Biology subjects

Ghimire, S.

Publications and source records attributed to Ghimire, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction

Extravasation, the exit of circulating cancer cells from blood vessels, is a critical yet poorly understood step in metastatic dissemination. Here we show that pancreatic ductal adenocarcinoma (PDAC) cells can breach endothelial barriers through two mechanistically distinct modes of extravasation. MIA PaCa-2 cells breach endothelial junctions via filopodia-like protrusions, enabling access to and spread across the basal extracellular matrix (ECM). By contrast, AsPC-1 cells remain rounded atop the endothelium and cross the barrier by triggering rapid retraction of neighbouring endothelial cells. These distinct extravasation modes were also observed in zebrafish larvae. In the mouse lung, AsPC-1 cells arrest, survive, induce endothelial detachment from the basal lamina, and extravasate through this retraction mechanism before metastatic outgrowth. Mechanistically, AsPC-1-secreted factors are sufficient to destabilise endothelial monolayers, and AsPC-1 cells also induce endothelial apoptosis; however, blocking apoptosis does not prevent barrier disruption. By contrast, treatment with saracatinib, a Src-family kinase inhibitor, protects endothelial barriers, limits early vascular disruption in the lung, and delays metastatic outgrowth. Together, these findings reveal that PDAC cells can extravasate via mechanistically distinct routes, suggesting that effective anti-metastatic strategies may need to target multiple modes of endothelial barrier breach rather than a single pathway.

cell biology↗

bioRxiv2026

Timed STING Inhibition Mitigates Gastrointestinal GvHD While Preserving Graft-versus-Leukemia Activity After Allo-HSCT

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is curative for hematological malignancies but limited by graft-versus-host disease (GvHD), in which donor T cells damage host tissues. Current prophylaxis broadly suppresses donor immunity, often compromising the beneficial graft-versus-leukemia (GvL) response, highlighting the need for strategies that uncouple GvHD from GvL. The cGAS-STING pathway can be strongly activated during conditioning-induced tissue damage and represents a potential therapeutic target. However, its context-dependent roles in inflammation and homeostasis have constrained its clinical translation. Here, we show that "timed" administration of the covalent STING inhibitor H151 before conditioning reduced GvHD-associated mortality without impairing GvL in murine allo-BMT models. Donor T cell activation and effector function were preserved, indicating that the protective effect operates at the level of GvHD target tissues rather than through systemic immunosuppression. Timed STING inhibition protected the intestinal epithelium by limiting apoptosis, preserving intestinal stem cell function, and sustaining metabolic fitness during conditioning-induced injury, independently of type I interferon (IFN-I) signaling. In allo-HSCT patients, low intestinal STING expression is associated with reduced transplant-related mortality. Together, these findings identify timed STING inhibition as a tissue-protective prophylactic strategy that could be incorporated into existing conditioning regimens to enhance efficacy while minimizing toxicity.

immunology↗

bioRxiv2026

The autophagy core protein Atg18 regulates exosome release and rescues pathogenic dysfunction associated to Parkinson Sac domain mutation in Synaptojanin

Macroautophagy, a catabolic process conserved across evolution, participates in fundamental aspects of synaptic function and neuronal survival. Exosomes are extracellular vesicles that mediate cell communication, including emerging roles mediating brain intercellular signaling, synaptic function and neuronal survival. Indeed, both autophagy and exosome release interact with each other, but this interplay is poorly characterized at the neuronal synapse, especially in the context of neurodegenerative diseases. Here, we report that at the presynaptic compartment the autophagy protein Atg18a/WIPI2 regulates exosome release at the level of the multivesicular body. The Parkinson disease mutation R258Q in the protein Synaptojanin inhibits synaptic autophagy, and causes locomotion deficits, seizures and neurodegeneration. We found that this mutation also reduces exosome release and that the dopaminergic overexpression of Atg18a in Synaptojanin mutant animals restores exosome release, locomotion and dopaminergic survival without restoring synaptic autophagy. Our data reports a novel function of Atg18a in the regulation of exosome release and spotlights the role of exosome release in the pathogenesis of Parkinson disease.

neuroscience↗

bioRxiv2026

Compartmentalized cytokine networks and systemic immune remodeling in bovine mammary H5N1 infection.

Highly pathogenic avian influenza A H5N1 has recently expanded its mammalian host range; in 2024, genotype B3.13 emerged in U.S. dairy cattle with pronounced mammary tropism. In the past, Influenza A virus immunology has been characterized primarily in respiratory infection models, whereas this study delineates immune responses after intramammary infection. An intramammary H5N1 challenge in Jersey cows in the early dry-off period enabled integration of dose- and compartment-resolved (alveoli versus teat cistern) cytokine and chemokine profiles with peripheral leukocyte dynamics and H5/N1-specific antibody responses. Infection-induced quarter-restricted, monophasic inflammatory networks peaking at 3-7 days post-infection, coordinated peripheral myeloid expansion and IFN-{gamma}-competent lymphocyte activation, and rising antibody titers across quarters.

microbiology↗

bioRxiv2026

Filopodia-mediated trans-endocytosis

Cell-cell communication in tissues is influenced by contact geometry and molecular signalling. Here, we demonstrate that epithelial intercellular filopodia can penetrate neighbouring cells to form micrometre-long, double-membrane "impact sites" and, in some instances, initiate trans-endocytosis. Using super-resolution live imaging and three-dimensional electron microscopy in cell models, xenografts, and patient-derived tissues, we observe widespread intercellular filopodia and extensive interdigitation at the cell-cell interface. Filopodia impact sites in the recipient cell recruit PACSIN2 into dynamic "PACSIN2 fingers" and are specifically enriched for caveolin-1 and dynamin-2, while clathrin and CLIC pathway markers are not enriched. Most contacts are transient and resolved by retraction, but some undergo scission, with recipient cells internalising filopodial tips across both homotypic and heterotypic interactions, including cancer-endothelium contacts. Correlative light and FIB-SEM analysis reveals that internalised tips are often double-membraned, closely associated with endoplasmic reticulum tubules, and can traffic to lysosomes. These findings define a protrusion-driven, curvature-dependent uptake pathway at cell-cell interfaces and identify filopodia as exchange organelles in epithelial collectives.

cell biology↗

bioRxiv2025

Robust Colonization of Nasal Microbiota Across the Respiratory Tract and the Gut Modulates Innate Immune Response in a Germ-Free Pig Model

The use of antibiotics in swine production has contributed to improved health and growth rates but also led to significant challenges, including the emergence of antibiotic-resistant bacteria and disruptions in the microbiome. This study employs a germ-free pig model to investigate the transplantation of the nasal microbiome into the respiratory tract, exploring its potential to colonize multiple body sites and its impact on host immunity. Using germ-free piglets inoculated with nasal microbiota from healthy donors, we examined the dynamics of microbial community formation across the respiratory and gastrointestinal tracts and assessed the effects of antibiotic intervention. Our findings reveal that specific taxa, predominantly from the phyla Proteobacteria and Firmicutes, cross colonized both respiratory as well as gastrointestinal tract. This cross- colonization highlights the adaptability of nasal microbiota and suggests a significant role in modulating host immunity through the gut-lung axis. The administration of the antibiotic tulathromycin on day 11 post-inoculation altered both nasal and gut microbiota compositions, reducing microbial diversity and impacting immune gene expression and cytokine profiles. These results underscore the complex interactions within the gut-lung axis and emphasize the implications of antibiotic use on microbial health and host immunity. Understanding these interactions provides crucial insights into alternative strategies for managing health in swine production without relying on antibiotics. Our study advocates for a reevaluation of antibiotic practices and supports the development of microbiome-centered interventions in swine health management.

microbiology↗

bioRxiv2025

12 weeks of voluntary wheel running restores glucagon sensitivity in middle-aged mice

Aerobic exercise training is a potent intervention for the treatment and prevention of age-related metabolic disease, which is characterized by both insulin and glucagon resistance. While insulin resistance is a key driver of metabolic disease in aging, glucagon signaling is equally critical in maintaining both glucose and lipid homeostasis, particularly during exercise. Previous studies have established the glucagon sensitizing effects of exercise training in younger animals. Most studies in rodents employ rigorous and carefully dosed forced exercise protocols. This forced exercise is a stressful paradigm. We implemented a voluntary wheel running (VWR) intervention to assess the effects of aging and exercise training on glucagon sensitivity. We initiated 12-weeks of VWR in young adult (6-month-old) and middle-aged (12-month-old) C57BL/6NCrl male mice. Glucagon sensitivity, as assessed by glucagon stimulated hyperglycemia, was decreased in middle-aged compared to young adult sedentary mice (P=0.046). While VWR did not affect glucose clearance, circulating insulin, glucagon, or insulin sensitivity, regardless of age, VWR improved glucagon responsivity only in middle-aged mice (P=0.031). VWR increased hepatic glycogen content and increased glucagon-stimulated glycogen depletion, regardless of age (P<0.01). Results from these studies suggest that exercise training can enhance liver glucagon action in aging mice without otherwise altering glucose homeostasis. New and NoteworthyFew studies have examined the impact of aging on glucagon sensitivity. Here we show that glucagon sensitivity declines from young adulthood to middle age. Yet, 12 weeks of voluntary wheel running, an exercise intervention without the stress of forced treadmill running or swimming, restores glucagon sensitivity in middle-aged male mice without otherwise altering glucose homeostasis.

physiology↗

bioRxiv2025

Glucagon receptor signaling is indispensable for the healthspan effects of caloric restriction in aging male mice

Obesity and type 2 diabetes mellitus accelerate aging, shortening the duration of healthspan. Conversely, chronic calorie restriction (CR) extends healthspan. Research aimed at understanding the mechanism by which CR slows aging has focused heavily on insulin and downstream signaling cascades. Glucagon, a hormone that counter-regulates insulin, is commonly affected by these same interventions. To investigate the role of glucagon in aging we used dietary manipulation, global and liver-specific glucagon receptor knockout, and pharmacological glucagon receptor activation. We found that globally eliminating glucagon receptor signaling (Gcgr KO) decreases median lifespan by 35% in lean mice. These lifespan shortening effects are more robust in diet-induced obese mice (54%). Extending these findings to metabolic health, we found that glucagon receptor signaling is indispensable to the metabolic response to chronic CR in young and aged mice. While CR decreased liver fat, serum triglyceride, and serum cholesterol in WT mice, these metabolic benefits were absent in Gcgr KO mice. In line with these observations, we found that critical nutrient sensing pathways known to improve aging are dysregulated in mice lacking glucagon receptor signaling at the liver (Gcgrhep-/-). Liver-specific deletion of the glucagon receptor decreases hepatic AMP Kinase activation in aging mice, regardless of diet. Further, CR decreases hepatic mTOR activity in WT mice, but not in Gcgrhep-/- mice. Together, these findings propose that glucagon signaling plays a critical role in both normal aging and the lifespan and healthspan extension driven by caloric restriction.

physiology↗

bioRxiv2025

LSD1 serine 166 is a phosphorylation switch for chromatinlandscaping, gene activation, and tissue remodeling

LSD1 is a histone 3 (H3) demethylase that can either repress or activate gene expression. We discover here that the so far enigmatic balance between these two activities in non-hormonal cancer cells is regulated by phosphorylation of serine 166 (S166) on LSD1. SET-mediated Protein Phosphatase 2A (PP2A) inhibition in KRAS mutant cells promotes S166 phosphorylation. Endogenous LSD1 S166 alanine mutant (S166A) cells display H3 lysine 9 demethylation and acetylation, euchromatin, and gene activation. Mechanistically this is explained by the impaired interaction of S166A mutant LSD1 with repressor proteins SNAI2 and MYBP1. Functionally LSD1 S166A mutant cells display augmented beta1 integrin activity and stress fiber formation, and the mutant xenograft tumors have altered tumor microenvironment associated with increased macrophage recruitment. Collectively, PP2A-regulated S166 of LSD1 is a phosphorylation switch for epigenetic gene activation in non-hormonal cancer cells. Conceptually we demonstrate how dephosphorylation of one amino acid on a non-histone protein shapes chromatin landscape in cancer cells, and modify tumor stroma, and immune cell content. Highlights* Mechanism for gene activation by LSD1 in non-hormonal cancers * Single phosphorylation switch in a non-histone protein controls epigenetic landscape * Epigenetic protein phosphorylation in cancer cells shapes tumour immune microenvironment * Novel function for Protein Phosphatase 2A (PP2A) in epigenome regulation via LSD1 Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/653937v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@19548b3org.highwire.dtl.DTLVardef@1d7fd4dorg.highwire.dtl.DTLVardef@13707b3org.highwire.dtl.DTLVardef@1da7b71_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Dietary Protein Sources Shape Gut Microbiome: Insights from Meta-analysis and Machine Learning

BackgroundDietary proteins shape gut microbial ecology, yet the taxonomic and functional consequences of plant- versus animal-based proteins remain poorly defined. Although digestibility and fermentation profiles differ by protein type, a systematic evaluation of how these differences influence microbial diversity, community structure, and metabolic capacity is lacking. This meta-analysis integrates taxonomic, machine learning, and functional inference approaches to identify microbial and metabolic signatures associated with dietary protein source in murine models. MethodsFollowing PRISMA guidelines, we analyzed 16S rRNA sequencing data from 10 murine studies (n = 187) comparing plant- and animal-protein diets. Alpha diversity was assessed using Shannon, Inverse Simpson, and Chao1 indices, and beta diversity with Aitchison distances. Differentially abundant taxa were identified using LEfSe and class-weighted Random Forest models. Functional potential was inferred with PICRUSt2, and taxon-pathway relationships were explored using correlation and network analyses. ResultsPlant-protein diets increased gut microbial diversity across all alpha diversity metrics and were associated with higher representation of saccharolytic and nitrogen-recycling genera such as Bacteroides, Muribaculaceae, and Allobaculum. Animal-protein diets favored proteolytic taxa, including Clostridium sensu stricto 1 and Colidextribacter. Microbial community structure differed significantly between diets (ANOSIM R = 0.663, p < 0.001). Random Forest models achieved >88% accuracy (AUC = 0.995) in predicting dietary groups, and LEfSe identified consistent discriminating taxa. Functional profiling showed that plant-based diets enriched pathways linked to short-chain fatty acid and aromatic amino acid metabolism, whereas animal-based diets favored sulfur- and branched-chain amino acid-associated pathways. Network analysis identified Muribaculaceae as a plant-associated hub and Lactobacillus as an animal-associated hub. ConclusionDietary protein source significantly influences gut microbiota composition and functional potential in mice. Plant- and animal-based proteins generate distinct metabolic signatures with implications for nitrogen cycling, sulfur metabolism, and microbial ecology. Future controlled dietary studies that harmonize protein source with other macronutrient variables are needed to isolate protein-specific effects. Statement of SignificanceThis study presents the first standardized meta-analysis of murine protein-intervention microbiome datasets, integrating taxonomic, machine learning, and predicted functional profiling to identify robust microbial and metabolic signatures that differentiate plant- from animal-based protein diets. By harmonizing evidence across diverse studies, it clarifies foundational ecological responses to protein source and provides mechanistic hypotheses that can inform future controlled nutrition and microbiome research

microbiology↗

bioRxiv2025

Unraveling Enteroendocrine Cell lineage dynamics and associated gene regulatory networks during intestinal development

Enteroendocrine cells (EECs) are rare intestinal epithelial cells producing multiple hormones that regulate essential aspects of digestion and energy. EEC subtypes, their hormone repertoire and differentiation mechanisms from intestinal stem cells have been characterized in the adult intestine. However, although EECs need to be functional from birth, as their absence causes severe intestinal malabsorption in newborns, the mechanisms underlying EEC subtype specification during development are largely unknown. We used mouse embryos, human pluripotent stem cell derived intestinal organoid models and single-cell transcriptomics to characterize EEC lineages and dynamics during development. Our findings demonstrate that in both mice and humans, the majority of EECs are specified during development through similar differentiation trajectories as observed in the adult intestine. This suggests that EEC subtypes specification occurs independently of fully organized crypt-villus structures and stimulation by diet or microbiota. However, the emergence of certain EEC subtypes depends on tissue maturation. Finally, our integrative approach infers lineage-specific regulators dynamically, identifying new candidates controlling EEC differentiation in the developing human gut. HIGHLIGHTSO_LIMost enteroendocrine cells (EECs) are specified during development. C_LIO_LICrypt-villus organization, diet or microbiota are not essential for EEC formation. C_LIO_LIIn pluripotent stem cell derived human intestinal organoids (HIOs), EECs differentiate along 3 main trajectories, one driven by maturation processes. C_LIO_LINovel Gene Regulatory Networks are identified governing human EEC differentiation in HIOs. C_LI

developmental biology↗

bioRxiv2025

A microbial metabolite protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration

Changes in the intestinal microbiome and microbiota-derived metabolites predict clinical outcomes after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Here, we report that desaminotyrosine (DAT), a product of bacterial flavonoid metabolism, correlates with improved overall survival and reduced relapse rates in allo-HSCT patients. In preclinical mouse models, treatment with synthetic DAT prevents graft-versus-host disease by protecting the intestinal barrier and promoting intestinal regeneration and contributes to graft-vs.-leukemia responses. DATs beneficial effects on intestinal regeneration remain effective despite broad-spectrum antibiotics-induced dysbiosis, also when administered by fecal microbiota transfer with flavonoid-degrading F. plautii. Mechanistically, DAT promotes mTORC1-dependent activation and proliferation of intestinal stem cells, with concomitant engagement of the innate immune receptor STING required to mitigate metabolic stress and maintain an undifferentiated stem cell state independently of type-I interferon responses. Additionally, DAT can skew T cells towards an effector phenotype to modulate graft-versus-leukemia responses. Our data uncover DATs dual, tissue- and immune-modulating properties and underscore its potential in precision microbiome-based therapies to improve tissue regeneration and minimize immune-mediated side effects.

immunology↗

bioRxiv2024

RiboTag-based RNA-Seq uncovers oligodendroglial lineage-specific inflammation in autoimmune encephalomyelitis

Oligodendroglial lineage cells (OLCs) are critical for neuronal support functions, including myelination and remyelination. Emerging evidence reveals their active roles in neuroinflammation, particularly in conditions like Multiple Sclerosis (MS). This study explores the inflammatory translatome of OLCs during the early onset of experimental autoimmune encephalomyelitis (EAE), an established MS model. Using RiboTag-based RNA sequencing in genetically modified Olig2-Cre RiboTag mice, we identified 1,556 upregulated and 683 downregulated genes in EAE OLCs. Enrichment analysis indicated heightened immune-related pathways, such as cytokine signaling, interferon responses, and antigen presentation, while downregulated genes were linked to neuronal development and myelination. Notably, OLCs expressed cytokines/chemokines, and their receptor, highlighting their active involvement in neuroinflammatory signaling. Functional studies demonstrated that interferon-gamma (IFN-{gamma}) signaling in OLCs exacerbates EAE pathology by enhancing antigen presentation and chemokine production, whereas interferon-beta (IFN-{beta}) signaling showed minimal impact. These findings provide novel insights into the inflammatory role of OLCs in EAE and suggest therapeutic potential in targeting OLC-mediated neuroinflammation for MS and related disorders.

neuroscience↗

bioRxiv2024

Restoring the Multiple Sclerosis Associated Imbalance of Gut Indole Metabolites Promotes Remyelination and Suppresses Neuroinflammation

In multiple sclerosis (MS) the circulating metabolome is dysregulated, with indole lactate (ILA) being one of the most significantly reduced metabolites. We demonstrate that oral supplementation of ILA impacts key MS disease processes in two preclinical models. ILA reduces neuroinflammation by dampening immune cell activation as well as infiltration; and promotes remyelination and in vitro oligodendrocyte differentiation through the aryl hydrocarbon receptor (AhR). Supplementation of ILA, a reductive indole metabolite, restores the gut microbiomes oxidative/reductive metabolic balance by lowering circulating indole acetate (IAA), an oxidative indole metabolite, that blocks remyelination and oligodendrocyte maturation. The ILA-induced reduction in circulating IAA is linked to changes in IAA-producing gut microbiota taxa and pathways that are also dysregulated in MS. Notably, a lower ILA:IAA ratio correlates with worse MS outcomes. Overall, these findings identify ILA as a potential anti-inflammatory remyelinating agent and provide insights into the role of gut dysbiosis-related metabolic alterations in MS progression. One Sentence SummaryIndole lactate, a postbiotic metabolite reduced in MS, corrects gut microbiome metabolic imbalances associated with remyelination and neuroinflammation.

neuroscience↗

bioRxiv2024

Tissue-adapted Tregs harness inflammatory signals to promote intestinal repair from therapy-related injury

Intestinal stem cells (ISC) promote tissue repair after genotoxic or immune-mediated injury. However, ISCs are particularly sensitive to various stressors and primary targets of overwhelming immune responses such as interferon-{gamma} (IFN{gamma})-mediated killing. In mouse models of gut damage and biopsies from patients having undergone allo-hematopoietic stem cell transplantation, we observed IFNy expression by intestinal Treg cells. Treg cells leverage combined IFN{gamma} and interleukin 10 (IL-10) stimulation of ISCs to nurture the growth of intestinal organoids through the activation of the mTORC1 and Myc pathways. Similarly, Treg cells or the combined addition of recombinant IFN{gamma} and IL-10 promote the regeneration of organoids after irradiation. Exposure of organoids to Wnt- or EGF-free culture conditions revealed distinct growth factor-like properties of IFN{gamma} and IL-10. While IFN{gamma} induced epithelial proliferation and differentiation, combined addition of IFN{gamma} and IL-10 led to balanced proliferation, ensuring ISC maintenance. Our results uncover a context-dependent role of inflammatory signaling in ISC, through which Treg cells promote epithelial repair.

immunology↗

bioRxiv2024

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers

Leukocyte extravasation is a key component of the innate immune response, while circulating tumor cell extravasation is a critical step in metastasis formation. Despite their importance, the mechanisms underlying leukocyte and tumor cell extravasation remain incompletely understood. Here, we developed an imaging pipeline that integrates fast, label-free live-cell imaging with deep learning-based image analysis to quantitatively track and compare the initial steps of extravasation--cell landing and arrest on an endothelial monolayer--under physiological flow conditions. We find that pancreatic ductal adenocarcinoma (PDAC) cells exhibit variable adhesion strength and flow sensitivity. Remarkably, some PDAC cells demonstrate comparable endothelial engagement as leukocytes, preferentially arresting at endothelial junctions, potentially due to increased stiffness at these sites, which leads to exposure to the underlying basal extracellular matrix. PDAC cells also tend to cluster in regions with high, heterogeneous expression of the endothelial CD44 receptor. Simulations suggest that clustering results from the combination of CD44-mediated attachment and localized flow disturbances that facilitate subsequent cell attachment. Targeting CD44 using siRNA or function-blocking antibodies, or degrading its ligand hyaluronic acid (HA), almost completely abolishes PDAC cell attachment. Overall, we demonstrate that cancer and immune cells share both common and unique features in endothelial adhesion under flow, and identify CD44 and HA as key mediators of PDAC cell arrest.

cell biology↗

bioRxiv2024

Emergent metabolic interactions in resistance to Clostridioides difficile invasion

Commensal gut bacteria are key contributors to the resilience against pathogen invasion. This is exemplified by the success of fecal microbiota transplantation in treating recurrent Clostridioides difficile infection. Yet, characteristics of communities that can confer colonization resistance and the underlying mechanisms remain largely unknown. Here we use a synthetic community of 14 commensal gut bacteria to uncover inter-species interactions and metabolic pathways underpinning the emergent resilience against C. difficile invasion. We challenged this synthetic community as well as fecal-matter-derived communities with antibiotic treatment and C. difficile in a continuous flow bioreactor. Using generalized Lotka-Volterra and genome-scale metabolic modelling, we identified interactions between Escherichia coli and Bacteroides/Phocaeicola sp. as key to the pathogens suppression. Metabolomics analysis further revealed that fructooligosaccharide metabolism, vitamin B3 biosynthesis, and competition for Stickland metabolism precursors contribute to suppression. Analysis of metagenomics data from patient cohorts and clinical trials attested the in vivo relevance of the identified metabolic pathways and the ratio between Bacteroides and Escherichia in successful colonization resistance. The latter was found to be a much stronger discriminator than commonly used alpha diversity metrics. Our study uncovers emergent microbial interactions in pathogen resistance with implications for rational design of bacteriotherapies.

systems biology↗

bioRxiv2024

IL-13 decreases susceptibility to airway epithelial SARS-CoV-2 infection but increases disease severity in vivo

Treatments available to prevent progression of virus-induced lung diseases, including coronavirus disease 2019 (COVID-19) are of limited benefit once respiratory failure occurs. The efficacy of approved and emerging cytokine signaling-modulating antibodies is variable and is affected by disease course and patient-specific inflammation patterns. Therefore, understanding the role of inflammation on the viral infectious cycle is critical for effective use of cytokine-modulating agents. We investigated the role of the type 2 cytokine IL-13 on SARS-CoV-2 binding/entry, replication, and host response in primary HAE cells in vitro and in a model of mouse-adapted SARS-CoV-2 infection in vivo. IL-13 protected airway epithelial cells from SARS-CoV-2 infection in vitro by decreasing the abundance of ACE2- expressing ciliated cells rather than by neutralization in the airway surface liquid or by interferon-mediated antiviral effects. In contrast, IL-13 worsened disease severity in mice; the effects were mediated by eicosanoid signaling and were abolished in mice deficient in the phospholipase A2 enzyme PLA2G2D. We conclude that IL-13-induced inflammation differentially affects multiple steps of COVID-19 pathogenesis. IL-13-induced inflammation may be protective against initial SARS-CoV-2 airway epithelial infection; however, it enhances disease progression in vivo. Blockade of IL-13 and/or eicosanoid signaling may be protective against progression to severe respiratory virus-induced lung disease. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPrior to this study, various pieces of evidence indicated the significant role of cytokines in the pathogenesis and progression of COVID-19. Severe COVID-19 cases were marked by cytokine storm syndrome, leading to immune activation and hyperinflammation. Treatments aimed at modulating cytokine signaling, such as IL-6 receptor antagonists, had shown moderate effects in managing severe COVID-19 cases. Studies also revealed an excessive production of type 2 cytokines, particularly IL-13 and IL-4, in the plasma and lungs of COVID-19 patients, which was associated with adverse outcomes. Treatment with anti-IL-13 monoclonal antibodies improved survival following SARS-CoV-2 infection, suggesting that IL-13 plays a role in disease severity. Type 2 cytokines were observed to potentially suppress type 1 responses, essential for viral clearance, and imbalances between these cytokine types were linked to negative COVID-19 outcomes. These findings highlighted the complex interactions between cytokines and the immune response during viral infections, underscoring the importance of understanding IL-13s role in COVID-19 and related lung diseases for developing effective therapeutic interventions. Added value of this studyIn this study, we explored the impact of IL-13-induced inflammation on various stages of the SARS-CoV-2 infection cycle using both murine (in vivo) and primary human airway epithelial (in vitro) culture models. Our findings indicated that IL-13 provided protection to airway epithelial cells against SARS-CoV-2 infection in vitro, partly by reducing the number of ACE2- expressing ciliated cells. Conversely, IL-13 exacerbated the severity of SARS2-N501YMA30-induced disease in mice, primarily through Pla2g2d-mediated eicosanoid biosynthesis. Implications of the available evidenceCurrent evidence indicates that PLA2G2D plays a crucial role in the IL-13-driven exacerbation of COVID-19 in mice, suggesting that targeting the IL-13-PLA2G2D axis could help protect against SARS-CoV-2 infection. These insights are important for clinical research, especially for studies focusing on drugs that modify IL-13 signaling or modulate eicosanoids in the treatment of asthma and respiratory virus-induced lung diseases.

cell biology↗