CD151 Maintains Endolysosomal Protein Quality to Inhibit Vascular Inflammation.

BACKGROUND: Tetraspanin CD151 is highly expressed in endothelia and reinforces cell adhesion, but its role in vascular inflammation remains largely unknown. METHODS: In vitro molecular and cellular biological analyses on genetically modified endothelial cells, in vivo vascular biological analyses on genetically engineered mouse models, and in silico systems biology and bioinformatics analyses on CD151-related events. RESULTS: Endothelial ablation of Cd151 leads to pulmonary and cardiac inflammation, severe sepsis, and perilous COVID-19, and endothelial CD151 becomes downregulated in inflammation. Mechanistically, CD151 restrains endothelial release of proinflammatory molecules for less leukocyte infiltration. At the subcellular level, CD151 determines the integrity of multivesicular bodies/lysosomes and confines the production of exosomes that carry cytokines such as ANGPT2 (angiopoietin-2) and proteases such as cathepsin-D. At the molecular level, CD151 docks VCP (valosin-containing protein)/p97, which controls protein quality via mediating deubiquitination for proteolytic degradation, onto endolysosomes to facilitate VCP/p97 function. At the endolysosome membrane, CD151 links VCP/p97 to (1) IFITM3 (interferon-induced transmembrane protein 3), which regulates multivesicular body functions, to restrain IFITM3-mediated exosomal sorting, and (2) V-ATPase, which dictates endolysosome pH, to support functional assembly of V-ATPase. CONCLUSIONS: Distinct from its canonical function in strengthening cell adhesion at cell surface, CD151 maintains endolysosome function by sustaining VCP/p97-mediated protein unfolding and turnover. By supporting protein quality control and protein degradation, CD151 prevents proteins from (1) buildup in endolysosomes and (2) discharge through exosomes, to limit vascular inflammation. Also, our study conceptualizes that balance between degradation and discharge of proteins in endothelial cells determines vascular information. Thus, the IFITM3/V-ATPase-tetraspanin-VCP/p97 complexes on endolysosome, as a protein quality control and inflammation-inhibitory machinery, could be beneficial for therapeutic intervention against vascular inflammation.

Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts.

BACKGROUND: Fibroblast-to-myofibroblast conversion is a major driver of tissue remodelling in organ fibrosis. Distinct lineages of fibroblasts support homeostatic tissue niche functions, yet their specific activation states and phenotypic trajectories during injury and repair have remained unclear. METHODS: We combined spatial transcriptomics, multiplexed immunostainings, longitudinal single-cell RNA-sequencing and genetic lineage tracing to study fibroblast fates during mouse lung regeneration. Our findings were validated in idiopathic pulmonary fibrosis patient tissues in situ as well as in cell differentiation and invasion assays using patient lung fibroblasts. Cell differentiation and invasion assays established a function of SFRP1 in regulating human lung fibroblast invasion in response to transforming growth factor (TGF)ß1. MEASUREMENTS AND MAIN RESULTS: We discovered a transitional fibroblast state characterised by high Sfrp1 expression, derived from both Tcf21-Cre lineage positive and negative cells. Sfrp1 + cells appeared early after injury in peribronchiolar, adventitial and alveolar locations and preceded the emergence of myofibroblasts. We identified lineage-specific paracrine signals and inferred converging transcriptional trajectories towards Sfrp1 + transitional fibroblasts and Cthrc1 + myofibroblasts. TGFß1 downregulated SFRP1 in noninvasive transitional cells and induced their switch to an invasive CTHRC1+ myofibroblast identity. Finally, using loss-of-function studies we showed that SFRP1 modulates TGFß1-induced fibroblast invasion and RHOA pathway activity. CONCLUSIONS: Our study reveals the convergence of spatially and transcriptionally distinct fibroblast lineages into transcriptionally uniform myofibroblasts and identifies SFRP1 as a modulator of TGFß1-driven fibroblast phenotypes in fibrogenesis. These findings are relevant in the context of therapeutic interventions that aim at limiting or reversing fibroblast foci formation.

Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis.

Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with single-cell RNA sequencing and induced a multilineage circuit of fibrogenic cell states in hPCLS. We showed that these cell states were highly similar to the in vivo cell circuit in a multicohort lung cell atlas from patients with pulmonary fibrosis. Using micro-CT-staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state, and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the hPCLS model provided evidence that the basaloid cell state was derived from alveolar type 2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in hPCLS, and antifibrotic drug treatments showed highly cell type-specific effects. Our work provides an experimental framework for perturbational single-cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration, and pathology. We further demonstrate that hPCLS offer an avenue for scalable, high-resolution drug testing to accelerate antifibrotic drug development and translation.

Mass spectrometry-based autoimmune profiling reveals predictive autoantigens in idiopathic pulmonary fibrosis.

Autoimmunity plays a role in certain types of lung fibrosis, notably connective tissue disease-associated interstitial lung disease (CTD-ILD). In idiopathic pulmonary fibrosis (IPF), an incurable and fatal lung disease, diagnosis typically requires clinical exclusion of autoimmunity. However, autoantibodies of unknown significance have been detected in IPF patients. We conducted computational analysis of B cell transcriptomes in published transcriptomics datasets and developed a proteomic Differential Antigen Capture (DAC) assay that captures plasma antibodies followed by affinity purification of lung proteins coupled to mass spectrometry. We analyzed antibody capture in two independent cohorts of IPF and CTL-ILD patients over two disease progression time points. Our findings revealed significant upregulation of specific immunoglobulins with V-segment bias in IPF across multiple cohorts. We identified a predictive autoimmune signature linked to reduced transplant-free survival in IPF, persisting over time. Notably, autoantibodies against thrombospondin-1 were associated with decreased survival, suggesting their potential as predictive biomarkers.

Transcriptomic and Proteomic Changes Driving Pulmonary Fibrosis Resolution in Young and Old Mice.

Bleomycin-induced pulmonary fibrosis in mice mimics major hallmarks of idiopathic pulmonary fibrosis. Yet in this model, it spontaneously resolves over time. We studied molecular mechanisms of fibrosis resolution and lung repair, focusing on transcriptional and proteomic signatures and the effect of aging. Old mice showed incomplete and delayed lung function recovery 8 weeks after bleomycin instillation. This shift in structural and functional repair in old bleomycin-treated mice was reflected in a temporal shift in gene and protein expression. We reveal gene signatures and signaling pathways that underpin the lung repair process. Importantly, the downregulation of WNT, BMP, and TGFß antagonists Frzb, Sfrp1, Dkk2, Grem1, Fst, Fstl1, and Inhba correlated with lung function improvement. Those genes constitute a network with functions in stem cell pathways, wound, and pulmonary healing. We suggest that insufficient and delayed downregulation of those antagonists during fibrosis resolution in old mice explains the impaired regenerative outcome. Together, we identified signaling pathway molecules with relevance to lung regeneration that should be tested in-depth experimentally as potential therapeutic targets for pulmonary fibrosis.

An integrated cell atlas of the lung in health and disease.

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.

Multi-isotope fingerprints of recent environmental samples from the Baltic coast and their implications for bioarchaeological studies.

Stable isotopes in coastal regions are influenced by the so-called sea spray effect which masks the actual terrestrial isotope fingerprint with a marine isotope signal. The sea spray impact on plants was investigated by analyzing different stable isotope systems (δ13Ccellulose, δ18Ocellulose, δ18Osulfate, δ34Ssulfate, δ34Stotal S, δ34Sorganic S, 87Sr/86Sr) in recent environmental samples (plants, soil, water) collected close to the Baltic Sea. All these isotopic systems are influenced by the sea spray, either by the uptake of ions (HCO3-, SO42-, Sr2+) of marine origin, thus exhibiting a marine isotopic signature, or by biochemical reactions associated with, e.g., salinity stress. A shift towards seawater values is observed for δ18Osulfate, δ34S, and 87Sr/86Sr. Cellulose becomes enriched in 13C and 18O due to sea spray, further enhanced (δ13Ccellulose) or mitigated (δ18Ocellulose) by salinity stress. The effect differs both regionally and seasonally, probably as a result of, e.g., differences in wind strength or prevailing wind direction, as well as between plants collected only few meters apart, in either the open field or at more wind-protected sites, reflecting samples more or less influenced by sea spray. The stable isotope data of recent environmental samples are compared to previously analyzed archaeological bone samples of animals from the Viking Haithabu and Early Medieval Schleswig sites located close to the Baltic Sea. Potential regions of origin can be predicted based on the magnitude of the (recent) local sea spray effect. This enables the identification of probably non-local individuals. The insights into sea spray mechanisms, biochemical reactions in plants, as well as seasonal, regional, and small-scale differences in stable isotope data will help to interpret multi-isotope fingerprints at coastal sites. Our study demonstrates the usefulness of environmental samples for bioarchaeological studies. Moreover, the detected seasonal and small-scale differences require adjusted sampling strategies for, e.g., isotopic baselines in coastal areas.

Climate change-related growth improvements in a wide niche-breadth tree species across contrasting environments.

BACKGROUND AND AIMS: The vulnerability and responsiveness of forests to drought are immensely variable across biomes. Intraspecific tree responses to drought in species with wide niche breadths that grow across contrasting climatically environments might provide key information regarding forest resistance and changes in species distribution under climate change. Using a species with an exceptionally wide niche breath, we tested the hypothesis that tree populations thriving in dry environments are more resistant to drought than those growing in moist locations. METHODS: We determined temporal trends in tree radial growth of 12 tree populations of Nothofagus antarctica (Nothofagaceae) located across a sharp precipitation gradient (annual precipitation of 500-2000 mm) in Chile and Argentina. Using dendrochronological methods, we fitted generalized additive mixed-effect models to predict the annual basal area increment as a function of year and dryness (De Martonne aridity index). We also measured carbon and oxygen isotope signals (and estimated intrinsic water-use efficiency) to provide potential physiological causes for tree growth responses to drought. KEY RESULTS: We found unexpected improvements in growth during 1980-1998 in moist sites, while growth responses in dry sites were mixed. All populations, independent of site moisture, showed an increase in their intrinsic water-use efficiency in recent decades, a tendency that seemed to be explained by an increase in the photosynthetic rate instead of drought-induced stomatal closure, given that δ18O did not change with time. CONCLUSIONS: The absence of drought-induced negative effects on tree growth in a tree species with a wide niche breadth is promising because it might relate to the causal mechanisms tree species possess to face ongoing drought events. We suggest that the drought resistance of N. antarctica might be attributable to its low stature and relatively low growth rate.

Identification and quantification of the sea spray effect on isotopic systems in α-cellulose (δ13C, δ18O), total sulfur (δ34S), and 87Sr/86Sr of European beach grass (Ammophila arenaria, L.) in a greenhouse experiment.

The sea spray effect can severely influence the isotopic signature of terrestrial individuals in coastal regions. To further specify this effect, beach grass was grown in a greenhouse under controlled environmental conditions and sprayed with mineral salt solution containing different mineral salts but only traces of NaCl (group 1). Another group of plants was sprayed with salty water from the Schlei inlet and the Baltic Sea, respectively (group 2). Control plants were only sprayed with tap water. Isotope analyses were conducted on the unwashed and washed plants (δ13Ccellulose, δ18Ocellulose, δ34Stotal S, 87Sr/86Sr), soil (δ18Osulfate, δ34Ssulfate, 87Sr/86Sr), and spray as well as irrigation water (δ18Osulfate, δ34Ssulfate, 87Sr/86Sr). Moreover, elemental analyses were performed on the water samples. The sea spray effect was visible in all isotopic systems under study. The uptake of SO42-, HCO3-, and Sr2+ directly affected plants of group 1, while plants of group 2, sprayed with salty water, additionally showed salinity stress in the case of α-cellulose and total sulfur due to biochemical reactions of the plants. Very high concentrations in HCO3- or SO42- also affected the plants' isotopic signatures. The impact of the sea spray and additional stress reactions were quantified. Our study is the first experiment creating an artificial sea spray effect in a greenhouse. This experiment for the first time enables the identification and quantification of the sea spray effect in environmental samples. The marine signature taken up by the plants and recorded by the investigated isotopic systems is apparently high and should have an impact on the isotopic fingerprints of animal consumers at the coast, as evidenced for archaeological animals from the Viking Haithabu and the early medieval Schleswig sites located close to the Baltic Sea. This result demonstrates the potential of greenhouse experiments as an isotopic predictor of the past local sea spray effect.

The discovAIR project: a roadmap towards the Human Lung Cell Atlas.

The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell-cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions.

Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'.

The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for 'reverse phenotyping'. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.

Multidisciplinary dataset for geological and environmental studies in the lake of Cavazzo (Southern Alps).

The present dataset was collected to evaluate the environmental stressors on a lacustrine basin in the Eastern Alps of glacial origin that has been affected in recent years by natural and anthropogenic events such as the construction of a hydroelectric power plant and a series of strong earthquakes during 1976-1977. We collected sediment cores in different sites from the lake margins to the depocenter and performed a multiproxy analysis of sediment sample to highlight lake stratigraphy and major changes occurring at a decadal scale (Polonia et al., [1]). The integrated analyses of sedimentological, geochemical, isotopic, mineralogical and micropaleontological analyses aimed at reconstructing changes in sediment composition and define the triggering mechanisms of altered environmental conditions. The dataset demonstrates that evaluating ex post the effects of artificial modification in a natural environment during relatively long time spans (decades) can provide important insights for managing and protection strategies in similar environments worldwide.

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers.

The correspondence of cell state changes in diseased organs to peripheral protein signatures is currently unknown. Here, we generated and integrated single-cell transcriptomic and proteomic data from multiple large pulmonary fibrosis patient cohorts. Integration of 233,638 single-cell transcriptomes (n = 61) across three independent cohorts enabled us to derive shifts in cell type proportions and a robust core set of genes altered in lung fibrosis for 45 cell types. Mass spectrometry analysis of lung lavage fluid (n = 124) and plasma (n = 141) proteomes identified distinct protein signatures correlated with diagnosis, lung function, and injury status. A novel SSTR2+ pericyte state correlated with disease severity and was reflected in lavage fluid by increased levels of the complement regulatory factor CFHR1. We further discovered CRTAC1 as a biomarker of alveolar type-2 epithelial cell health status in lavage fluid and plasma. Using cross-modal analysis and machine learning, we identified the cellular source of biomarkers and demonstrated that information transfer between modalities correctly predicts disease status, suggesting feasibility of clinical cell state monitoring through longitudinal sampling of body fluid proteomes.

Functional Hypogonadism and Testosterone Deficiency in Aging Males With and Without HIV-infection.

INTRODUCTION: HIV infection has become a chronic, well-treatable disease and the focus of caretakers has shifted to diagnosis and treatment of comorbidities. Hypogonadism in elderly men with HIV might be of particular relevance, however, little is known about its epidemiology in contrast to non-infected peers and men with other chronic medical conditions, such as type 2 diabetes. This study aimed at comparing the prevalence of testosterone deficiency and functional hypogonadism in men ≥ 50 years in these three groups. PATIENTS AND METHODS: Multi-center, cross-sectional substudy of the German-wide 50/2010 study, including men aged 50 years or older with HIV-infection, type 2 diabetes, and controls. RESULTS: Altogether, 322 men were included (mean age: 62 years (SD±7.9)). The prevalence of testosterone deficiency in men living with HIV, type 2 diabetes, and controls was 34.5, 44.9, and 35.0%, respectively; the prevalence of functional hypogonadism was 7.7, 14.3 and 3.5%, respectively. Single-factor ANOVA demonstrated significant differences between the groups for total testosterone (p<0.001), SHBG (p<0.001), as well as for free testosterone concentrations (p=0.006). Comorbidities were, however, most important single factor in multi-factor analysis. DISCUSSION: Despite a comparable prevalence of testosterone deficiency, functional hypogonadism was more frequent in men living with HIV when compared to non-infected controls. This was the result of a higher burden of symptoms that might, however, also be secondary to other conditions. Number of comorbidities was a more important factor than belonging to one of the groups.

Injury triggers fascia fibroblast collective cell migration to drive scar formation through N-cadherin.

Scars are more severe when the subcutaneous fascia beneath the dermis is injured upon surgical or traumatic wounding. Here, we present a detailed analysis of fascia cell mobilisation by using deep tissue intravital live imaging of acute surgical wounds, fibroblast lineage-specific transgenic mice, and skin-fascia explants (scar-like tissue in a dish - SCAD). We observe that injury triggers a swarming-like collective cell migration of fascia fibroblasts that progressively contracts the skin and form scars. Swarming is exclusive to fascia fibroblasts, and requires the upregulation of N-cadherin. Both swarming and N-cadherin expression are absent from fibroblasts in the upper skin layers and the oral mucosa, tissues that repair wounds with minimal scar. Impeding N-cadherin binding inhibits swarming and skin contraction, and leads to reduced scarring in SCADs and in animals. Fibroblast swarming and N-cadherin thus provide therapeutic avenues to curtail fascia mobilisation and pathological fibrotic responses across a range of medical settings.

Inhibition of LTßR signalling activates WNT-induced regeneration in lung.

Lymphotoxin ß-receptor (LTßR) signalling promotes lymphoid neogenesis and the development of tertiary lymphoid structures1,2, which are associated with severe chronic inflammatory diseases that span several organ systems3-6. How LTßR signalling drives chronic tissue damage particularly in the lung, the mechanism(s) that regulate this process, and whether LTßR blockade might be of therapeutic value have remained unclear. Here we demonstrate increased expression of LTßR ligands in adaptive and innate immune cells, enhanced non-canonical NF-κB signalling, and enriched LTßR target gene expression in lung epithelial cells from patients with smoking-associated chronic obstructive pulmonary disease (COPD) and from mice chronically exposed to cigarette smoke. Therapeutic inhibition of LTßR signalling in young and aged mice disrupted smoking-related inducible bronchus-associated lymphoid tissue, induced regeneration of lung tissue, and reverted airway fibrosis and systemic muscle wasting. Mechanistically, blockade of LTßR signalling dampened epithelial non-canonical activation of NF-κB, reduced TGFß signalling in airways, and induced regeneration by preventing epithelial cell death and activating WNT/ß-catenin signalling in alveolar epithelial progenitor cells. These findings suggest that inhibition of LTßR signalling represents a viable therapeutic option that combines prevention of tertiary lymphoid structures1 and inhibition of apoptosis with tissue-regenerative strategies.

Mitochondrial Regulation of the 26S Proteasome.

The proteasome is the main proteolytic system for targeted protein degradation in the cell and is fine-tuned according to cellular needs. Here, we demonstrate that mitochondrial dysfunction and concomitant metabolic reprogramming of the tricarboxylic acid (TCA) cycle reduce the assembly and activity of the 26S proteasome. Both mitochondrial mutations in respiratory complex I and treatment with the anti-diabetic drug metformin impair 26S proteasome activity. Defective 26S assembly is reversible and can be overcome by supplementation of aspartate or pyruvate. This metabolic regulation of 26S activity involves specific regulation of proteasome assembly factors via the mTORC1 pathway. Of note, reducing 26S activity by metformin confers increased resistance toward the proteasome inhibitor bortezomib, which is reversible upon pyruvate supplementation. Our study uncovers unexpected consequences of defective mitochondrial metabolism for proteasomal protein degradation in the cell, which has important pathophysiological and therapeutic implications.

Sea spray correction in δ13Ccarbonate, δ18Ocarbonate, δ18Ophosphate, and δ34Scollagen values of coastal humans - A methodological approach.

The so-called sea spray effect influences animals and humans living in coastal regions. As a consequence, δ13Ccarbonate, δ18Ocarbonate, δ18Ophosphate, and δ34Scollagen isotope values of affected individuals are more positive than otherwise expected. However, the effect is hidden in the case of humans who actually might have consumed marine food what would (partly) explain their isotopic signature. In order to correct for the sea spray effect in humans the dietary proportions were calculated based on the δ13Ccollagen and δ15Ncollagen isotope values using stable isotope mixing models. Four different programs (SISUS, simmr, IsotopeR, MixSIAR) were applied which resulted in quite different calculated diets. Each individual human can be corrected for the sea spray effect using the calculated proportion of terrestrial food (e.g. domesticated mammals, plants) and the approximated sea spray effect for each isotopic system. The differences in the calculated food proportions detected for the different mixing model programs, however, lead to differences in the correction procedure. We suggest using the dietary proportions as obtained by probabilistic SISUS rather than those of the Bayesian programs (simmr, IsotopeR, MixSIAR). The correction against the sea spray effect using the dietary proportions calculated by SISUS was supported by Gaussian Mixture Model (GMM) clustering which also enables the identification of probably non-local individuals in the dataset.

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis.

The cell type specific sequences of transcriptional programs during lung regeneration have remained elusive. Using time-series single cell RNA-seq of the bleomycin lung injury model, we resolved transcriptional dynamics for 28 cell types. Trajectory modeling together with lineage tracing revealed that airway and alveolar stem cells converge on a unique Krt8 + transitional stem cell state during alveolar regeneration. These cells have squamous morphology, feature p53 and NFkB activation and display transcriptional features of cellular senescence. The Krt8+ state appears in several independent models of lung injury and persists in human lung fibrosis, creating a distinct cell-cell communication network with mesenchyme and macrophages during repair. We generated a model of gene regulatory programs leading to Krt8+ transitional cells and their terminal differentiation to alveolar type-1 cells. We propose that in lung fibrosis, perturbed molecular checkpoints on the way to terminal differentiation can cause aberrant persistence of regenerative intermediate stem cell states.