Biology subjects

Lehmann, M.

Publications and source records attributed to Lehmann, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Mitochondrial PEX14 supports peroxisome biogenesis

Peroxisomes are essential for cellular homeostasis and human health due to their central metabolic and physiological functions. The peroxisomal membrane protein PEX14 is indispensable for matrix protein import into peroxisomes. Recent studies support a hybrid model in which pre-peroxisomal vesicles originating from both, mitochondria and the endoplasmic reticulum, fuse to generate peroxisomes. PEX14 has repeatedly been observed at mitochondria in biogenesis disease models or upon protein overexpression, but such localization has generally been interpreted as aberrant mislocalization. Whether endogenous PEX14 naturally localizes to mitochondria and contributes to peroxisome biogenesis has remained unknown. Here, using high-content and super-resolution microscopy, we demonstrate that endogenous PEX14 localizes to the mitochondrial outer membrane. We show that ectopically expressed PEX14 accumulates at mitochondria, and PEX14 variants unable to access mitochondria and restricted to peroxisomes fail to rescue the PEX14 knockout phenotype. Vice versa, a mitochondria-targeted PEX14 variant supports peroxisome biogenesis. Our results identify the physiological mitochondrial pool of PEX14 in human cells and establish it as an essential intermediate in de novo peroxisome biogenesis.

cell biology↗

bioRxiv2026

Sleep-dependent modulation of thalamic brain temperature estimates in humans

Mammalian thermal physiology is geared towards dissipating heat during sleep. Brain temperature typically decreases during non-rapid-eye-movement (NREM) sleep in all mammalian species measured to date, yet non-invasive confirmation in healthy humans is lacking: the only available human study used invasive recordings in epileptic patients without a wake control condition. Magnetic resonance spectroscopy (MRS) enables brain temperature mapping non-invasively, using the temperature-sensitive chemical shift of water relative to N-Acetyl-Aspartate as an internal reference. First, we validated that with metabolite cycling (MC), a MRS approach that enables the simultaneous acquisition of metabolite and water information without conventional water suppression, can be used to determine estimates of brain temperature in an ex vivo sheep head. Next, we determined that by using a temporal resolution of ~4 minutes, we obtained high-quality spectra without losing excessive temporal resolution. We then re-analyzed an existing set of MRS data (acquired with the MC sequence) of the thalamus in young adults (n=9) who slept in the evening for up to 2 hours in the scanner, to assess sleep-evoked changes in estimates of brain temperature. Of the nine participants, five participants took part in the subsequent wake-only experiment, allowing to control for the potential impact of circadian time and body posture on estimates of brain temperature. Sleep-wake states were quantified with standard polysomnography, confirming that the participants managed to sleep in the scanner. On average, they spent 39.4+/-15.7 min in N2 sleep, 24.8+/-18.1 min in N3 sleep, 10.0+/-4.9 min in N1 sleep, and 37.0+/-19.6 min awake. Estimates of brain temperature were correlated across the sleep and wake-only experiment within the same participant (R^2=0.29, P<0.0001). When participants entered NREM sleep, estimates of brain temperature decreased by 0.2 degrees Celcius. Moreover, the deeper NREM sleep, the more pronounced the decrease in estimates of brain temperature (P=0.014). These data suggest that an evening nap consisting of NREM sleep decreases thalamic temperature. Considering the profound impact temperature can have on brain functioning, these brain temperature changes could be a pathway through which sleep impacts the brain.

neuroscience↗

bioRxiv2026

Molecular Structure, DNA Binding, and Photophysical Properties of SYTOX Orange and SYTOX Green

Fluorescent dyes are critical to visualizing nucleic acids in many applications. SYTOX Orange and SYTOX Green are cyanine dyes, used in dead cell staining and increasingly in single-molecule assays to probe DNA supercoiling and processing. However, their structures and effects on DNA mechanics are not or only partially known. We determine the structure of SYTOX Orange to be (E)-2-((2-(4 ((diethyl(methyl)ammonio)methyl)phenyl)-6-methoxy-1-methylquinolin-4(1H)-ylidene)methyl)-4-methyloxazolo[4,5-b]pyridin-4-ium, identical to SYBR Gold except for an aza-benzoxazol core that is fundamentally different from other dyes in the SYTOX and SYBR families. We report SYTOX Green to be (Z)-2-(bis(3-(trimethylammonio)propyl)amino)-4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)-1-phenylquinolin-1-ium, similar to PicoGreen. Using magnetic tweezers, we characterize the effect of SYTOX Orange and SYTOX Green on DNA mechanics. They lengthen and unwind DNA consistent with intercalation and the DNA unwinding angles per dye are 21.1(1){degrees} and 20.5(1){degrees} for SYTOX Orange and Green, respectively. Both dyes leave the DNA bending persistence length and plectoneme size almost unaltered (<10% change up to 1 {micro}M), which is advantageous in assays probing DNA supercoiling. Their photophysical properties reveal close agreement between single-molecule manipulation and optical absorbance and fluorescence spectroscopy. Our comprehensive set of complementary measurements relates mechanical and optical properties to the molecular structures and provides recommendations for their use in applications.

biophysics↗

bioRxiv2026

fastder: fast, annotation-agnostic detection of expressed regions from RNA-seq coverage and splicing data

Background.Features from RNA-seq experiments are usually counted using a curated annotation (GENCODE, Ensembl, etc) as reference. This approach constrains RNA-seq counts to what the annotation considers a valid gene, transcript or exon, and misses transcription outside them. Moreover, reference annotations are known to be incomplete, and inadequate in some experiments altering splicing, and some diseases. To circumvent these constraints, annotation-free detection of expressed regions aims to detect the actual regions being expressed in a sample or samples. For large scale usage, the recount3 resource holds uniformly processed coverage tracks and splice junctions for over 8,000 human and over 10,000 mouse RNA-seq studies, with several hundred thousand samples in total. This opens an opportunity for scalable tools to call expressed regions that are annotation free. Results.We present fastder, a C++ tool to detect expressed regions directly from recount3 coverage and splice junctions files, with no read alignment steps. It also can run on local raw reads, after aligning them with STAR, making it suitable to analyze species beyond human and mouse. fastder calls expressed regions by bump hunting expression coverage files, and stitches them into spliced multi-exon structures using the splice junction data. On simulated RNA-seq with unannotated expression features, fastder calls exons at a base-level accuracy on par with derfinder and golden standard for the task. Exon precision improves with sequencing depth. We compare fastders performance against a coverage-only baseline, derfinder and groHMM. fastder extends the functionality of those by assigning strands to the expressed regions, and by also producing multi-exon regions. It runs about 15 to 20 times faster than derfinder and groHMM, within bounded memory. We showcase its use with two recount3-derived examples, including the recovery of cryptic exons from a TDP-43 knockdown experiment; and the GTEx data clustering based on the topology of the expressed regions alone, without taking the expression levels into account. Conclusions.fastder makes annotation-agnostic detection of expressed-regions fast enough to run at recount3 scale. As limitation, it detects expressed regions and the junctions between them, not different isoforms from the same gene.

genomics↗

bioRxiv2026

Human-restricted Salmonella exploit preassembled flagella for intracellular motility and vacuolar escape

Human-restricted typhoidal Salmonella enterica serovars cause systemic infections known as enteric fever, whereas most non-typhoidal serovars cause self-limiting gastroenteritis. Both groups rely on flagella-mediated motility during intestinal colonization and invasion, yet their intracellular flagellar programs appear to diverge after host cell entry. Non-typhoidal Salmonella are thought to rapidly silence flagellar expression intracellularly, whereas human-restricted S. Paratyphi A maintains flagellar gene expression and uses motility to evade xenophagy. However, the fate and function of flagella assembled before invasion have remained unclear. Here, we used fluorescence microscopy to follow preassembled flagella during epithelial cell invasion across typhoidal and non-typhoidal Salmonella. We show that intracellular bacteria remain flagellated during invasion across epithelial cell lines, serovars, and invasion conditions, indicating that Salmonella do not universally shed or lose preassembled flagella upon host cell entry. We demonstrate that internalized flagella are disassembled within Salmonella-containing vacuoles, whereas cytosolic flagella are targeted by autophagy. We further show that S. Paratyphi A uses flagella assembled before invasion to power intracellular motility and promote escape from the Salmonella-containing vacuole, and that intracellular motility is a phenotype shared by typhoidal Salmonella. Together, these findings reveal that human-restricted Salmonella can exploit preassembled flagella inside host cells as part of an intracellular pathogenic strategy. We propose that intracellular motility represents an adaptation to the human epithelial environment that may promote vacuolar escape and host restriction. ImportanceFlagella are best known for driving bacterial motility before host cell invasion, but their fate and function after intracellular entry remain poorly understood. This study shows that Salmonella do not universally lose their flagella during epithelial cells invasion. Instead, both typhoidal and non-typhoidal Salmonella serovars enter host cells with intact preassembled flagella, but only human-restricted typhoidal serovars use them for intracellular motility. This distinction separates flagellar presence from flagellar function and identifies intracellular motility as a serovar-specific behavior associated with human-restricted systemic disease. The findings suggest that typhoidal Salmonella have adapted to the human epithelial intracellular environment by maintaining a motile state that may promote escape from the Salmonella-containing vacuole and favor cytosolic lifestyle. More broadly, this work reframes flagella not only as extracellular colonization factors but also as intracellular determinants of pathogen behavior, host adaptation, and disease outcome.

microbiology↗

bioRxiv2026

Lifespan Analysis of the Lung Epithelium Reveals Inflammatory Reprogramming and Regenerative Decline

Aging is a major risk factor for chronic lung diseases, associated with chronic low-grade inflammation (inflammaging) and impaired epithelial regeneration. How epithelial-intrinsic aging intersects with inflammaging across the lifespan remains poorly understood. Here, we systematically analyzed lung epithelial cells from neonatal, young adult, and aged mice to define age-dependent changes in regenerative capacity. RNA sequencing revealed lifespan-associated shifts characterized by early repression of developmental and WNT/{beta}-catenin programs and progressive activation of DNA damage, inflammation, and senescence signatures. Functionally, neonatal epithelial cells exhibited markedly enhanced organoid-forming capacity compared with young and aged cells. Aged organoids maintained a pro-inflammatory secretory profile indicative of cell-intrinsic inflammaging, and transfer of the aged secretome or TNF- to young cultures significantly impaired regeneration. Comparison of freshly isolated cells and long-term organoid cultures revealed sustained repression of regenerative pathways with age, consistent with stable epigenetic imprinting. Pharmacological inhibition of DNA methylation and WNT signalling partially restored regenerative capacity in adult organoids. Together, these findings identify epigenetic reprogramming and epithelial-intrinsic inflammaging as key determinants of age-dependent regenerative decline.

cell biology↗

bioRxiv2026

Alveolar Epithelial Cell Loss of the Mitochondrial Regulator TFAM Drives Progressive Lung Fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by failed alveolar epithelial repair and progressive fibrotic remodeling. Although aberrant reprogramming of alveolar type 2 (AT2) cells and accumulation of transitional AT2 states are increasing recognized as central features of IPF, the epithelial-intrinsic mechanisms that initiate these pathogenic states remain incompletely understood. Here, we identify mitochondrial transcription factor A (TFAM), a regulator of mitochondrial DNA maintenance, as a critical regulator of AT2 cell homeostasis. TFAM expression was reduced in AT2 cells from human IPF lungs. Inducible AT2 cell-specific Tfam deletion in mice caused spontaneous fibrotic remodeling and increased susceptibility to bleomycin-induced lung injury. TFAM-deficient AT2 cells acquired KRT8+ transitional and p21+ senescence-associated features before the onset of fibrotic transformation, accompanied by impaired oxidative phosphorylation, redox imbalance, mitochondrial superoxide accumulation, repression of mtDNA-encoded respiratory genes, and disrupted mitochondrial ultrastructure. TFAM-deficient AT2 cells developed a profibrotic secretory program that promoted extracellular matrix deposition and fibroblast activation. We further identified insulin-like growth factor-binding protein 2 (IGFBP2) as a secreted mediator induced in TFAM-deficient AT2 cells. IGFBP2 was elevated in AT2 cells in human IPF lung tissue and bronchoalveolar lavage fluid (BALF) from patients with IPF. IGFBP2 was detected in supernatants from fibrotic human precision-cut lung slices (hPCLS). IGFBP2 neutralization attenuated profibrotic remodeling in fibrotic hPCLS. Collectively, our findings identify TFAM-dependent mitochondrial homeostasis as an epithelial checkpoint linking AT2 cell-state stability to impaired epithelial-mesenchymal crosstalk driving pulmonary fibrosis.

pathology↗

bioRxiv2026

Local IFNγ signaling contributes to the regenerative decline of aged alveolar progenitor cells

The lungs are highly susceptible to chronic disease in advanced age, likely due to the uniquely compromised repair function of alveolar type II (AT2) cells, facultative progenitor cells that maintain the gas exchange surface. Using aging mouse models, single-cell sequencing, and ex vivo organoid assays, we found that homeostatic aged AT2 cells exhibited an Interferon {gamma} (IFN{gamma}) response associated with IFN{gamma}+ CD8+ T cells in tertiary lymphoid structures (TLS). Aged AT2 cells exhibit impaired regeneration in organoid assays and lost markers of an IFN{gamma} response outside the lung microenvironment, demonstrating that elevated local IFN{gamma} influences the state of AT2 cells. Neutralization of IFN{gamma} signaling and immunoproteasome knockout mice with attenuated IFN{gamma} levels partially rescued aged AT2 cell regeneration. Our findings demonstrate that local IFN{gamma} signaling in aging lungs actively represses alveolar regeneration, establishing chronic inflammatory signaling as a cause of age-related decline in the lung. Halting chronic inflammatory processes restored alveolar regeneration and may provide a means to improve lung health in old age.

cell biology↗

bioRxiv2026

Cellular protein delivery through membrane potential driven water pores

Providing immediate access for functional proteins inside living cells would unlock unprecedented control over cellular processes; however, commonly used endocytic delivery suffers from endosomal trapping and degradation. One of the most powerful non-endosomal delivery methods uses cell surface anchored cell penetrating peptide (CPP)-additives that allow proteins to enter cells directly. Nevertheless, the underlying molecular mechanism involved in direct entry via crossing the cell membrane (protein translocation through the cell) and the major driving forces remain controversially discussed. Here, we provide a stepwise molecular picture on how CPP-additives enable uptake of protein cargoes through direct membrane translocation. CPP-additives accumulate on the cell surface in nucleation zones, locally hyperpolarizing the membrane, and induce transient water pores that allow selective CPP-protein entry without compromising membrane integrity. These fundamental mechanistic insights provide a firm basis for rationally optimizing delivery strategies using highly cationic CPPs, ultimately resulting in innovative and smart protein delivery strategies to advance therapeutic protein applications. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/707441v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@14c1386org.highwire.dtl.DTLVardef@195f765org.highwire.dtl.DTLVardef@a52258org.highwire.dtl.DTLVardef@171dd7c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Structural studies suggest CCDC127 as a novel membrane contact site protein in the mitochondrial intermembrane space

Mitochondria feature a sophisticated membrane architecture, with a planar mitochondrial outer membrane (MOM) and a folded inner membrane (MIM). Due to the remarkable adaptability of mitochondria, a proteinaceous network in the intermembrane space (IMS) was proposed to confer both stability and flexibility. However, components of such scaffolds, tentatively termed the mitoskeleton, have remained largely elusive. The mitochondrial contact site and organizing system (MICOS), a central organizer of mitochondrial membrane architecture, was suggested to participate in mitoskeleton formation. Here, we structurally characterize the coiled-coil domain-containing 127 (CCDC127) protein, a putative interactor of MICOS. We show that CCDC127s amino-terminal transmembrane region is anchored in the MOM and the bulk soluble part exposed to the IMS. A crystal structure of CCDC127s central coiled-coil displays a parallel dimer which further oligomerizes into tetramers. We demonstrate that the carboxy-terminal helical bundle (CHB) domain dimerizes to create a peripheral membrane-binding site. Supported by electron microscopy data, we propose a structural model of CCDC127 as intramitochondrial membrane contact site protein mediating the structural organization of the IMS as part of the mitoskeleton.

molecular biology↗

bioRxiv2025

Lipid-induced Caveolin1-Lipid droplet trafficking is associated with lipid droplet growth

Caveolae are 50-100 nm sized plasma membrane invaginations involved in cellular lipid uptake and lipid accumulation. Several caveolin1 and cavin1 mutations are associated to human lipodystrophy. Interestingly, previous research identified caveolae proteins at lipid droplets although their specific cellular function at lipid droplets and in lipid trafficking is not understood. Here, we show that extracellular dietary lipids like oleic acid and cholesterol shift caveolae at the plasma membrane to highly spherical invaginations. Within 3 hours of lipid treatment caveolin1 accumulates specifically to lipid droplets. Correlative fluorescence FIB-SEM and split-APEX proteomics revealed no caveolar vesicles at the lipid droplet but caveolin1 alone. Mechanistically, caveolin1-lipid droplet trafficking is regulated by EHD2 at the plasma membrane level, followed by caveolin1 localization to EEA1- and Rab5-positive endosomes within 1 hour of oleic acid treatment, and subsequently lipid droplet accumulation. Caveolin1-lipid droplet trafficking does not depend on lysosomal activity. Surprisingly, the deletion of the central caveolin1 {beta}-barrel (Cav1-F160X), a mutation found in lipodystrophy patients, abolished caveolin1-lipid droplet trafficking and lipid droplet growth. Taken together, our results show that dietary lipids induce caveolae uptake, caveolin1 accumulation to lipid droplets and a caveolin1-dependent lipid droplet growth.

cell biology↗

bioRxiv2025

Targeting p16INK4a reverses alveolar epithelial cell dysfunction and induces lung regeneration in emphysema

Pulmonary emphysema involves impaired regenerative capacity of alveolar type 2 epithelial cells (AT2), the main progenitor cells in alveoli. However, the mechanisms underlying dysfunctional epithelial repair remain unclear. In a mouse model of elastase-induced emphysema, we observed an accumulation of activated AT2s in the lung, associated with an overexpression of p16INK4a (p16), a cell cycle inhibitor known to influence stem cell fate. Deletion of p16 promoted the transition of AT2 into alveolar type 1 (AT1) cells, resulting in tissue regeneration in both mice and alveolar organoids. Pharmacological targeting of the p16 pathway using senolytic agents recapitulate this regenerative effect, further supporting the role of p16 as a key brake on epithelial plasticity. These findings demonstrate that alveolar epithelial cell dysfunction can be reversed by p16 deletion or by eliminating p16+ cells, thereby reactivating the AT2-to-AT1 transition and promoting endogenous alveolar regeneration. This work identifies the p16 pathway as a promising therapeutic target for restoring damaged alveoli in emphysema.

cell biology↗

bioRxiv2025

Single cell decomposition of multicellular aging programs associated with impaired lung regeneration

Aging impairs the regenerative capacity of mammalian organs and is a major risk factor for organ fibrosis. Mechanisms underlying persistent fibrosis after lung injury in old individuals remain unclear. We used longitudinal single-cell RNA-seq after lung injury and dissected aging effects computationally and experimentally at baseline and during repair. In old mice, sustained fibroblast activation in the resolution phase of fibrosis was associated with prolonged epithelial senescence and persistent epithelial-mesenchymal crosstalk. Single-cell interpretable tensor decomposition analysis revealed that aging most strongly affected T/B-lymphocytes and macrophages. Notably, we identified a Granzyme K-high CD8+ T cell state that was unique to aged mice, co-localized with epithelial progenitors, and its co-culture or Gzmk treatments in lung organoids impaired progenitor function by inducing stem cell senescence. In summary, our study highlights the effects of immune aging on epithelial progenitor function and provides a time-resolved high resolution map of lung regeneration in the context of aging.

cell biology↗

bioRxiv2025

Role of Chloroplast Lipid-Remodelling Protein 23 During Cold Acclimation in Arabidopsis thaliana

Cold acclimation is a crucial physiological process that enables plants to adapt to low temperatures. A key aspect of this adaptation is lipid remodeling, which preserves membrane fluidity and integrity under cold stress. Proteins of the chloroplast envelope membranes are increasingly recognized for their role in acclimation to changing environmental conditions. While lipid synthesis occurs at the inner envelope membrane, little is known about specific proteins involved in lipid remodeling during cold acclimation. In this study, we investigate the role of Chloroplast Lipid Remodeling Protein 23 (CLRP23) as a component of the inner chloroplast envelope membrane. Subcellular fractionation combined with protease protection assays provided evidence for its orientation toward the intermembrane space. To explore its function, we analyzed the physiological performance and lipid composition in CLRP23-deficient mutant plants. Under cold stress, we observed significant impairments in photosynthesis and exaggerations in galactolipid response, suggesting CLRP23 is involved in lipid remodeling. Lipid overlay assays, supported by in silico docking analyses, demonstrate that CLRP23 can directly interact with chloroplast lipids, including galactolipids. Complementary transcriptomic and proteomic analyses reveal broader effects on cold-responsive pathways, supporting the view that CLRP23 contributes to the integration of membrane and metabolic responses during acclimation. These findings expand our understanding of protein-mediated processes during cold acclimation.

plant biology↗

bioRxiv2025

Expression levels of the Band-7 protein FLOTILLIN modulate salt tolerance, growth and development in the moss Physcomitrium patens

The Band-7 proteins, known as FLOTILLINs (FLOT), are present at the plasma membranes of most land plants. They function in clathrin-independent endocytosis and contribute to nodule formation following symbiotic infections. This study reveals that the single FLOT variant in Physcomitrium patens is located at the thylakoid membranes in chloroplasts, serving an unanticipated function. Phenotypic analysis of knockout and overexpression lines demonstrates that PpFLOT overexpression significantly impairs the high salinity tolerance of P. patens. Additionally, liquid protonema cultures of PpFLOT-OEX lines exhibited a distinct color change due to necrotic events and developed brachycyte-like cells. These changes correlate with the strength of PpFLOT expression and do not occur when these lines are cultivated on solid medium. Our study found that PpFLOT-OEX lines display increased chlorophyll and H2O2 production. We also discovered that PpFLOT is regulated by ABA and light, and its high expression can potentially affect retrograde signaling. Metabolomics and proteomics analyses revealed changes in the pigment and lipid composition as well as differentially accumulated proteins in PpFLOT mutant lines. We also observed changes in the expression of ion-transport related genes, accumulation of lipids crucial during pathogen defense, and differentially accumulated proteins taking part in multiple metabolomic pathways. Consequently, our study suggests a novel role for chloroplastic PpFLOT in plant terrestrialization, as it is putatively involved in Ca2+ and reactive oxygen species (ROS) signaling in response to abiotic and biotic stress, along with the light-dependent regulation of chlorophyll biosynthesis.

plant biology↗

bioRxiv2025

A silicon rhodamine-fused glibenclamide to label and detect malaria-infected red blood cells

The malaria parasite Plasmodium falciparum affects the lives of millions of people worldwide every year. The detection of replicating parasites within human red blood cells is of paramount importance, requiring appropriate diagnostic tools. Herein, we design and apply a silicon rhodamine-fused glibenclamide (SiR-glib). We first test this far-red fluorescent, fluorogenic and endoplasmic reticulum-targeting sulfonylurea in mammalian cells and pancreatic tissues, before characterizing its labeling performance in red blood cells infected with the asexual developmental stages of Plasmodium falciparum. We further combine SiR-glib with a portable smartphone-based microscope to easily and rapidly identify parasitized red blood cells, providing proof of principle for diagnostic use in rural endemic areas without major healthcare facilities.

biochemistry↗

bioRxiv2024

Expandable, Functional Hepatocytes Derived from Primary Cells Enable Liver Therapeutics

Liver disease affects millions annually in the United States, with orthotopic transplantation as the only curative option for many patients. However, the scarcity of donor organs highlights a need for alternative cell-based therapies. Hepatocyte-based approaches are promising due to the cells inherent synthetic, metabolic, and detoxifying functions, but they face critical barriers, including the lack of a scalable source of functional hepatocytes and poor engraftment. In this study, we developed a scalable process for expanding primary human hepatocytes (PHHs) while preserving their identity and function. By leveraging heterocellular aggregation with stromal cells, we generated cryopreserved "seed" constructs that maintained viability and function post-thaw. Seeds demonstrated enhanced metabolic and detoxification functions and robust engraftment across multiple anatomic sites outside of the liver. Our approach addresses key limitations of hepatocyte-based therapies, offering a stable, scalable, and clinically viable platform for liver cell therapy applications.

bioengineering↗

bioRxiv2024

SenSet, a novel human lung senescence cell gene signature, identifies cell-specific senescence mechanisms

Cellular senescence is a major hallmark of aging. Senescence is defined as an irreversible growth arrest observed when cells are exposed to a variety of stressors including DNA damage, oxidative stress, or nutrient deprivation. While senescence is a well-established driver of aging and age-related diseases, it is a highly heterogeneous process with significant variations across organisms, tissues, and cell types. The relatively low abundance of senescence in healthy aged tissues represents a major challenge to studying senescence in a given organ, including the human lung. To overcome this limitation, we developed a Positive-Unlabeled (PU) learning framework to generate a comprehensive senescence marker gene list in human lungs (termed SenSet) using the largest publicly available single-cell lung dataset, the Human Lung Cell Atlas (HLCA). We validated SenSet in a highly complex ex vivo human 3D lung tissue culture model subjected to the senescence inducers bleomycin, doxorubicin, or irradiation, and established its sensitivity and accuracy in characterizing senescence. Using SenSet, we identified and validated cell-type specific senescence signatures in distinct lung cell populations upon aging and environmental exposures. Our study presents the first comprehensive analysis of senescent cells in the healthy aging lung and uncovers cell-specific gene signatures of senescence, presenting fundamental implications for our understanding of major lung diseases, including cancer, fibrosis, chronic obstructive pulmonary disease, or asthma.

genomics↗