Biology subjects

Sauler, M.

Publications and source records attributed to Sauler, M..

15 recordsLinked to original sources

bioRxiv2026

SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics

Spatially resolved transcriptomic (SRT) data requires spatial domain identification to enable tissue microenvironment-specific downstream analyses. Here we present SPEAK (Spatial Prompting with Expert-Aligned Knowledge), a large language model (LLM)-based method to identify spatial domains from SRT data by taking advantage of the prior knowledge from both LLM and human experts. SPEAK constructs a spatial context prompt for each cell/spot based on cell types and marker genes of its neighboring cells, enabling zero-shot inference, expert-guided fine-tuning, and prototype updating through two-stage prompting. Applications to STARmap, Visium, MERFISH and Xenium datasets showed advantages of SPEAK over existing spatial domain identification methods in domain prediction accuracy, robustness to limited prior knowledge, biological interpretability, and capacity for efficient expert-guided fine-tuning with generalizability to other tissue sections.

bioinformatics↗

bioRxiv2026

AT2-intrinsic Z-AAT expression drives conserved inflammatory and proteotoxic stress responses and predisposes to emphysema

Individuals homozygous for the SERPINA1 "Z" mutation with alpha-1 antitrypsin deficiency (AATD) are highly susceptible to emphysema. This predisposition has classically been attributed to a relative deficiency of circulating alpha-1 antitrypsin (AAT) reaching the lungs and associated protease-antiprotease imbalance. Accumulating evidence suggests that the presence of misfolded Z-AAT protein either in the circulation, the lung interstitium, or within resident lung cells could contribute to emphysema pathogenesis. We have shown that type 2 alveolar epithelial cells (AT2s), progenitor cells of the lung alveolus, heterogeneously retain Z-AAT and exhibit a transcriptional disease signature in AATD patient samples. However, a lack of model systems that faithfully recapitulate AT2 biology and associated Z-AAT expression has limited our ability to study this phenomenon. Here, we apply syngeneic induced pluripotent stem cell-derived AT2s (iAT2s) and a novel mouse model featuring AT2-specific inducible human SERPINA1 expression to interrogate the cell-instrinsic consequences of Z-AAT expression, validating findings in an independent dataset of human COPD lung tissue comparing ZZ to MM SERPINA1 genotypes. We find further evidence of Z-AAT retention within AT2s and identify shared AT2 transcriptomic disease signatures conserved across model systems, characterized by innate immune and inflammatory signaling, NF-{kappa}B activation, and endoplasmic reticulum stress. Mice with AT2-specific Z-AAT expression additionally demonstrate increased susceptibility to elastase-induced emphysema, providing functional evidence for AT2-intrinsic contributions to AATD-associated lung disease. Within iAT2s, a subpopulation of Z-AAT expressing cells exhibits activation of the PERK-eIF2 signaling axis and markers of an alveolar basal intermediate (ABI) state, emerging cell-autonomously in the absence of mesenchymal co-culture.Together, these data provide evidence that Z-AAT expression in AT2s induces heterogenous cell-intrinsic stress responses including proteotoxic stress, inflammatory signaling, and aberrant cell fate adoption, and is sufficient to result in predisposition to injury, supporting a potential contribution of AT2-intrinsic Z-AAT toxicity to human AATD-associated emphysema pathogenesis.

cell biology↗

bioRxiv2025

Single cell transcriptomics in a treatment-segregated cohort exposes a STAT3-regulated therapeutic gap in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic pulmonary disease of unknown etiology. Since approved IPF drugs only slow disease progression, novel therapeutics are required that improve clinical outcomes. Here we report a single cell lung RNA-Seq and gene regulatory network analysis of the largest IPF cohort assembled to date. Segregating this cohort based on status of treatment with approved first-generation IPF antifibrotics (untreated, nintedanib- and pirfenidone-treated), we describe for the first time the transcriptional landscape of untreated IPF across 40 lung cell types, and the elements of this program that are impacted by these antifibrotics. On average, nearly 60% of the untreated IPF-dysregulated transcriptome is refractory to treatment with these drugs, a transcriptional deficit we refer to as the IPF therapeutic gap. Gene regulatory network analysis indicated a dominant functional footprint for the transcription factor STAT3 in both untreated IPF and the IPF therapeutic gap. Validating our analysis in a translational precision cut lung slice platform that recapitulates IPF explants, pharmacological inhibition of STAT3 reduced the IPF therapeutic gap in numerous lung cell types. Finally, we resolved a STAT3-anchored master regulatory network comprising numerous profibrotic transcription factors in IPF alveolar fibroblasts, a critical fibrotic lineage. Our study represents a comprehensive resource for translational lung fibrosis research and introduces a strategy for drug discovery that is adaptable to human disease more broadly.

cell biology↗

bioRxiv2025

A Tunable Pulmonary Organoid Model Demonstrates Compositionally Driven Epithelial Plasticity and Immune Polarization

Summary/AbstractAberrant epithelial regeneration and immune remodeling are hallmarks of chronic lung diseases such as idiopathic pulmonary fibrosis (IPF), COPD, and post-viral syndromes. Yet how cellular context shapes these trajectories remains unresolved. We present a tunable, primary rat-derived lung organoid model that systematically varies immune, epithelial, and mesenchymal inputs to reveal how composition alone dictates epithelial plasticity and macrophage polarization. Across organoid conditions that varied by relative starting lineage ratios, we observed the spontaneous emergence of disease-relevant transitional cell states, including Sox9+ stressed progenitors, RAS-like intermediates, and hillock-like cells, alongside distinct macrophage activation profiles. In mesenchyme-rich contexts, epithelial-immune-mesenchymal crosstalk appeared to reinforce inflammatory signaling and stabilize transitional persistence, while immune-dominant inputs favored ATI-like repair and squamous remodeling. Hillock-like cells displayed context-specific polarization and expressed immune-regulatory genes, suggesting a role as epithelial orchestrators that help calibrate inflammatory response during regeneration. Connectomic analysis via NICHES revealed that regenerative outcomes were associated with dynamic multicellular signaling networks that integrate stress sensing, immune coordination, and epithelial resilience. This platform provides a tractable system for modeling milieu-specific repair and regenerative mechanisms and could inform therapeutic strategies aimed at redirecting epithelial fate in chronic lung disease.

bioengineering↗

bioRxiv2025

The ferroptosis inhibitor NUPR1 coordinates the mitochondrial response to oxidative stress and cell metabolism during COPD pathogenesis in the lung

Chronic obstructive pulmonary disease (COPD) is characterized by chronic injury and oxidative stress leading to progressive lung tissue destruction. Emerging evidence suggests that regulated cell death pathways, particularly ferroptosis, contribute to COPD pathology. We previously identified the stress response protein and known ferroptosis inhibitor nuclear protein 1 (NUPR1) as markedly downregulated in lung tissue from COPD patients. Here, we demonstrate that NUPR1 inhibition exacerbates iron accumulation, enhances lipid peroxidation, impairs mitochondrial function, disrupts cellular metabolism, and increases oxidative stress in lung epithelial cells. Furthermore, Nupr1 knockout mice exhibit mitochondrial abnormalities, increased oxidative damage, and lung tissue changes consistent with COPD pathology. Collectively, our findings establish NUPR1 as a critical regulator of ferroptosis, stress responses, mitochondrial integrity, and metabolic balance in the lung, highlighting its potential contribution to COPD pathogenesis.

cell biology↗

bioRxiv2025

Integrative Single-Cell RNA and ATAC Sequencing Reveals the Impact of Chronic Cigarette Smoking on Lung Epithelial Responses to Influenza and Hyperoxia

Cigarette smoke (CS) is a significant risk factor for developing acute respiratory distress syndrome (ARDS), but the cellular and molecular mechanisms linking smoking to ARDS susceptibility remain unclear. Our goal was to improve our understanding of these mechanisms. To address this, we established a mouse model comparing long-term CS exposure to non-smoking controls, examining responses to influenza infection and hyperoxia-induced lung injury. The mice were divided into six groups (n=1 per group): control (CON), cigarette smoke (CS), hyperoxia (HYP), influenza infection (FLU), cigarette smoke plus hyperoxia (CS+HYP), and cigarette smoke plus influenza infection (CS+FLU). Single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) were performed on lung tissues. Quality control analysis using Seurat (v5.1.0) and Signac (v1.13.1) retained 78,402 cells from scRNA-seq and 84,144 cells from scATAC-seq, with 32,305 matched cells identified across both datasets. Differential gene expression analysis revealed significant smoking-associated alterations in cellular responses to influenza infection and hyperoxia exposure. Pathway enrichment indicated heightened immune responses, inflammatory signaling, and cellular survival pathways in smoking-exposed animals. Integration of scRNA-seq and scATAC-seq identified key transcription factors (TFs), including those involved in immune regulation, tissue repair, and chromatin remodeling mediating these responses. Overall, this study underscores the role of chronic cigarette smoke exposure in exacerbating pathways critical to ARDS pathogenesis, providing potential targets for therapeutic intervention.

bioinformatics↗

bioRxiv2024

A Nerve-Fibroblast Axis in Mammalian Lung Fibrosis

Fibrosis contributes to incurable pathologies in vital organs including the lung. Myofibroblasts are fibrogenic effector cells that accumulate via incompletely understood mechanisms. We discovered that 1-adrenoreceptor expressing myofibroblasts receive sympathetic nerve-derived noradrenergic inputs in fibrotic mouse and human lungs. We combined optical clearing, whole lung imaging, cell-specific gene deletion in sympathetic nerves and myofibroblasts, pharmacologic interventions, sympathetic nerve co-culture and precision-cut lung slices, with analysis of bronchoalveolar lavage fluid, lung tissues, single-cell RNA sequencing datasets, and isolated lung fibroblasts from patients with diverse forms of pulmonary fibrosis to characterize a fibrogenic unit comprised of aberrantly patterned sympathetic nerves and 1-adrenoreceptor subtype D expressing myofibroblasts. The discovery of this previously undefined nerve-fibroblast axis that is conserved across species demonstrates the pivotal contribution of nerves to tissue remodeling and heralds a novel paradigm in fibrosis research.

cell biology↗

bioRxiv2024

Cell type-specific expression of angiotensin receptors in the human lung with implications for health, aging, and chronic disease

The renin-angiotensin system is a well-characterized regulator of tissue homeostasis whose clinical relevance has expanded to include lung disorders such as chronic obstructive pulmonary disease (COPD)-associated emphysema, idiopathic pulmonary fibrosis, and COVID-19. Despite this interest, the cell-specific localization of angiotensin receptors in the human lung has remained poorly defined, in part due to limitations of available antibody reagents. Here, we define the expression patterns of the two predominant angiotensin receptors, AGTR1 and AGTR2, using complementary bulk and single-nucleus transcriptomic datasets from human lung tissue. We demonstrate that these receptors exhibit mutually exclusive, compartment-specific localization, with AGTR1 expressed in lung pericytes and AGTR2 expressed in alveolar epithelial type 2 cells. AGTR1 is detectable in isolated lung pericytes, and spatial colocalization with pericyte markers confirmed within the airspace microvasculature compartment by RNAscope. Airspace pericyte abundance was reduced in an experimental emphysema model but restored by pharmacologic attenuation of AGTR1 signaling commensurate with airspace repair. In COPD lungs, AGTR1 expression showed heterogeneous, disease-associated dysregulation across stromal populations, including upregulation in alveolar fibroblasts. Bulk transcriptomics also revealed aging-associated redistribution of AGTR1 expression into stromal compartments. Angiotensin II and cigarette smoke impaired pericyte migration toward endothelial cells, while combined exposure suppressed pericyte proliferation. Together, these findings identify AGTR1 as a new highly selective marker of lung pericytes and a regulator of pericyte behaviors within the airspace microvasculature. These findings provide a cell-resolved framework for angiotensin signaling with direct relevance to airspace resilience and therapeutic targeting.

bioinformatics↗

bioRxiv2024

Epidermal Growth Factor Receptor Regulates Beclin-1 in Hyperoxia

While delivery of supplemental oxygen is a life-saving therapy, exposure to high levels of oxygen, called hyperoxia, is associated with increased mortality in the intensive care unit (ICU). Hyperoxia leads to oxidant-mediated acute lung injury (ALI) and pulmonary cell death, called hyperoxic acute lung injury (HALI). Elucidation of molecular mechanisms in HALI could identify therapeutic targets in ALI. In the current study, we examined in vivo effects of HALI on Beclin-1 (BCN1), a molecule that regulates autophagy and cell death. Effects of HALI on BCN1 and autophagy markers were examined in wildtype mice. Analysis of BCN1 and autophagy was completed via Western blot, RT-qPCR, and immunohistochemistry. In wildtype mice, HALI led to increased BCN1 in the lung and in the alveolar epithelium. HALI resulted in significant alterations in markers of autophagy in the lung, including reduced microtubule-associated protein 1B-light chain (LC3B)-II/-I ratios, suggesting reduced autophagic flux. HALI caused increased LDH release in human alveolar type-II cells derived from induced pluripotent stem cells (AT2siPSC), as well as reduced LC3B-II/-I ratios. We previously showed that inhibition of the tyrosine kinase receptor epidermal growth factor receptor (EGFR) is protective in HALI. EGFRWa5/+ mice, which have genetically reduced EGFR activity and improved survival in HALI, showed increased total BCN1, reduced phosphorylated-(p-)/total BCN1 ratios, and decreased LC3B-II/-I ratios in the lung in HALI compared with wildtype. Administration of wortmannin, a phosphatidylinositol-3 kinase (PI3K) inhibitor which decreases BCN1-mediated autophagy, led to increased mortality in HALI in wildtype mice. These data support that regulation of BCN1 and autophagy by EGFR is a protective mechanism in HALI, a pathway which warrants further study for its therapeutic potential. KEY MESSAGESHALI is associated with increased mortality in the ICU and causes alveolar epithelial cell death, but the role of BCN1 in HALI is not well defined. This study shows that BCN1, a molecule involved in autophagy and cell death, is regulated by EGFR in HALI in vivo. These results are significant because regulation by BCN1 and autophagy by EGFR is a novel pathway in HALI with therapeutic potential that warrants further study.

cell biology↗

bioRxiv2022

Spatiotemporal coordination of stem cell behavior following alveolar injury

Tissue repair requires a highly coordinated cellular response to injury. In the lung, alveolar type 2 (AT2) cells act as stem cells and can replace both themselves and alveolar type 1 cells (AT1); however, the complex orchestration of AT2 stem cell activity following lung injury is poorly understood owing to the inability of tracking individual stem cells and their dynamic behavior over time. Here, we apply live time lapse imaging to ex vivo mouse precision cut lung slice (PCLS) culture and in vivo mouse lung to track individual GFP-labeled AT2 cells following induction of alveolar injury by bleomycin. We observe highly dynamic movement of AT2 cells, including migration within and between alveoli. To map the dynamic evolution of AT2 cell behavior, we introduce Live Cell Encoder (LCE-PHATE), a novel method for converting static snapshots from time lapse imaging into single points representative of entire, dynamic cellular trajectories. Applying LCE-PHATE, we observe the emergence of at least three distinct morphokinetic AT2 cell states associated with AT2 stem cell injury response. Finally, small molecule-based inhibition of Rho-associated protein kinase (ROCK) pathway significantly reduced motility of AT2 stem cells following injury and reduced expression of Krt8, a marker of intermediate progenitor cells. Together, our results uncover motility of alveolar stem cells as a new injury response mechanism in the lung and reveal properties of stem cell motility at high cellular resolution.

cell biology↗

bioRxiv2022

Lung spatial profiling reveals a T cell signature in COPD patients with fatal SARS-CoV-2 infection

RationalePeople with pre-existing lung diseases like chronic obstructive pulmonary disease (COPD) are more likely to get very sick from SARS-CoV-2 disease 2019 (COVID-19), but an interrogation of the immune response to COVID-19 infection, spatial throughout the lung structure is lacking in patients with COPD. ObjectivesTo profile the immune microenvironment of lung parenchyma, airways, and vessels of never- and ever-smokers with or without COPD, whom all died of COVID-19, using spatial transcriptomic and proteomic profiling. FindingsThe parenchyma, airways, and vessels of COPD patients, compared to control lungs had: 1) significant enrichment for lung resident CD45RO+ memory T cells; 2) downregulation of genes associated with T cell antigen-priming and memory T cell differentiation; 3) higher expression of proteins associated with SARS-CoV-2 entry and major receptor ubiquitously across the ROIs and in particular the lung parenchyma, despite similar SARS-CoV-2 structural gene expression levels. ConclusionsThe lung parenchyma, airways, and vessels of COPD patients have increased T-lymphocytes with a blunted memory T cell response and a more invasive SARS-CoV-2 infection pattern, and may underlie the higher death toll observed with COVID-19.

immunology↗

bioRxiv2022

In utero delivery of miRNA induces epigenetic alterations and corrects pulmonary pathology in congenital diaphragmatic hernia

Structural fetal diseases, such as congenital diaphragmatic hernia (CDH) can be diagnosed prenatally. Neonates with CDH are healthy in utero as gas exchange is managed by the placenta, but impaired lung function results in critical illness from the time a baby takes its first breath. During fetal development, lungs are capable of remarkable growth and the fetus does not yet require lung function for gas exchange. MicroRNA (miR) 200b and its downstream targets in the TGF{beta} pathway are critically involved lung branching morphogenesis. Here we characterize the expression of miR200b and the TGF{beta} pathway at different gestational times using a rat model of CDH. Fetal rats with CDH are deficient in miR200b at gestational day 18. We demonstrate that NPs loaded with miR200b given systemically to fetal rats result in changes in the TGF{beta} pathway; these epigenetic changes improve lung size, lung morphology, and lung vascularization. This is the first demonstration of in utero epigenetic therapy to improve lung growth and development in a pre-clinical model. With refinement, this technique could be applied to fetal cases of CDH or other forms of impaired lung development in a minimally invasive fashion. eTOC SynopsisIn utero treatment with NPs loaded with miR200b improves lung development in a rat model of CDH. miR200b treatment epigenetic changes in the TGF{beta}, leads to larger lungs with more airspace and favorable pulmonary vascular remodeling. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/482144v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@3531caorg.highwire.dtl.DTLVardef@57ff5aorg.highwire.dtl.DTLVardef@13d6ee9org.highwire.dtl.DTLVardef@3cb3d8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

A lung targeted miR-29 Mimic as a Therapy for Pulmonary Fibrosis

microRNAs are non-coding RNAs that negatively regulate gene networks. Previously, we reported a systemically delivered miR-29 mimic MRG-201 that reduced fibrosis in animal models, but at doses prohibiting clinical translation. Here, we generated MRG-229, a next-gen miR-29 mimic with improved chemical stability, conjugated with the internalization moiety BiPPB (PDGFbetaR-specific bicyclic peptide). In TGF-b-treated human lung fibroblasts and precision cut lung slices, MRG-229 decreased COL1A1 and ACTA2 gene expression and reduced collagen production. In bleomycin-treated mice, intravenous or subcutaneous delivery of MRG-229 downregulated profibrotic gene programs at doses more than ten-fold lower than the original compound. In rats and non-human primates, and at clinically relevant doses, MRG-229 was well tolerated, with no adverse findings observed. In human peripheral blood decreased mir-29 concentrations were associated with increased mortality in two cohorts potentially identified as a target population for treatment. Collectively, our results provide support for the development of MRG-229 as a potential therapy in humans with IPF. One Sentence SummaryOne Sentence Summary: A stabilized, next-generation miR-29 mimic has been developed that demonstrates efficacy at commercially viable doses with a robust safety margin in non-human primates.

molecular biology↗

bioRxiv2020

Integrated Single Cell Atlas of Endothelial Cells of the Human Lung

BackgroundDespite its importance in health and disease, the cellular diversity of the lung endothelium has not been systematically characterized in humans. Here we provide a reference atlas of human lung endothelial cells (ECs), to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium, both in health and disease. MethodsWe reprocessed control single cell RNA sequencing (scRNAseq) data from five datasets of whole lungs that were used for the analysis of pan-endothelial markers, we later included a sixth dataset of sorted control EC for the vascular subpopulation analysis. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by immunohistochemistry and in situ hybridization. Signaling network between different lung cell types was studied using connectomic analysis. For cross species analysis we applied the same methods to scRNAseq data obtained from mouse lungs. ResultsThe six lung scRNAseq datasets were reanalyzed and annotated to identify over 15,000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including pan-endothelial, pan-vascular and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial and venous ECs we found previously indistinguishable subpopulations; among venous EC we identified two previously indistinguishable populations, pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary EC we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1 and TBX2 and general capillary EC. We confirmed that all six endothelial cell types, including the systemic-venous EC and aerocytes are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-Receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. Our manuscript is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). ConclusionOur integrated analysis provides the comprehensive and well-crafted reference atlas of lung endothelial cells in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.

cell biology↗

bioRxiv2020

Decreased miR-24-3p potentiates DNA damage responses and increases susceptibility to COPD

Activation of the DNA damage response (DDR) due to chronic exposure to cigarette smoke (CS) is implicated in the pathogenesis of Chronic Obstructive Pulmonary Disease (COPD). However, not all smokers develop COPD and the pathologic consequences of CS exposure are heterogenous. Cellular mechanisms that regulate the DDR and contribute to disease progression in susceptible individuals are poorly understood. Because microRNAs are well known regulators of the DDR, we evaluated microRNA expression arrays performed on lung samples from 172 subjects with and without COPD. We identified miR-24-3p as the microRNA best correlated with radiographic emphysema ({rho}=-0.353, P=1.3e-04) and validated this finding in multiple cohorts. In a CS-exposure mouse model, miR-24-3p inhibition increased emphysema severity. In human airway epithelial cells, miR-24-3p suppressed apoptosis through the BH3-only protein BIM and suppressed homology-directed DNA repair and the DNA repair protein BRCA1. Finally, we found BIM and BRCA1 were increased in COPD lung tissue and inversely correlated with miR-24-3p expression. We concluded that decreased miR-24-3p expression increases COPD susceptibility and potentiates the DDR through BIM and BRCA1.

cell biology↗