Biology subjects

Sharma, S.

Publications and source records attributed to Sharma, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Differential roles for IL-4Rα and IL-13Rα1in immune cell infiltration and epithelial remodeling in experimental eosinophilic gastritis

RationaleEosinophilic gastritis (EoG) is a chronic inflammatory disease characterized by infiltration of eosinophils and mast cells, epithelial remodeling, and fibrosis. Although EoG is increasingly recognized as a distinct type 2 inflammatory disease, the cellular and molecular events that drive disease pathogenesis remain poorly understood. This is due in part to the absence of robust and physiologically relevant experimental models that recapitulate human disease. MethodsExperimental EoG was induced in wild type and Il13ra1-/-mice by repeated intragastric oxazolone challenges in skin-sensitized mice. IL-4R1 was neutralized using antibodies. Gastric histopathology was determined by H&E, anti-Ki67, chloroacetate esterase and anti-MBP staining. Gastric RNA was subjected to RNA sequencing. ResultsExperimental EoG resulted in robust gastric eosinophilia, mastocytosis, epithelial remodeling, and subepithelial fibrosis. Transcriptomic profiling of gastric tissue revealed broad upregulation of type 2 cytokine and epithelial-remodeling genes, including Il4ra, Il4i1, Ccl5, Muc4, Mmp10, Mcpt1/2, Areg, Pparg and Tff2. The transcriptome profile of experimental EoG was markedly distinct from that of experimental EoE despite both models being initiated by oxazolone, suggesting that identical inflammatory triggers elicit tissue-specific and context-dependent transcriptional programs. Blockade of IL-4R signaling abrogated both eosinophil and mast cell infiltration and attenuated epithelial remodeling, whereas genetic deletion of Il13ra1 selectively suppressed epithelial remodeling without affecting inflammatory cell recruitment. ConclusionThese findings establish experimental EoG as a robust model for dissecting the cellular and molecular mechanisms driving gastric type 2 inflammation. They further define receptor-specific roles for IL-4R and IL-13R1 in coordinating immune infiltration and epithelial remodeling in EoG.

immunology↗

bioRxiv2026

Efflux pump regulation and metabolic rewiring define the ceiling of efflux-mediated drug resistance in Mycobacteria

Multidrug-resistant efflux pumps play a critical role in antimicrobial resistance, yet the physiological limits of their overexpression remain poorly understood. While gene amplifications and regulatory mutations commonly drive this overexpression, these pumps remain transcriptionally inactive under normal cellular conditions due to their high energetic cost, making it challenging to assess their full impact on resistance evolution and the maximum attainable minimum inhibitory concentration (MIC). To delineate the extent and spectrum of efflux-based resistance, we subjected Mycobacterium smegmatis mc{superscript 2}155(Msm) wild-type and efflux pump-deleted strains ({Delta}lfrA and {Delta}efpA) to adaptive laboratory evolution in the presence of a broad-spectrum efflux substrate ethidium bromide (EtBr). Despite prolonged selection, resistance plateaued at 8-16x MIC, revealing an intrinsic ceiling to efflux-based adaptation. Evolved populations integrated multiple layers of adaptation: enhanced efflux kinetics, reduced intracellular EtBr accumulation, and mutations spanning global regulators, ribosomal genes, and membrane components. Notably, deletion of specific pumps ({Delta}lfrA) triggered compensatory upregulation of alternative efflux systems, highlighting functional redundancy. Beyond efflux activation, evolved strains exhibited metabolic reprogramming, including downregulation of the tricarboxylic acid cycle and upregulation of lipid biosynthesis and {beta}-oxidation, which altered NAD/NADH homeostasis and membrane potential. Extending this adaptive evolution approach to Mycobacterium tuberculosis H37Ra (Mtb) demonstrated that these adaptive constraints and metabolic alterations are conserved across mycobacterial species. Together, these results uncover fundamental limits to efflux evolution and reveal how bacteria integrate regulatory and metabolic plasticity to maximize drug resistance. Targeting these interconnected networks may offer a powerful strategy to contain the rise of multidrug resistance. ImportanceEfflux pumps are widely recognized as major contributors to antimicrobial resistance; however, the extent to which resistance can be driven solely by efflux remains unclear. Here, we define the limits of efflux-mediated resistance using adaptive laboratory evolution to ethidium bromide in Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that resistance reproducibly plateaus despite continued selection and the presence of multiple efflux pumps in the genome, indicating a physiological ceiling to efflux-based adaptation. This limit is achieved through distinct evolutionary trajectories involving regulatory mutations that converge on enhanced efflux activity. Importantly, upregulation of efflux pumps is coupled to extensive cellular remodelling, including metabolic rewiring, and changes in membrane energetics, revealing system-wide trade-offs associated with resistance. Together, our findings demonstrate that efflux-driven resistance is constrained by cellular physiology and shaped by global adaptive costs, thereby refining current models of antimicrobial resistance and identifying vulnerabilities that may be exploited to limit the evolution of resistance.

systems biology↗

bioRxiv2026

Hyperglycemia transcriptionally regulates the paranodal protein (Caspr1) in retinal neurons and modulates neurite extension

Hyperglycemia is a hallmark of diabetes, affecting neuronal structure and function by altering molecular signalling pathways. Here, we explore the role of hyperglycemia in regulating Caspr1 expression and its downstream effects on neurite outgrowth. Caspr1, a critical protein implicated in neurodegenerative diseases, was found to be significantly downregulated in N2a and 661W cell lines cultured under hyperglycemic conditions (25mM glucose) and, as a result, promoted neurite outgrowth. Knockout of Caspr1 using CRISPR-Cas9 further confirmed its inhibitory role on neurite outgrowth, as Caspr1-deficient cells exhibited enhanced neurite elongation. Caspr1 downregulation was mediated by decreased expression of C/EBP, a key transcription factor with a binding site on the Caspr1 promoter. Overexpression of C/EBP restored Caspr1 promoter activity and mRNA levels, establishing C/EBP as a critical regulator. Additionally, hyperglycemia was observed to inhibit Akt phosphorylation, which further contributed to Caspr1 downregulation. Adding insulin to the culture medium under hyperglycemic conditions shows inhibition of Akt phosphorylation and downregulation of Caspr1, resulting in a shorter length of neurites in retinal neurons. In vivo, studies in diabetic mouse models and diabetic patient samples demonstrated reduced expression of Caspr1 in retinal tissues. These results suggest that hyperglycemia regulates Caspr1 expression through Akt and C/EBP pathways, promoting neurite outgrowth in retinal neurons. In contrast, adding insulin to the medium under hyperglycemia downregulates the Caspr1 expression and reduces neurite length in retinal neurons. Targeting this pathway may offer new therapeutic approaches to mitigate neurodegeneration in diabetic retinopathy.

cell biology↗

bioRxiv2025

Efficacy of immunostimulant feed additive ShrimpGuard, for the preventive management of White Spot Syndrome Virus (WSSV) infection in shrimps

White spot syndrome virus (WSSV) is a virulent lethal viral pathogen affecting shrimp aquaculture worldwide. Current solutions for WSSV management can be divided into three categories; farm management, selective breeding or genetic engineering to get WSSV resistant varieties of shrimp, and developing vaccine or drug-like solutions specifically targeting WSSV. At present, farm management or good farming practice is the most reliable way of managing the problem, anti-WSSV vaccine, or anti-WSSV drugs that are reliable and scalable in the market are not available. We have developed a feed additive named "ShrimpGuard" using our SOLAQ (Solutions for Agriculture and Aquaculture) platform that specifically provides Shrimp protection against the WSSV infection. Here we report protection observed in both laboratory and farm demonstrations, in Penaeus vannamei. Collectively, these studies show that Shrimp-Guard does not cause any adverse effects on shrimp health and is able to provide significant protection to shrimp against WSSV infection. Briefly, the immune parameters of shrimp respond to ShrimpGuard treatment with increase observed in Total haemocyte count, and activity of prophenoloxidase. Further, survival rates of shrimp treated with ShrimpGuard after WSSV infection was between 80-100 % compared to 0% survival observed in untreated shrimp. The ShrimpGuards performance was tested in production farms and it was found that ShrimpGuard is safe for farm-based applications and the data obtained shows a positive impact on shrimp yield after ShrimpGuard treatment.

immunology↗

bioRxiv2025

The protein turnover and trafficking of Chlamyopsin6 is regulated by IFT88 and IFT52 in the Chlamydomonas reinhardtii

Microbial rhodopsin-based optogenetics has been widely applied to diverse mammalian and plant cell types for controlling membrane potential mediated responses. However, trafficking of optogenetically active protein to the desired subcellular organelle is still a major concern in optogenetic field. This could be resolved by studying the trafficking mechanism of optogenetically active protein in the native system. Current study is focused on the trafficking of two of the microbial rhodopsins named Chalmyopsin5 and Chlamyopsin6 in a green alga, Chlamydomonas reinhardtii. Chlamyopsin5 and Chlamyopsin6 are modular in nature and possess rhodopsin, histidine kinase, response regulator and cyclase domain in tandem. Immunolocalization of Chlamyopsin5 and Chlamyopsin6 in wild strain suggests their different subcellular localization; Chlamyopsin5 in eyespot and Chlamyopsin6 in flagella. Extensive immunocytochemistry of Chlamyopsin5 and Chlamyopsin6 was performed in different intraflagellar transport (IFT) components-defective strains of Chlamydomonas to dissect their trafficking mode to the destined subcellular compartment. Our results indicated the trafficking of Chlamyopsin5 to the eyespot to be independent of IFT machinery while Chlamyopsin6 to the flagella to be IFT dependent. Further, we demonstrate that IFT88 and IFT52 stabilizes Chlamyopsin6 and IFT20 interacts with Chlamyopsin6 in Chlamydomonas. Protein interactome of Chlamyopsin5 and Chlamyopsin6 indicate their role in nitrogen assimilation, gametogenesis and photoprotection in co-ordination with other photoreceptors. Collectively, our study enabled us to understand the targeting of Chlamyopsins to the subcellular compartment (eyespot and flagella). This study is important to expand optogenetic application of microbial type modular rhodopsin with histidine kinase and response regular. Further research in this direction is required to resolve the current challenge of targeting of optogenetic protein to desired subcellular compartment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/693822v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@2691edorg.highwire.dtl.DTLVardef@367a61org.highwire.dtl.DTLVardef@9c85c6org.highwire.dtl.DTLVardef@128f9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

LPC 18:2-Driven Apoptosis In Neutrophils Is Non-Inflammatory and Lipid Raft Dependent

Lysophosphatidylcholines (LPCs) are potent bioactive lipids whose fatty acid compositions dictate their immunomodulatory effects. Here, we delineate how unsaturated LPC 18:2 and saturated LPC 16:0 differentially regulate neutrophil survival and inflammatory programs. LPC 18:2 markedly increased reactive oxygen species (ROS) generation and caspase-3/7 activation, mitochondrial membrane depolarization, and cytochrome c release, features consistent with intrinsic apoptosis. In contrast, LPC 16:0 induced robust LDH and HMGB-1 release, indicating membrane rupture and pyroptosis-like death. Bulk RNA sequencing revealed that LPC 16:0 strongly upregulated inflammatory and cytokine gene expression. Disruption of lipid-raft integrity abolished LPC 18:2-induced ROS and apoptosis, underscoring the dependence of these effects on membrane organization. Collectively, these results identify LPC 18:2 as a non-inflammatory, mitochondria-dependent inducer of neutrophil apoptosis, whereas LPC 16:0 promotes inflammatory, lytic death programs. These findings highlight how lipid saturation determines neutrophil fate and immune tone, providing mechanistic insight into how distinct LPC species shape inflammation and tissue injury.

immunology↗

bioRxiv2025

Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants

Abstract (Summary)Genome-wide association studies (GWAS) have mapped thousands of congenital heart disease (CHD)-associated variants within non-coding regions of the genome. Non-coding variants can alter regulatory mechanisms, such as transcription factor (TF) binding control of gene expression, potentially contributing human diseases. However, with the increasing number of disease-associated variants, comprehensive functional validation remains a significant challenge. In this work, we developed a novel method called SNP Bind-n-Seq to evaluate >3,000 CHD-risk variants for allelic binding for the cardiac TFs NKX2-5, GATA4, and TBX5 in a high-throughput manner. These binding affinity data sets were coupled with a massively parallel reporter assay (MPRA) to screen CHD-risk variant genotype-dependent regulatory activity. We identified 170 variants that exhibit allelic TF binding and 187 that modulate gene expression. Combining both approaches revealed three high-confidence variants with genotype-dependent TF binding, genotype-dependent transcriptional activity, and eQTL behavior in cardiac cells. Collectively, this study provides the first combined high-throughput biochemical and functional genomic evaluation of thousands of CHD-risk variants. HighlightsO_LIAllelic binding affinity measurements of [~]9,600 variants for NKX2-5, GATA4, and TBX5 C_LIO_LIEvaluaFon of >3,000 CHD-risk variants for genotype-dependent regulatory acFvity C_LIO_LIInteracFon networks idenFfy funcFonal variants and genes involving cardiac eQTLs C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/691900v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1f2dc96org.highwire.dtl.DTLVardef@1700929org.highwire.dtl.DTLVardef@696ec4org.highwire.dtl.DTLVardef@1e724d8_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

INVA8001, a Novel and Highly Selective Chymase Inhibitor, Ameliorates Liver Inflammation, Fibrosis, and Hyperplasia in Mdr2 Knockout Mice

Background and aimsMast cells (MCs) play a significant role in autoimmune diseases by mediating inflammatory responses, innate and adaptive responses, angiogenesis, and various pathological processes. MC numbers are significantly increased in chronic liver disease and liver cancer, and degranulation leads to a release of MC mediators, including chymase, which increases inflammation, activates hepatic stellate cells (HSCs), ultimately leading to fibrosis. Primary sclerosing cholangitis (PSC) is a chronic, progressive cholestatic liver disease characterized by inflammation, fibrosis, ductular reaction, and eventual liver failure. MCs and their mediators, particularly chymase, have been implicated in PSC pathogenesis; however, targeting chymase therapeutically has remains largely unexplored. In this study, we aimed to evaluate the efficacy of INVA8001, a highly selective chymase inhibitor, on PSC pathogenesis in the Mdr2 knockout mouse (Mdr2-/- mice) model of PSC. Approach and ResultsWe evaluated the levels of chymase and other MC markers in liver biopsy samples collected from late-stage PSC patients. The effect of chymase inhibition was evaluated using a highly selective and potent small molecule chymase inhibitor, INVA8001, in Mdr2-/- mice. Ten-week-old male Mdr2-/- mice were injected intraperitoneally (IP) with 20 mg/kg of INVA8001 daily for two weeks and varying parameters of disease pathogenesis, including MC activation, inflammation, fibrosis, biliary pathology, and cholestasis were evaluated. In addition, histological, immunohistochemical, biochemical, and molecular analyses were conducted to evaluate the effects of INVA8001 treatment in Mdr2-/- mice. The liver biopsies of PSC patients showed an increased number of chymase-positive cells compared with control samples (collected from non-diseased patients). INVA8001 treatment resulted in a reduction of MC accumulation, inflammation, histological damage, fibrosis, ductular reaction, and biliary senescence in Mdr2-/- mice. The current data show the pathophysiological role of chymase in PSC and the impact of a selective chymase inhibitor on PSC disease pathogenesis. This can further be extrapolated to various MC-driven diseases such as chronic urticaria, atopic dermatitis, asthma, metabolic dysfunction-associated steatohepatitis (MASH), and eosinophilic gastrointestinal diseases, among others, where chymase is central to the disease pathogenesis. ConclusionsOur findings identify chymase as a key driver of PSC pathogenesis establishing INVA8001 as a promising new therapeutic candidate for hepatobiliary disorders, including PSC. Chymase inhibition simultaneously targets MC activation, inflammation, fibrosis, and biliary senescence, and offers a multifaceted approach to treating PSC and other MC-related disorders.

pathology↗

bioRxiv2025

Bruch's Membrane Contributes to the Structural Integrity of the Human Eye

PurposeTo investigate the contribution of the Bruchs membrane and sclera tissues to the overall structural integrity of the ocular wall. MethodsTwenty-three human globes were subjected to biomechanical testing. A piece of sclera measuring 5 x 5 mm was carefully removed at the nasal region, 2 mm away from the optic nerve head. The intraocular pressure was increased at approximately 1 mmHg/s until Bruchs membrane-uvea-retina-tissue layer (BMUR) ruptured. Next, strips of sclera and Bruchs membrane-choriocapillaris (BMC) complex were isolated from the superior fundus region. Uniaxial tension tests were performed at a strain rate of 0.01/s and sampling rate of 15 Hz. The tangent moduli of the BMC and sclera at 0.01, 0.02 and 0.03 strains were compared. ResultsThe rupture pressure of the BMUR was 98.1 {+/-} 21.4 mmHg. The tangent moduli of the BMC at 0.01, 0.02 and 0.03 strains were 2.96 {+/-} 1.44 MPa, 7.68 {+/-} 1.78 MPa and 9.43 {+/-} 2.11 MPa, respectively, and the tangent moduli of the sclera at 0.01, 0.02 and 0.03 strains were 1.09 {+/-} 0.80 MPa, 2.72 {+/-} 1.67 MPa and 5.69 {+/-} 3.27 MPa, respectively. ConclusionThe BMUR was able to sustain relatively high IOP before rupturing. The uniaxial tensile tests showed that the BMC tangent moduli were about 3 times of those of the sclera at strains of 0.01 and 0.02. Although the sclera is approximately 47 times thicker, the BMC is still likely to make a significant contribution (3.51% to 7.42% at strain <0.03) to the overall structural strength of the ocular wall.

bioengineering↗

bioRxiv2025

HIV-1 latency reversing agents converge on phosphoregulation of nuclear protein complexes

Despite the success of antiretroviral therapy (ART), HIV-1 persists in latently infected cells, posing a central barrier to a cure. "Shock-and-kill" strategies using latency-reversing agents (LRAs) have shown some promise in reactivating viral gene expression ex vivo, but have yielded little clinical efficacy, underscoring the need for deeper insight into the molecular mechanisms that govern reactivation. Here, we performed deep quantitative phosphoproteomics of J-Lat 10.6 cells treated with diverse LRAs: SAHA, PMA, or prostratin. We identified 48,476 confidently localized phosphorylation sites mapping to 6,672 proteins, with SAHA inducing the most extensive changes. Regulated phosphoproteins were enriched in chromatin organization, transcription, RNA processing, nuclear transport, and cytoskeletal remodeling. Although LRAs regulated overlapping pathways, they elicited divergent kinase activities and site-specific phosphorylation patterns. A reproducible core of 3,502 phosphorylation sites on 1,432 proteins mapped to 39 nuclear protein complexes, including the spliceosome, Mediator, NF-{kappa}B, and RNA polymerase II. Remarkably, 20 protein complexes were phosphoregulated by all three LRAs, but at distinct sites, revealing convergence on shared nuclear machinery through distinct mechanisms. This study provides a comprehensive map of protein complex phosphorylation remodeling during HIV-1 reactivation and highlights signaling mechanisms that could guide the rational design of next-generation LRAs with improved efficacy and reduced toxicity.

microbiology↗

bioRxiv2025

Peroxiredoxin 1 safeguards the nucleolar genome from oxidative damage

Peroxiredoxin 1 (PRDX1) is a highly conserved, thiol-dependent peroxidase that rapidly scavenges reactive oxygen species to modulate redox signaling. PRDX1-null mice exhibited genomic instability, shortened lifespan, and accelerated tumorigenesis, including development of lymphomas, sarcomas, and carcinomas. Despite extensive characterization of these phenotypes, the molecular mechanism by which PRDX1 loss causes genomic instability remains poorly understood. Here we show that PRDX1 deficiency alters nucleolar morphology, impairs RNA Polymerase I (POL-I)-dependent transcription of pre-ribosomal RNAs and triggers nucleolar genomic instability. This oxidative stress-induced nucleolar dysfunction promotes the stability of secondary DNA structures, such as RNA-DNA hybrids and G-quadruplex DNA, contributing to nucleolar genomic instability. We demonstrate that PRDX1 loss reduces nascent rRNA levels and impairs rRNA processing, further affecting ribosome biogenesis. Mechanistically, we established that PRDX1 loss triggers activation of the nucleolar DNA damage response including activation of DNA repair kinase ATM and the nucleolar factor TCOF1 within the nucleolus, and recruitment of the MRE11-RAD50-NBS1 (MRN) complex subunit NBS1 to ribosomal DNA (rDNA) loci. NBS1 accumulation correlates with the repression of rDNA transcription by POL-I, potentially delaying rRNA synthesis, and safeguarding the nucleolar genome from further oxidative damage. Collectively, these findings uncover a previously unrecognized, but critical role, for PRDX1 in maintaining nucleolar integrity and ribosomal biogenesis through redox-dependent regulation of rDNA transcription and processing machinery.

molecular biology↗

bioRxiv2025

Genetic Ablation and Multi-Omics Profiling Reveal CEP55 as a Key Driver of Tumorigenesis in Diverse Cancer Models

BackgroundCEP55 is a centrosomal protein with emerging oncogenic roles. It is overexpressed in many cancers, where it drives genomic instability, phenocopies PTEN loss and hyperactivates the PI3K/AKT pathway, thereby promoting aggressive and therapy-resistant tumors. MethodsWe developed an inducible Cep55 knockout (KO) mouse model as well as generated primary, immortalized (SV40), and transformed (E1A/Ras) mouse embryonic fibroblasts (MEFs) for functional and proteomic assays. Tumorigenesis was studied using E1A/Ras MEF transplantation and a Pten-deficient genetically engineered mouse model (GEMM). Multi-omics apparatus including proteomics, and spatial transcriptomics, histopathology, immunobloting and functional assays were employed to elucidate underlying mechanisms. Findings were cross-validated using human cancer datasets. ResultsCep55 ablation remodeled the extracellular matrix (ECM), disrupted integrin and oncogenic signaling, reduced AKT/ERK activation, and induced stress pathways. Cep55 knockouts (KO) cells showed impaired proliferation, migration, invasion, and adhesion. In vivo, unlike the embryonic lethality observed in constitutive KOs, the inducible Cep55 deletion was well-tolerated in adult mice. Strikingly, tumors derived from Cep55-null EIA/RAS-transformed MEFs exhibited delayed onset and progression. In the genetically engineered cancer-prone mouse model, Cep55 deletion on a Pten-deficient background led to a greater than seven-fold increase in median survival. Spatial transcriptomics on cancerous tissues revealed that CEP55 regulates ECM remodeling, integrin expression, trafficking, and cell adhesion, supporting its critical role in tumor progression to metastasis. ConclusionCEP55 is dispensable for adult homeostasis but essential for tumorigenesis, especially with PTEN loss. Its deletion suppresses transformation, delays tumor growth, and prolongs survival, supporting CEP55 as a therapeutic target in PTEN-deficient cancers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/685219v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@3d81e8org.highwire.dtl.DTLVardef@1bd5a7org.highwire.dtl.DTLVardef@167ecf3org.highwire.dtl.DTLVardef@1f57b95_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Protectin D1/GPR37 signaling enhances macrophage-dependent efferocytosis to attenuate experimental abdominal aortic aneurysm formation

Abdominal aortic aneurysms (AAAs) are chronic inflammatory vascular disorders characterized by progressive aortic dilation and destruction of the vascular wall, often culminating in rupture. Current management is limited to surgical repair, with no approved targeted pharmacologic therapies. In this study, we investigated the immunomodulatory role of Protectin D1 (PD1), a specialized pro-resolving lipid mediator, through G-protein-coupled receptor 37 (GPR37) signaling on macrophages in mitigating AAA progression and preventing aortic rupture. Single cell-RNA sequencing analysis of human tissue demonstrated significant differences in PD1/GPR37 axis-related genes in macrophages in AAAs compared to control aortic tissue. Using an established murine AAA model, PD1 administration significantly attenuated aortic diameter, pro-inflammatory cytokine and matrix metalloproteinase (MMP2) expression, as well as maintained aortic morphology in a GPR37-dependent manner. Importantly, PD1 treatment prevented preformed AAA progression to aortic rupture in another preclinical elastase+BAPN model of aortic rupture, by attenuating aortic diameter, tissue inflammation as well as decreasing macrophage infiltration, preserving elastin integrity, and restoring smooth muscle -actin expression in the aortic wall. Mechanistically, PD1 enhanced macrophage efferocytosis of apoptotic vascular smooth muscle cells in the murine aortic tissue as well as in isolated macrophages via GPR37-dependent manner and attenuated the inflammatory paracrine secretion of macrophage-specific paracrine release of TNF- and IL-{beta}. These findings suggest that PD1/GPR37 signaling on macrophages promotes inflammation-resolution by enhancing efferocytosis of apoptotic SMCs conferring protection against aortic inflammation and remodeling to mitigate AAA formation and rupture. Significance StatementThis study elucidates the protective role of specialized proresolving lipid mediator, Protectin D1, by activating macrophages via GPR37 receptors, to enhance the clearance of apoptotic smooth muscle cells to mitigate aortic inflammation and vascular remodeling during abdominal aortic aneurysm formation. We observed that several key inflammation related genes were associated with PD1/GPR37-dependent signaling in macrophages of human AAAs. Detailed analysis in experimental models delineated the signaling pathway where upregulating macrophage-dependent efferocytosis via immunomodulation by Protectin D1 attenuated aortic inflammation and remodeling, indicating a potential mechanism for therapeutic intervention in the pathobiology of AAAs to prevent aortic rupture.

immunology↗

bioRxiv2025

Wnt7a is a Novel Lymphangiocrine Factor Driving Cholangiocyte Proliferation during Liver Regeneration

The significance of lymphatic vessels (LVs) and lymphatic endothelial cells (LyECs) during liver regeneration remains unexplored. We aimed to characterize contribution of LVs and LyECs in liver regeneration using two-thirds partial hepatectomy (PHx) models. An increased number and diameter of CD31+PDPN+ LVs was observed at day 2 and 5 post-PHx. Proteomic analysis of LyECs and ELISA studies in conditioned media of LyECs revealed that one of the secreted proteins, Wnt7a was uniquely expressed at day 2 post PHx. In vitro studies confirmed that Wnt7a is a potent stimulator of proliferation for both hepatocytes and cholangiocytes. In vivo inhibition of lymphangiogenesis and reduction in Wnt7a led to a decline in the percentage of CK19+ cholangiocytes and bile ducts. Western blot analysis showed that Wnt7a activated the downstream Frizzled 7 receptor and non-canonical planar-cell-polarity pathway to drive the proliferation of cholangiocytes. In vivo, Wnt7a loss-of-function experiments in zebrafish along with inhibitor studies in rat models of PHx further re-iterated clear links between Wnt7a and proliferation of bile ducts. Pro-regenerative effects of Wnt7a were demonstrated in a model of small-for-size syndrome (80% PHx), where administering recombinant Wnt7a enhanced both cholangiocyte and hepatocyte proliferation. Elevated Wnt7a levels were seen in donors of liver transplant patients at day 1 and 2 post-hepatectomy and Wnt7a also facilitated growth of human cholangiocyte organoids in vitro. Our findings uncover the novel role of Wnt7 as one of the key lymphangiocrine signals that facilitates proliferation of cholangiocytes during liver regeneration. HighlightsO_LINumber of functional lymphatic Vessels (LVs) and lymphangiogenesis is enhanced between day 2 and day 5 after partial hepatectomy (PHx) in rat models and liver transplant donors. C_LIO_LIWnt7a released from lymphatic endothelial cells (LyECs) acts as a potent lymphangiocrine factor, stimulating proliferation of hepatocytes and cholangiocytes in vitro, across both rodent and human models. C_LIO_LIInhibition of lymphagiogenesis during PHx transiently reduces number of cholangiocytes during early liver regeneration. C_LIO_LIWnt7a signals through Frizzled 7 receptor to activate p-AKT, p-JAK1 and p-STAT3 proteins in cholangiocytes. C_LIO_LIAdministration of recombinant Wnt7a in 80% PHx models induces proliferation of hepatocytes and bile ducts. C_LI

physiology↗

bioRxiv2025

Fibroblast specialisation across microanatomy in a single-cell atlas of healthy human Achilles tendon

Tendons are transitional tissues linking muscle to bone, enabling locomotion and fine motor control. The cellular biology across the Achilles tendon unit is poorly understood, yet critical for interpreting normal function and pathological changes across its microanatomically-defined functional zones. We generated a spatially-resolved transcriptomic atlas of human Achilles tendon, sampling the tendon-bone junction (enthesis), midbody, myotendinous junction, and adjoining muscle. Six fibroblast subtypes were identified, with distinct transcriptional profiles and spatial distributions, suggesting specialised functional roles across the tendon-muscle unit. Two dominant fibroblast types were specifically positioned in the tendon mid-substance and paratenon (vessel-rich region surrounding the tendon fibrils); other populations included perineural, myotendinous junction-specific, muscle-specific, and lining-layer fibroblasts. These findings demonstrate how cellular diversity across a transitional tissue may underlie microanatomical-specific roles. This atlas provides a foundation for understanding cellular functions across the tendon-muscle unit and will be essential for comparisons with diseased tissue, identifying pathogenic mediators and treatment targets for autoimmune and degenerative pathologies of the Achilles tendon.

genomics↗

bioRxiv2025

Calcium: Modulator of Post-transcriptional and post-translational process in mESCs

Calcium ion (Ca2+) is a ubiquitous intracellular and extracellular messenger that regulates several cellular activities. Previous findings have reported the presence of active Ca2+ receptors in mouse embryonic stem cells (mESCs) but the fundamental requirement of Ca2+ signalling remains unclear. We have noted the presence of high Ca2+ in undifferentiated mESCs and showed that its depletion exerts G2/M cell cycle arrest, spontaneous differentiation of mESCs towards mesoderm lineage and mitochondrial biogenesis. Further, our data demonstrates that Ca2+ regulates the homeostasis and stability of Oct4 and Nanog at the post-translational level through pCamkII dependent mechanism independent of polyubiquitin system, JAK-STAT3 pathway, transcriptional and translational control. Our data also signifies the role of Ca2+ at the post-transcriptional level in regulating p-bodies and stress granule markers (Dcp1a, XRN1, Tudor and EDC4), splicing-dependent and 3UTR-dependent NMD activity. Together, this study identifies the broad role of Ca2+ in modulating key processes in mESCs. HighlightsCa2+ is present at elevated levels in mESCs and is important for pluripotency Ca2+ depletion accelerates G2/M cell cycle arrest and mesoderm differentiation Ca2+ regulates pluripotency and p-bodies markers at the post-translational level Ca2+ regulates Oct4, Nanog, dcp1a through pCaMKII dependent mechanism

cell biology↗

bioRxiv2025

Extreme weather risk shrinks range size estimates and alters biodiversity predictions

Extreme weather events, including heat waves, cold snaps, and droughts, are increasing in frequency and intensity with expected but little understood consequences for biodiversity. Extreme weather events can push organisms beyond their physiological thermal or hydric tolerances and thus limit where they can persist, affecting their geographic distributions. Species might be especially sensitive to extreme weather at the edges of their geographic ranges, where they are often already living near their physiological limits. However, the influence of climatic variability and extreme weather is often ignored in favor of climatic means when estimating distributional and richness patterns. Here we link hundreds of millions of citizen science bird observations from 2004-2024 to high-resolution extreme weather risk maps to explore how climatic variability and extreme weather risk alters summer and winter distributions and biodiversity patterns for 535 North American species. We find that species distribution models accounting for historical extreme weather risk performed better at predicting richness and the presence of individual species across 220 well-surveyed sites. Models incorporating extreme weather predicted narrower geographic distributions than models relying on only climatic means, with species ranges shrinking an average of 6% in summer and 10% in winter and range truncation observed at the range edges. These effects were observed in both seasons but were particularly strong in winter, a time with greater short-term weather variability than summer. Richness estimates were substantially lower when extreme weather was accounted for, especially in the US southwest and central plains (up to 30-40 fewer species), regions highly prone to extreme heat, cold and drought. Our results suggest that more mechanistically informed biodiversity predictions that account for extreme weather are critical for reliably predicting shifting distributional and biodiversity patterns.

ecology↗

bioRxiv2025

Unmasking Early Microglial Remodeling in an Alzheimer's Disease Mouse Model

Early neuroimmune remodeling is a critical yet understudied component of Alzheimers disease (AD) pathogenesis. To investigate microglial contributions to AD development prior to overt plaque deposition, we developed an open-source morphometric pipeline to systematically quantify hippocampal microglial structure and activation states in pre-plaque 5xFAD mice. Across [~]11,000 cells, we extracted multidimensional parameters including area, circularity, convex hull, branch points, nearest-neighbor distance, and nuclear features, alongside Iba1 and CD68 intensity measurements. While no significant overt gliosis was observed at this early stage, microglia from 5xFAD mice exhibited subtle trends toward increased structural complexity compared to wild-type controls. Importantly, significant sex-specific differences were detected within the CA1 subregion: male 5xFAD microglia displayed hyper-ramified morphologies consistent with enhanced surveillance states, whereas female microglia demonstrated greater density and a more reactive phenotype. Correlation analyses revealed a conserved association between microglial complexity and Iba1/CD68 expression, independent of sex or genotype, underscoring a fundamental link between cytoskeletal remodeling and phagolysosomal activity. These findings highlight the capacity of morphometric profiling to sensitively detect early, region-specific, and sex-dependent shifts in microglial phenotype before amyloid deposition. By integrating quantitative morphology with canonical molecular markers, this framework provides a robust and unbiased approach for characterizing microglial activation trajectories. Such early readouts may inform biomarker discovery and therapeutic strategies aimed at modulating microglial responses to delay or prevent AD progression.

neuroscience↗