Biology subjects

Ali, S.

Publications and source records attributed to Ali, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Scarless regeneration requires post-translational proteolytic regulation via macrophage-derived Legumain

Macrophages express proteolytic factors in response to injury but how proteases are deployed and regulated during regeneration are incompletely defined. Beyond their transcriptomic expression, activity of individual proteases is defined both by their unique substrate specificity and post-translational modifications of their active forms. Here we show a key role for the lysosomal protease Legumain in controlling ECM dynamics and post-translational processing of the regenerative proteome. Injury interface-targeted Ctsla localization and post-translational processing requires Lgmn in macrophages. Extracellular cues from physical remodeling control differentiation state and injury response of ligament resident fibroblasts. Loss of ECM turnover, including localized Fibronectin 1a/b remodeling, impairs dedifferentiation in legumain mutants and leads to fibrotic scarring. Taken together, we demonstrate a role for macrophage-derived lysosomal proteases as specialized tools required to fine-tune proteome composition and function in regeneration.

cell biology↗

bioRxiv2026

StainAI-Web: An Interactive Platform for Whole-Slide Microglial Morphology Analysis

Microglial morphology analysis has emerged as a critical approach in neuroinflammation research. The increasing availability of high-resolution and whole-slide histology images has created strong demand for robust, scalable analytical methods capable of efficiently processing these datasets. Existing approaches may require code-based local computation or prolonged processing times for whole-slide images, while manual morphology quantification remains labor-intensive. To address these limitations, we introduce StainAI-Web, a server that performs rapid, automated microglial morphology detection across whole-slide immunohistochemistry images in the cloud. The system provides interactive grayscale preprocessing and supports ROI-based regional quantification, allowing users to define specific tissue regions and systematically compare microglial populations across regions. An interactive visualization module dynamically updates quantitative summaries of morphological distributions as ROIs are selected or modified. Analysis results, including structured JSON files and morphology-annotated overlays, are downloadable for downstream analysis or integration into external computational pipelines. These integrated features provide an accessible framework for efficient and reproducible whole-slide microglial morphology analysis. The StainAI-Web is available at https://stainaiviewer.azurewebsites.net/.

bioinformatics↗

bioRxiv2026

The androgen receptor polyglutamine tract sets the transcriptional balance between muscle growth and atrophy

The androgen receptor (AR) mediates the potent anabolic effects of testosterone and other androgens on skeletal muscle, yet the transcriptional mechanisms coupling this hormonal signal to muscle growth remain unresolved. AR is a ligand-inducible transcription factor whose N-terminal transactivation domain (NTD) harbours a polymorphic polyglutamine (polyQ) tract that, when pathologically expanded, causes spinal and bulbar muscular atrophy (SBMA). To define how the NTD and its polyQ tract shape muscle transcription, we combined an engineered AR allelic series in human myogenic cells with super-resolution and single-molecule imaging, genome-wide binding and expression maps, and human population genetics. Under physiological conditions, androgen-activated AR assembles into dynamic transcriptional condensates and drives an anabolic programme in skeletal muscle through activation of the AP-1 pathway. Progressive expansion of the polyQ tract destabilises AR chromatin binding and shifts its occupancy from promoters to low-affinity distal enhancers, tracking with imaging signatures of muscle aging. In SBMA, this culminates in aberrant transactivation of ectodysplasin A2 receptor (EDA2R), a marker of senescence and inflammation, which engages non-canonical NF-{kappa}B signalling to drive muscle atrophy. Silencing Eda2r attenuated muscle wasting in SBMA mice, establishing this axis as therapeutically actionable. Together, these findings reveal a fundamental mechanism of skeletal-muscle homeostasis and open therapeutic avenues for the many conditions in which muscle atrophy is central.

molecular biology↗

bioRxiv2026

An immunophenotype-coupled transcriptomic atlas of mouse hematopoietic progenitors

Decoding the bone marrow (BM) hematopoietic progenitor compartment is central to understanding the development of mature immune cells in health and disease. Single-cell multimodal approaches are transforming the analysis of this heterogeneous compartment by simultaneously capturing transcriptomic and proteomic information. Still, integrated studies covering the full spectrum of murine hematopoietic stem and progenitor cells (HSPCs) remain scarce. Here, we report a Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) based atlas of 9,281 low-frequency mouse BM HSPCs, profiled using a 123 antibody-derived tag (ADT) panel coupled with genome-wide single-cell transcriptomes. Multimodal analysis resolved 28 progenitor stages across eight blood lineages, each defined by distinctive surface marker and transcription factor (TF) profiles, and provided novel marker combinations to dissect transcriptionally closely related progenitor stages. Classical mouse progenitor surface markers, such as CD117, CD34, and CD115, were detected in accordance with well-established lineage relationships, whereas CD43 and CD48 showed, unexpectedly, broader expression patterns. Neglected surface molecules such as CD27, CD36, CD106, and PIR-A/B are nominated as novel stage-specific markers. ADT versus transcriptome comparison revealed transcription-translation inconsistencies for markers, including CD54 and CD68. A CITE-seq-guided gating strategy translates these population definitions into FACS-compatible panels for prospective isolation and functional interrogation of previously unresolved progenitor stages. Comprehensive TF network analysis delineated lineage- and stage-specific transcriptional programs. This contributes to clarifying unresolved ontogenies and functions, including the lympho-myeloid dual origin of pDCs or rapid neutrophil turnover. This new and comprehensive resource enables exploration of mouse hematopoietic progenitor states driving discoveries in hematology and immunology.

immunology↗

bioRxiv2026

Systemic Nanobubbles Enable Ultrasound-Guided STING Immunotherapy in Breast Cancer

Activation of the STING pathway can induce potent antitumor immunity, but effective delivery of STING agonists to the tumor while limiting systemic exposure remains challenging. We previously developed MUSIC, an ultrasound-guided platform that uses microbubbles (MBs) to deliver the STING agonist 2'3'-cGAMP and locally activate antitumor immunity. However, the vascular confinement of MBs and the need for intratumoral administration limit the potential for systemic tumor targeting. To overcome these limitations, we developed SONATA (Systemic Oncotherapy using Nanobubbles for Acoustically-guided Tumor Activation), which employs nanobubbles (NBs) that are approximately 10-fold smaller than conventional MBs, enabling systemic administration and tumor extravasation. Following NB accumulation within tumors, ultrasound exposure triggers localized cGAMP release, facilitating delivery to targeted CD11b+ antigen-presenting cells (APCs) and STING activation with spatial and temporal control. NBs are composed of the same components as MBs, including phospholipid shells and a perfluorobutane core and are functionalized with anti-CD11b antibodies to target CD11b+ APCs and spermine-modified dextran to stably load cGAMP through nanocomplex formation. Upon ultrasound activation, SONATA induced phosphorylation of STING, TBK1, and IRF3 and increased IFN-{beta} production in bone marrow-derived macrophages. In an orthotopic breast cancer model, intravenously administered SONATA combined with tumor-localized ultrasound significantly inhibited tumor growth compared with controls. Furthermore, SONATA synergized with immune checkpoint blockade prolonged the median survival of tumor-bearing mice. Collectively, these findings establish SONATA as a systemically administered immunotherapy platform that enables ultrasound-guided, spatially controlled STING activation.

bioengineering↗

bioRxiv2026

Reinforcement Learning via Brain Feedback for real-time fMRI-based adaptive stimulus generation

Traditional fMRI studies rely on predefined task paradigms, where fixed stimulus designs limit the flexibility with which brain-stimulus relationships can be explored. Here, we introduce Reinforcement Learning via Brain Feedback (RLBF), a framework and open-source software package for adaptive stimulus optimization using real-time fMRI. RLBF reverses the conventional direction of inference by using neural responses to guide the exploration of stimulus spaces through reinforcement learning, enabling optimization of predefined brain targets such as regional activity or multivariate neural signatures. The accompanying Python-based software provides a modular framework integrating real-time fMRI data processing, reinforcement learning agents, adaptive stimulus generation, simulation-based testing, and experiment monitoring. Its flexible architecture allows researchers to customize preprocessing pipelines, reward functions, stimulus spaces, and RL strategies for diverse closed-loop neuroimaging applications. We validate the framework in a proof-of-concept study (N=10), demonstrating real-time optimization of a simple visual stimulus space by adapting checkerboard contrast and frequency to maximize primary visual cortex (V1) responses within a single 10-minute fMRI session. RLBF provides an extensible foundation for brain-guided stimulus optimization and enables new approaches for investigating neural specificity, individualized brain-stimulus relationships, and adaptive experimental design.

bioinformatics↗

bioRxiv2026

Cellular senescence is associated with age-related loss of liver zonation and hepatocyte function

The liver is organized into tightly regulated zones with distinct metabolic functions but zonation erodes with age. Cellular senescence contributes to aging and liver diseases, however, its impact on aging biology is ill-defined. As part of The Cellular Senescence Network Consortium, we used multiple spatial transcriptomics approaches (GeoMx, Visium, CosMx) with snRNA-seq to profile senescence signatures, zonation markers, and metabolic pathways in livers from wild-type (WT) mice of multiple ages. We observed a loss of canonical zone signatures in aged mouse livers characterized by "expansion" of midlobular (zone 2) marker gene expression, accompanied by diminished expression of zone 3 marker genes by middle-age (18 months), indicative of loss of cell identity. Multiple analytic approaches identified distinct age-, zone- and sex-specific senescence signatures, which were significantly associated with zonation markers changes. This was recapitulated in Ercc1 mutant models of accelerated senescence, supporting a causal role of senescent cells in liver aging. A "no-zone" hepatocyte-like cluster expanded with age and with the strongest Senescence-Associated Secretory Phenotype (SASP) profile. Gene expression profiles from senescent hepatocytes implicate decreased WNT signaling and increased BMP as contributing to age-related loss of zonation. Together, these data elucidate the role of senescent cells in driving aging biology in non-diseased liver through disruption of cell:cell signaling and the loss of metabolic and cell identity gene expression necessary for hepatocyte function.

cell biology↗

bioRxiv2026

Outbred Drosophila populations reveal diet-dependent genetic effects on development time

Metabolic effects of genetic variation often depend on diet, yet the loci underlying diet-dependent developmental responses remain incompletely defined. Here we combine multi-trait phenotyping of Drosophila Genetic Reference Panel lines with genome-wide mapping in newly developed Drosophila Recombinant Populations. High sugar causes genotype- and life-stage-dependent changes in metabolic and life-history traits, with development time emerging as a highly heritable, sugar-sensitive phenotype. Mapping in 16 outbred advanced intercross populations reveals distinct association landscapes under low- and high-sugar diets, with a concentrated low-sugar signal, a more distributed high-sugar pattern, and identified genotype-by-diet loci including tap, Eip75B and Cerk. Functional perturbation supports diet-dependent effects for several prioritized candidates. Allele-frequency analyses identify operationally defined thrifty-like variants associated with delayed development under high sugar and relatively earlier development under low sugar; these variants are enriched for cell-adhesion, neurodevelopmental, and morphogenetic processes. Together, these results establish an outbred Drosophila framework for dissecting how dietary sugar remodels the genetic architecture of development time.

genetics↗

bioRxiv2026

Phenotype-dependent subtyping exposes high MYC activity as a targetable dependency in LuAd

C-MYC (MYC) occupies a critical nexus of oncogenic signalling and deregulated expression of MYC is widespread across most human cancer types, suggesting that MYC should be an attractive target for therapeutic intervention. Although 30-40% of human Non-Small Cell lung cancers show low level amplification of c-MYC and genetic evidence has shown that c-Myc is a key downstream effector of KRas-driven lung tumourigenesis in mouse models, the functional contribution of MYC to human lung cancer remains unclear. We applied a phenotype-based classifier to the TCGA Lung Adenocarcinoma (LuAd) cohort and found that high MYC transcriptional activity identifies a subset of LuAd with significantly reduced survival. Application of the same methodology to a panel of genetically engineered mouse models identified multiple genotypes that give rise to the high MYC activity phenotype, disease positioning such models as reflective of a distinct subset of human LuAd. We show that high MYC activity predicts sensitivity to a small molecule dual-inhibitor of the MYC co-factors, EZH2 and G9A, HKMTi-1-005, and that treatment with HKMTi-1-005 strongly reduced MYC protein expression, induced B cell-mediated immune surveillance and suppressed growth of autochthonous KRasG12D-driven lung tumours. Statement of significanceThis work establishes the principle of indirectly targeting MYC in LuAd, via inhibition of associated enzymatic cofactors, EZH2 and G9A, and identifies a large subset of aggressive human LuAd with a high MYC activity signature that may benefit from this approach.

cancer biology↗

bioRxiv2026

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq

Functional genomics studies have provided critical insights into cell type-specific gene regulatory programs, but to date most have been conducted in wild-type tissues or cell cultures. Here, we present a gene expression functional atlas across the mouse brain. We use an enhanced in vivo Perturb-seq platform to analyze transcriptome-wide responses to loss of 1,947 disease-associated genes, profiling over 7.7 million cells spanning major brain regions and neuronal populations. We find striking cell-type-specific essentiality and transcriptional programs and show that closely related disease genes such as two NMDA receptor subunits can drive opposing transcriptional programs. Together, this work reveals insights into the genetics and mechanisms of neurodevelopmental, psychiatric, and neurodegenerative diseases in vivo, paving the way for the design of future genetic medicine.

genomics↗

bioRxiv2026

Comprehensive analysis of air and surface hospital microbiomes uncovers potential hotspots and avenues for transmission of diverse pathogens linked to hospital-acquired infections

Fomite-mediated and airborne transmission pathways play a significant role in the dissemination of healthcare associated pathogens, contributing to the burden of hospital-acquired infections (HAIs). Effective infection prevention and control therefore require robust surveillance approaches capable of capturing the complexity of air and surface microbial communities present in healthcare settings. However, to date such approaches are not widely employed. In this study we used a rapid and low-biomass optimized metagenomic workflow to detect clinically relevant pathogens, characterise genetic signatures such as antimicrobial resistance and virulence determinants, and profile the wider airborne microbiome, including unculturable taxa) essential for HAI surveillance. Air samples were collected from multiple clinical and non-clinical areas across three multi-storey healthcare units within a UK hospital, alongside to surface samples from a haematology/oncology ward with a documented history of outbreaks. Following DNA extraction and enrichment optimised for low-biomass samples, sequencing was performed using the Oxford Nanopore Technologies MinIon long-read platform. Metagenomics data were analysed using an in-house developed bioinformatics pipeline. Metagenomic profiling revealed high bacterial taxonomic diversity across sampled environments, with limited overlap between the airborne and surface communities. Approximately 0.3% of bacterial reads harboured a large variety of antimicrobial resistance genes (ARGs), virulence factors (VFs) and mobile genetics elements (MGEs) across different hospital sample groups. Notably, critical and emerging pathogens were detected across ten wards and were associated with clinically significant resistance determinants, including multiple blaOXA subtypes, vanA gene clusters, and multidrug efflux pumps conferring resistance to eight important classes of antibiotics, including carbapenems, cephalosporins, penams, and vancomycin. In addition, several plasmid replicons implemented in horizontal gene transfer (HGT) were identified within these pathogens, indicating an increased potential for the emergence and dissemination of multi-drug resistance within hospital associated microbial communities. Our findings highlight the importance of using rapid metagenomics-based methodologies for environmental surveillance in healthcare settings. Correspondingly, this study revealed that hospital air and surface microbiomes comprise complex and dynamic microbial communities that harbour diverse of ARGs and VFs with the potential for rapid transmission across the surface-air interface, particularly in high-risk/vulnerable patient areas where outbreaks are more likely to occur.

microbiology↗

bioRxiv2025

HP1 dimerization but not LLPS drives the condensation and segregation of H3K9me-marked chromatin

Heterochromatin protein 1 (HP1) is a conserved chromatin-associated factor implicated in the establishment and maintenance of H3K9me-marked heterochromatin, potentially through phase separation-mediated condensation. Whether HP1 promotes heterochromatin condensation primarily through its dimerization or liquid-liquid phase separation (LLPS) remains unresolved. Using the C. elegans HP1 orthologue HPL-2 and a combined in vitro-in vivo approach, we systematically dissected the molecular determinants of HPL-2 function in heterochromatin condensation. Through specific mutants, we demonstrate that HPL-2 dimerization is essential for condensing H3K9me chromatin arrays in vitro and for maintaining HPL-2 and H3K9me heterochromatin foci in C. elegans embryos, while LLPS enhances or stabilizes these foci. We further show that HPL-2 dimerization is sufficient to mediate segregation of H3K9me from unmodified chromatin arrays in vitro, forming spatially distinct H3K9me-enriched condensates. Surprisingly, HPL-2 mutants defective in heterochromatin foci formation cause only minor transcriptional changes among genes associated with H3K9me-marked heterochromatin, implying that HP1-dependent heterochromatin foci and gene silencing are not tightly coupled in vivo. Nonetheless, these mutant C. elegans exhibit profound physiological and developmental defects. Our findings establish dimerization as the principal molecular mechanism of HP1-driven H3K9me-chromatin condensation, elucidate an auxiliary role of LLPS, and reveal the uncoupling between HP1-dependent heterochromatin and transcriptional regulation.

biochemistry↗

bioRxiv2025

Shadow competition and the evolution of sensory capability in sit-and-wait predators

1Shadow competition occurs when an organism prevents another organisms access to a resource by intercepting that resource first, thereby casting a "shadow" over the competing organism. This competition is commonly seen in the case of sit-and-wait (or ambush) predators. Shadow competition is closely related to the sensory capabilities of the organism, such as the range at which a predator can detect prey as well as the field of view of prey detection. Here, we develop an agent-based model whereby stationary, sit-and-wait predators exert shadow competition for prey on other predators on an explicit spatial landscape. Three predator characteristics can evolve: location, sensory radius, and field of view. We vary the number of available prey, the location of the prey source, the cost of sensory perception, and the energy requirements of the predator to find how shadow competition affects the evolved predator characteristics. We find that predators evolve a long, narrow sensory cone as a result of shadow competition, and that shadow competition greatly limits the efficiency of the predator-prey system. Thus, shadow competition, and the spatial interaction of predators in general, can dramatically shape predator phenotype and behavior.

ecology↗

bioRxiv2025

Cannabidiol as a Prophylactic Agent Against Glioblastoma Growth: A Preclinical Investigation

PurposeGlioblastoma (GBM) is one of the most aggressive brain tumors, with limited treatment options and poor outcomes due to frequent relapse after surgery. This study aims to investigate whether pretreatment with inhaled cannabidiol (CBD) can inhibit GBM growth in a preclinical murine model. Specifically, we hypothesize that CBD pretreatment may reduce tumor progression and modulate the tumor microenvironment. MethodsC57BL/6 mice were pretreated with inhaled CBD for either 3 or 14 days, or a placebo, followed by intracranial implantation of glioblastoma cells. Tumor growth, immune checkpoint expression (IDO, PD-L1), and key biomarkers (MGMT, Ki67) were assessed to determine the impact of CBD pretreatment on tumor progression and the immune microenvironment. ResultsThe 14-day CBD pretreatment significantly reduced tumor growth compared to both the placebo and 3-day CBD groups. Additionally, this group showed lower expression of immune checkpoints (IDO, PD-L1) and reduced levels of MGMT and Ki67, suggesting enhanced tumor suppression. These results indicate that prolonged CBD pretreatment modulates the tumor microenvironment and may improve tumor control and reduce relapse risk. ConclusionThis study demonstrates that inhaled CBD pretreatment significantly inhibits GBM growth in a preclinical model. CBDs ability to reduce immune checkpoint expression and key biomarkers associated with tumor progression suggests that it could be an effective strategy for enhancing the efficacy of GBM therapies and potentially improving post-surgical outcomes. Further research is required to investigate its clinical potential and mechanisms of action.

cancer biology↗

bioRxiv2025

Glycosphingolipids Regulate Phosphatidylserine Transport at ER-PM Contact Sites

Plasma membrane (PM) localization of KRAS requires specific glycosphingolipids in the outer leaflet and phosphatidylserine (PS) in the inner leaflet. PM PS content is controlled by lipid transport proteins ORP5 and ORP8, which operate at ER-PM membrane contact sites (MCSs). Using high-resolution imaging, we now show that GSLs including GM3 and SM4, are required to maintain ORP5 and ORP8 localization to MCSs. Genetic deletion or pharmacologic inhibition of enzymes required for the biosynthesis of GM3 or SM4, displace PI4-kinase Type III (PI4KIII) and its adaptor EFR3A from the PM, thereby reducing PM phosphatidylinositol 4-phosphate (PI4P) content. PM interactions of ORP5 and ORP8 are also disrupted. Since ORP5 and ORP8 transport PS to the PM by counter-transporting PI4P to the ER, PM PS content is substantially reduced. We further show that GM3 and GM2 regulate the assembly of ER-PM-MCSs, such that the function of other MCS-localized macromolecular machineries including calcium release-activated calcium channels is abrogated when glycosphingolipid biosynthesis is blocked. Together, this study establishes glycosphingolipids as organizers of PS transport and ER-PM MCSs, expanding the regulators of MCSs beyond protein tethers to include glycosylated lipids and revealing how glycosphingolipids control KRAS function.

molecular biology↗

bioRxiv2025

SAGA (Simplified Association Genomewide Analyses): a user-friendly Pipeline to Democratize Genome-Wide Association Studies

Genome-wide association studies (GWAS) have enabled clinicians and researchers to identify genetic variants linked to complex traits and diseases(1-3). However, GWAS still face several challenges, particularly regarding accessibility and reproducibility (4-6). Conducting these analyses often requires substantial bioinformatics expertise for data preprocessing, software installation, and scripting(7-10). We then developed SAGA ("Simplified Association Genome-wide Analyses"), a BASH-based, open-source, fully automated pipeline that integrates three widely adopted tools--PLINK(11), GMMAT(12), and SAIGE(13)--for accessible, robust, and reproducible GWAS. After installation, users simply need to provide genotype and phenotype files in standard formats. The pipeline automates preprocessing, association testing, and visualization, outputting summary statistics, Manhattan plots, and quantile-quantile plots. SAGA enables robust GWAS for users without scripting experience, expanding access to complex genetic analyses.

bioinformatics↗

bioRxiv2025

Fine scale structural information substantially improves multivariate regression model for mRNA in-vial degradation prediction

The success of COVID-19 mRNA vaccines has made the in-solution stability optimization of mRNAs a key objective. However, we still lack a complete understanding of sequence metrics that influence mRNA in-solution stability. RNA secondary structure plays a critical role in protecting against hydrolysis, the primary degradation pathway under storage conditions. Yet, the structural metrics that best guide stability-focused mRNA design remain incompletely defined. Global metrics like minimum free energy and average unpaired probability have improved mRNA stability but fail to capture local structural variation relevant to RNA degradation. We demonstrate that base-pairing log odds provide fine-scale, orthogonal insight that complements global metrics and improves stability modeling. Further, by combining local and global features into a parsimonious four-feature regression model, dubbed Stability Regression Analysis using Nucleotide-Derived features (STRAND), we achieve a greater than two-fold reduction in prediction error compared to existing machine learning and deep learning approaches and demonstrate robust generalization across diverse transcript contexts. This compact and interpretable model provides an accurate and reliable framework for predicting mRNAs in-solution stability.

bioinformatics↗

bioRxiv2025

Distinct 2-phenyl-imidazo pyridine derivatives drive ER degradation and selectively impair proliferation of ER+ breast cancer cells via the aryl hydrocarbon receptor

X15695 is a 2-phenyl-imidazo[1, 2] pyridine derivative identified as an orally active, selective oestrogen receptor (ER) degrader that inhibits the proliferation of ER+ breast cancer cells. Here, we show that X15695 is an aryl hydrocarbon receptor (AHR) ligand that stabilises the AHR more efficiently than its classical ligand, indirubin. X15695 enables AHR to form a complex with the ER, promoting its proteasomal degradation. In the presence of oestradiol, X15695 outperforms the standard of care drug fulvestrant in suppressing the growth of ER+ breast cancer cells, either expressing the wild-type or clinically relevant ER mutant forms (Y537S and D538G), and of patient-derived xenograft organoids established from ER+ tumours. Using computational techniques, we discovered that a low pKa value resulting from electron-withdrawing substituents in the 2-phenyl-imidazo[1, 2] pyridine compounds is a key feature that identify them as potent AHR ligands, leading to the potential discovery of additional derivatives for future therapeutic development.

cancer biology↗