium resides at the interface between the circulation and the underlying tissue, where it senses biochemical and mechanical properties of both the blood as it flows through the vascular circuit and the vessel wall. The endothelium performs the bidirectional signaling between the blood and tissue compartments that is necessary to maintain homeostasis while physically separating both, facilitating a tightly regulated exchange of water, solutes, cells, and signals. Disruption in endothelial function contributes to vascular disease, which can manifest in discrete vascular locations along the artery-to-capillary-to-vein axis. Although our understanding of mechanisms that contribute to endothelial cell injury and repair in acute and chronic vascular disease have advanced, pathophysiological mechanisms that underlie site-specific vascular disease remain incompletely understood. In an effort to improve the translatability of mechanistic studies of the endothelium, the American Thoracic Society convened a workshop to optimize rigor, reproducibility, and translation of discovery to advance our understanding of endothelial cell function in health and disease.

A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models

Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. Here we report that SARS-CoV-2 replication is restricted at a post-entry step in a number of ACE2-positive airway-derived cell lines due to tonic activation of the cGAS-STING pathway mediated by mitochondrial DNA leakage and naturally occurring cGAS and STING variants. Genetic and pharmacological inhibition of the cGAS-STING and type I/III IFN pathways as well as ACE2 overexpression overcome these blocks. SARS-CoV-2 replication in STING knockout cell lines and primary airway cultures induces ISG expression but only in uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway in productively infected cells. Pharmacological inhibition of STING in primary airway cells enhances SARS-CoV-2 replication and reduces virus-induced innate immune activation. Together, our study highlights that tonic activation of the cGAS-STING and IFN pathways can impact SARS-CoV-2 cellular tropism in a manner dependent on ACE2 expression levels.