Biology subjects

Shemesh, A.

Publications and source records attributed to Shemesh, A..

12 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

Site-specific genome engineering of primary human natural killer cells for programmable anti-tumor function

Natural killer (NK) cells are emerging as a promising platform for engineered adoptive cell therapies. However, gene editing in NK cells remains challenging, and more effective strategies are needed. Here, we established a robust, feeder-free, and modular workflow for genome engineering in primary human NK cells, combining CRISPR/Cas9 with AAV6-mediated transgene delivery. Efficient site-specific transgene integration was achieved at various loci and can be coupled with concurrent disruption of the target locus in a single editing step. Furthermore, transgene expression was tunable according to the integration site and promoter. We applied this strategy to target a chimeric antigen receptor (CAR) transgene to a panel of inhibitory NK receptor loci, establishing a synergistic approach to enhance anti-tumor activity and facilitate the reliable comparison of CAR variants without expression bias. We identified TIGIT as an ideal locus that supports strong CAR expression and anti-tumor function. This genome engineering framework, which leverages multiple, complementary and precisely controlled genetic edits, can support the rational design of future NK-cell therapies tailored to overcome cell-intrinsic limitations and tumor-specific barriers.

immunology↗

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

FcεR1γ-based Activating Chimeric Antigen Receptors enhanced Natural Killer cell function against HLA-E+ cells

Fc{varepsilon}R1{gamma} is a transmembrane adaptor protein regulating NKp30, NKp46, and CD16 expression and function in human NK cells. HLA-E expression by cancer cells suppresses NK cell function through interaction with NKG2A. Here, we engineered human NK cells to express a modified Fc{varepsilon}R1{gamma} with a 4-1BB co-stimulatory motif. Fc{varepsilon}R1{gamma}41BB expression led to upregulation of NKp30, NKp46, and CD16 expression and enhanced NKp30 and CD16-mediated target cell lysis. Against cells expressing HLA-E, Fc{varepsilon}R1{gamma}41BB improved NK cell lytic function relative to Fc{varepsilon}R1{gamma}. We then generated an CD19ScFv-CD8hinge-Fc{varepsilon}R1{gamma}41BB(TM-IC) CAR (FCRG10). Engineering human NK cells to express FCRG10 led to upregulation of NKp30 and CD16, and improved NK cell-mediated cytotoxicity against cells co-expressing B7H6, CD19, and HLA-E relative to NK cells expressing the conventional CD19CAR41BB-CD3{zeta} with a CD8 transmembrane domain. Our results indicate that modification of Fc{varepsilon}R1{gamma} enhanced NK cell lytic function mediated by several activating receptors and improved CAR NK cell response in conditions favoring NK cell suppression by HLA-E. Our work may contribute to NK cell-based cancer immunotherapy mediated by co-recognition of stress-induced ligands, antibody-coated cells, and tumor-associated antigens.

immunology↗

bioRxiv2024

Spleen Tyrosine Kinase (SYK) negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy

NK cells express activating receptors that signal through ITAM-bearing adapter proteins. The phosphorylation of each ITAM creates binding sites for SYK and ZAP70 protein tyrosine kinases to propagate downstream signaling including the induction of Ca2+ influx. While all immature and mature human NK cells co-express SYK and ZAP70, clonally driven memory or adaptive NK cells can methylate SYK genes and signaling is mediated exclusively using ZAP70. Here, we examined the role of SYK and ZAP70 in a clonal human NK cell line KHYG1 by CRISPR-based deletion using a combination of experiments and mechanistic computational modeling. Elimination of SYK resulted in more robust Ca++ influx after cross-linking of the CD16 and NKp30 receptors and enhanced phosphorylation of downstream proteins, whereas ZAP70 deletion diminished these responses. By contrast, ZAP70 depletion increased proliferation of the NK cells. As immature T cells express both SYK and ZAP70 but mature T cells often express only ZAP70, we transduced the human Jurkat cell line with SYK and found that expression of SYK increased proliferation but diminished TCR-induced Ca2+ flux and activation. We performed transcriptional analysis of the matched sets of variant Jurkat and KHYG1 cells and observed profound alterations caused by SYK expression. As depletion of SYK in NK cells increased their activation, primary human NK cells were transduced with a CD19-targeting CAR and were CRISPR edited to ablate SYK or ZAP70. Deletion of SYK resulted in more robust cytotoxic activity and cytokine production, providing a new therapeutic strategy of NK cell engineering for cancer immunotherapy.

immunology↗

bioRxiv2024

CITE-seq analysis reveals human cytomegalovirus and diabetes-associated adaptive NK cell alterations in cardiovascular disease.

Coronary artery disease (CAD) is a leading cause of mortality worldwide with Diabetes and human cyto-megalovirus (HCMV) infection as risk factors. CADs influence on human NK cells is not well characterized. CITE-seq analysis of a CAD cohort of 61 patients revealed distinctly higher NK cell SPON2 expression and lower IFNG expression in severe CAD patients. Interestingly, HCMV+ patients displayed lower SPON2 ex-pression while diabetes status reversed the HCMV effect. Diabetes led to diminished adaptive Fc{varepsilon}RI{gamma}-/low NK cell frequencies and was associated with a higher PBMC IL15/TGFB transcript ratio, while TGFB in-creased in severe CAD. SPON2 expression corresponded to changes in conventional vs. adaptive NK cell frequencies, and SPON2/IFNG ratio decreased in inflamed plaque tissue with an increased adaptive NK cell gene signature and was increased in severe CAD patients. Our results indicate that the SPON2/IFNG ra-tio and adaptive NK cell gene signature associated with stenosis severity or inflammation in CAD.

immunology↗

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↗

bioRxiv2023

Ribosomal Protein SA (RPSA) is required for localized translation and sarcomere maintenance

Cardiomyocyte sarcomeres contain localized ribosomes, but the factors responsible for their localization and the significance of localized translation are unknown. Using proximity labeling, we identified Ribosomal Protein SA (RPSA) as a Z-line protein. In cultured cardiomyocytes, the loss of RPSA led to impaired local protein translation and reduced sarcomere integrity. By employing CAS9 expressing mice along with adeno-associated viruses expressing CRE recombinase and single-guide RNAs targeting Rpsa, we knocked out Rpsa in vivo and observed mis-localization of ribosomes and diminished local translation. These genetic mosaic mice with Rpsa knockout in a subset of cardiomyocytes developed dilated cardiomyopathy, featuring atrophy of RPSA-deficient cardiomyocytes, compensatory hypertrophy of unaffected cardiomyocytes, left ventricular dilation, and impaired contractile function. We demonstrate that RPSA C-terminal domain is sufficient for localization to the Z-lines and that if the microtubule network is disrupted RPSA loses its sarcomeric localization. These findings highlight RPSA as a ribosomal factor essential for ribosome localization to the Z-line, facilitating local translation and sarcomere maintenance.

cell biology↗

bioRxiv2022

Sex differences in coronary artery disease and diabetes revealed by scRNA-Seq and CITE-Seq of human CD4+ T cells

BackgroundDespite the decades-old knowledge that diabetes mellitus (DM) is a major risk factor for cardiovascular disease (CVD), the reasons for this association are only partially understood. Among the immune cells involved in CVD development, accumulating evidence supports the critical role of T cells as drivers and modifiers of this condition. CD4+ T cells are commonly found in atherosclerotic plaques. The activity and distribution of CD4+ T cell subsets differs between the sexes. MethodsPeripheral blood mononuclear cells (PBMCs) of 61 men and women who underwent cardiac catheterization were interrogated by single cell RNA sequencing (scRNA-Seq, [~]200,000 cells) combined with 49 protein markers (CITE-Seq). Coronary artery disease (CAD) was quantified using Gensini scores, with scores above 30 considered CAD+ and below 6 considered CAD-. Four pairs of groups were matched for clinical and demographic parameters. To test how DM changed cell proportions and gene expression, we compared matched groups of diabetic and non-diabetic subjects. We analyzed 41,782 single CD4+ T cell transcriptomes for sex differences in 61 mostly statin-treated coronary artery disease patients with and without DM. ResultsWe identified 16 clusters in CD4 T cells. The proportion of cells in CD4 cluster 8 (CD4T8, CCR2+ Em) was significantly decreased in CAD+, especially among DM+ participants. The proportions of cells in CD4T2, CD4T11, CD4T16 were increased and CD4T13 was decreased in CAD+ among DM+Statin+ participants. CD4T12 was increased in DM+ participants. In female participants, CD4T8, 12, and 13 were decreased compared to in male participants. In CD4 T cells, 31 genes showed significant and coordinated upregulation in both CAD and DM. The DM gene signature was partially additive to the CAD gene signature. ConclusionsWe conclude that CAD and DM are clearly reflected in PBMC transcriptomes and that significant differences exist between women and men and between subjects treated with statins or not.

immunology↗

bioRxiv2021

Natural Killer cell division regulates FcεRIγ expression downstream of mTOR activity

The expansion of human Fc{varepsilon}RI{gamma}-/low (FcR{gamma}-/low) natural killer (NK) cells accrues during viral infections; however, the molecular mechanisms regulating FcR{gamma} expression is not well defined and can have implication for host protection and NK cell immunotherapy. Our analysis of NK cell subsets in lung transplant patients during rapamycin treatment revealed significantly lower FcR{gamma} levels in the NK cell population. Moreover, lower FcR{gamma} levels in healthy donors were associated with low mTORC1/C2 activity and low T-bet expression. Cell division suppression by rapamycin or TGF{beta} suppressed FcR{gamma} upregulation during IL-2 receptor stimulation, whereas promoting NK cell division by co-inhibiting FOXO1 activity restored FcR{gamma} upregulation. These results suggest that the human FcR{gamma}-/low NK cell phenotype is associated with cell division suppression and reduced mTOR activity.

immunology↗

bioRxiv2020

Combined protein and transcript single cell RNA sequencing reveals cardiovascular disease and HIV signatures

Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single cell (sc)RNA sequencing in PBMCs. Among 31 participants in the WIHS Study, we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs and Louvain clustering, we identified 58 subsets among CD4 T, CD8 T, B, NK cells and monocytes. This resolution was superior to flow cytometry, mass cytometry or scRNA-sequencing without antibodies. Since the transcriptome was not needed for cell identification, combined protein and transcript scRNA-Seq allowed for the assessment of disease-related changes in transcriptomes and cell type proportion. As a proof-of-concept, we showed such differences between healthy and matched individuals living with HIV with and without cardiovascular disease. In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.

immunology↗