Biology subjects

Odeh, A.

Publications and source records attributed to Odeh, A..

9 recordsLinked to original sources

bioRxiv2026

An AI-assisted platform for quantitative histopathological analysis in interstitial lung disease

Interstitial lung diseases (ILDs) are heterogeneous pulmonary disorders characterized by chronic inflammation and/or fibrosis. 30-40% of ILD patients develop fibrotic disease that is associated with progressive respiratory decline and poor prognosis, particularly in idiopathic pulmonary fibrosis. Current antifibrotic therapies slow disease progression but do not reverse fibrosis, highlighting the need for improved therapeutic strategies. Robust histopathological evaluation in preclinical models is essential for drug development; however, conventional scoring systems are semi-quantitative, labor-intensive, subject to inter-observer variability, and rely on limited field sampling. Here, we introduce FibroSight, a standalone platform for compartment-resolved quantification of lung remodeling in Sirius Red-stained sections. By integrating deep learning- based structural segmentation with color-based feature extraction, FibroSight enables highly automated whole-lobe analysis without requiring complex computational setup. The platform quantifies complementary remodeling parameters, including parenchymal collagen fraction, parenchymal tissue density, nuclear area fraction, parenchymal airspace fraction, and airway- and vascular-associated remodeling. Validated in the bleomycin-induced fibrosis model, FibroSight-derived metrics strongly correlated with expert Ashcroft scoring and showed stronger associations with histological severity than corresponding outputs from a semi-automated ImageJ-based workflow. The platform further distinguished inflammatory from fibrotic remodeling in influenza-induced lung injury and demonstrated translational proof-of-concept applicability in human ILD biopsy specimens. By enabling scalable, reproducible, and multi-compartment histological quantification, FibroSight provides a practical framework for objective assessment of lung remodeling. This approach expands conventional fibrosis evaluation by integrating fibrotic, inflammatory, airway, and vascular-associated readouts, supporting more precise analysis of disease mechanisms and therapeutic responses in preclinical and translational ILD research.

pathology↗

bioRxiv2026

Hypertension-mediated cardiac fibrosis is a mechanical process initiated by smooth muscle cells

Hypertension represents the most prevalent chronic cardiovascular condition, typically culminating in pathological cardiac remodeling characterized by hypertrophy and extensive fibrosis. Although the cellular phenotypes associated with these changes are well-documented, the precise mechanisms by which hypertensive stress is sensed and transduced into a fibrotic program remain poorly defined. To elucidate these mechanisms, we investigated the role of Lysyl oxidase (LOX), an extracellular matrix (ECM)-modifying enzyme that is upregulated during hypertensive stress and associated with cardiovascular diseases. By employing cell-type specific Cre-Lox technology to conditionally delete Lysyl oxidase in either smooth muscle cells (SMCs) or fibroblasts, the primary ECM-secreting cell populations, we demonstrate that fibroblast-specific Lox deletion had no significant impact on the progression of cardiac fibrosis. Conversely, SMC-specific Lox deletion selectively inhibited the fibrotic response without affecting other remodeling parameters, such as cardiac hypertrophy. Notably, in the SMC-specific Lox knockout hearts, fibrosis was restricted to the perivascular niche and failed to propagate into the cardiac interstitium. We find that this transition is a mechanical, ECM-dependent process initiated by SMCs. Our results identify SMCs, rather than fibroblasts, as the primary sensors and initiators of the hypertensive fibrotic response. These findings demonstrate that fibrosis can be uncoupled from other hypertensive manifestations and identify SMC-mediated ECM modification as a potential therapeutic target for treating hypertensive heart disease.

cell biology↗

bioRxiv2025

Intracellular delivery of full-length antibodies via organ targeted lipid nanoparticles

Antibodies are proteins prized for their ability to bind to extracellular antigens with exceptionally high affinities and specificities. These features have motivated researchers to utilize antibody-antigen binding to inhibit intracellular disease targets in the proteome, yet delivery of antibodies into the cytosol of cells has long been a considerable challenge. Here, we outline the development of a novel lipid nanoparticle (LNP) platform for delivering antibodies into cells to selectively inhibit disease-relevant cytosolic targets. This approach efficiently delivers various therapeutic antibodies into multiple cancer cell lines, inhibiting key transcription factors in inflammatory and cancer signaling pathways. We further demonstrate systemic delivery of therapeutic antibodies in disease models, including alpha-synuclein-specific antibodies for Parkinsons disease and RelA-specific IgGs for acute lung injury using targeted LNP formulations. This work establishes a promising method for using LNPs for the delivery of antibody and antibody-derived therapeutics intracellularly to treat numerous proteome targets.

bioengineering↗

bioRxiv2025

FibroTrack: A Standalone Deep Learning Platform for Automated Fibrosis Quantification in Muscle and Cardiac Histology

Accurate fibrosis quantification is essential for understanding muscle and cardiac disease, yet current manual and semi-automated methods remain slow, subjective, and poorly reproducible. We introduce FibroTrack, a standalone deep learning platform with a graphical user interface (GUI) that fully automates fibrosis analysis across Sirius Red (SR), Massons Trichrome (MT), and immunohistochemistry (IHC) stainings. FibroTrack uniquely integrates LAB (lightness, green-red, blue-yellow) color space normalization with a You Only Look Once version 11 (YOLOv11) segmentation model trained on 2,034 histological images. This approach achieved >97% precision and demonstrated excellent concordance with blinded pathologists (Spearman correlation, r = 0.87-0.96). Automated outputs include segmented images and structured spreadsheets, ensuring high reproducibility and scalability. By combining advanced color analysis with state-of-the-art segmentation in an accessible tool, FibroTrack provides a novel, accurate, and clinically relevant solution for high-throughput fibrosis quantification in both preclinical research and pathology practice.

pathology↗

bioRxiv2025

Sphingomonas nivalis sp. nov., a novel psychrophilic bacteria isolated from a permanent snowfield in Glacier Peaks Wilderness Area, Washington State, USA

A novel chemoheterotrophic psychrophilic bacterium, designated as strain I4T was isolated form a permanent snowfield in Washington State, USA. Growth is extremely slow, regardless of temperate (tested between 4{degrees}-25{degrees} C) but was had marginal optimal growth at 8.5{degrees} C. I4T was determined to be able to utilize 102 of the 190 tested carbon sources, 70 or the 95 tested nitrogen sources, 34 or the 59 tested phosphorous sources, and 10 of the 35 tested sulfur sources. I4T was seen to grow from pH 5.0-5.5 but could grow as low as 4.5 pH and as high as 9.5 pH with specific amendments. The genome of I4T was sequenced and it is approximate 4.0 Mb and has a G + C content of 66.2 mol%. Phylogenomic analyses using two independent methods places I4T within the genus Sphingomonas with S. sanguinis being its closest relative. On the basis of its genomic, physiological, and morphological properties, I4T (=ATCC TSD-357T= NCIMB 15472T) is proposed as the type strain of a novel species, Sphingomonas nivalis sp. nov.

microbiology↗

bioRxiv2024

Enteropathogenic Escherichia coli induces Entamoeba histolytica Levy-like movement on fibronectin-rich substrate by reducing traction forces

Amebiasis, caused by Entamoeba histolytica, is a global health concern, affecting millions and causing significant mortality, particularly in areas with poor sanitation. Although recent studies have examined E. histolyticas interaction with human intestinal microbes, the impact of bacterial presence on the parasites motility, mechanical forces, and their potential role in altering invasiveness have not been fully elucidated. In this study, we utilized a micropillar-array system combined with live imaging to investigate the effects of enteropathogenic Escherichia coli on E. histolyticas motility characteristics, F-actin spatial localization, and traction force exerted on fibronectin-coated substrates. Our findings indicate that co-incubation with E. coli significantly enhances the motility of E. histolytica, as evidenced by the enhancement of Levy-like movement patterns, i.e., increased directionality and velocity. This increased motility is accompanied by a reduction in F-actin-dependent traction forces and podosome-like structures on fibronectin-coated substrates, but with increased F-actin localization in the upper part of the cytoplasm. These findings highlight the role of physical interactions and cellular behaviors in modulating the parasites virulence, providing new insights into the mechanistic basis of its pathogenicity. Author SummaryAmebiasis, caused by the protozoan parasite Entamoeba histolytica, is a major global health issue, affecting around 50 million people and resulting in 100,000 deaths annually. The disease is transmitted through contaminated food and water. Upon reaching the intestines, which are teeming with bacteria, E. histolytica begins its invasion by removing the protective mucus layer, followed by adhering to and detaching enterocytes, leading to the disruption and degradation of the epithelial barrier. Afterwards, E. histolytica invades along the fibronectin-rich basement membrane deep into the crypts of Lieberkuhn, eventually penetrating the fibronectin- rich lamina propria. This leads to further tissue destruction and potential dissemination to distant organs, causing severe complications. In our study, we explored how the presence of enteropathogenic bacteria affects the parasites motility and mechanical force generation, both of which are key to its pathogenicity. Using a micropillar-array system and live imaging, we found that exposure to enteropathogenic Escherichia coli significantly increases E. histolyticas motility while reducing its traction force on fibronectin-rich matrices. These changes in behavior highlight the role of bacterial interactions in enhancing the parasites virulence. Our findings provide important insights into the mechanistic basis of E. histolyticas pathogenicity, offering potential avenues for new treatments against amebiasis.

microbiology↗

bioRxiv2024

Fibroblast diversification is an embryonic process dependent on muscle contraction

Fibroblasts are the most common cell type found in connective tissues, known to play major roles in development, homeostasis, regeneration and disease. Although specific fibroblast subpopulations were associated with different biological processes, the mechanisms and unique activities underlying their diversity has not been thoroughly examined. Turning to skeletal muscle development, we set to dissect the variation of muscle-resident fibroblasts (mrFibroblasts). Our results demonstrate mrFibroblasts diversify following the transition from embryonic to fetal myogenesis prior to birth. We find mrFibroblast segregate into two major subpopulations occupying distinct niches, with interstitial fibroblasts residing between the muscle fibers, and delineating fibroblasts sheathing the muscle mass. We further show these subpopulations entail distinct cellular dynamics and transcriptomes. Notably, we find mrFibroblast subpopulations exert distinct regulatory roles on myoblast proliferation and differentiation. Finally, we demonstrate this diversification depends on muscle contraction. Altogether, these findings establish mrFibroblast diversify in a spatio-temporal embryonic process into distinct cell types, entailing different characteristics and roles.

developmental biology↗

bioRxiv2024

Coordination between cytoskeletal organization, cell contraction and extracellular matrix development, is depended on LOX for aneurysm prevention

Distinct, seemingly independent, cellular pathways affecting intracellular machineries or extracellular matrix (ECM) deposition and organization, have been implicated in aneurysm formation. One of the key genes associated with the pathology in both humans and mice is Lysyl oxidase (LOX), a secreted ECM-modifying enzyme, highly expressed in medial vascular smooth muscle cells. To dissect the mechanisms leading to aneurysm development, we conditionally deleted Lox in smooth muscle cells. We find that cytoskeletal organization is lost following Lox deletion. Cell culture assays and in vivo analyses demonstrate a cell-autonomous role for LOX affecting myosin light chain phosphorylation and cytoskeletal assembly resulting in irregular smooth muscle contraction. These results not only highlight new intracellular roles for LOX, but notably they link between multiple processes leading to aneurysm formation suggesting LOX coordinates ECM development, cytoskeletal organization and cell contraction required for media development and function.

cell biology↗

bioRxiv2021

Implications of central carbon metabolism in SARS-CoV-2 replication and disease severity

Viruses hijack host metabolic pathways for their replicative advantage. Several observational trans-omics analyses associated carbon and amino acid metabolism in coronavirus disease 2019 (COVID-19) severity in patients but lacked mechanistic insights. In this study, using patient- derived multi-omics data and in vitro infection assays, we aimed to understand i) role of key metabolic pathways in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) reproduction and ii) its association with disease severity. Our data suggests that monocytes are key to the altered immune response during COVID-19. COVID-19 infection was associated with increased plasma glutamate levels, while glucose and mannose levels were determinants of the disease severity. Monocytes showed altered expression pattern of carbohydrate and amino acid transporters, GLUT1 and xCT respectively in severe COVID-19. Furthermore, lung epithelial cells (Calu-3) showed a strong acute metabolic adaptation following infection in vitro by modulating central carbon metabolism. We found that glycolysis and glutaminolysis are essential for virus replication and blocking these metabolic pathways caused significant reduction in virus production. Taken together, our study highlights that the virus utilizes and re-wires pathways governing central carbon metabolism leading to metabolic toxicity. Thus, the host metabolic perturbation could be an attractive strategy to limit the viral replication and disease severity.

microbiology↗