Biology subjects

Bar, A.

Publications and source records attributed to Bar, A..

10 recordsLinked to original sources

bioRxiv2026

Drug-centric knowledge graph: representing therapeutic modality, pharmacology and multiscale biology

Biomedical knowledge graphs link targets to mechanisms, diseases and phenotypes, but target-centered representations omit much of what distinguishes therapeutic interventions. We introduce a drug-centric knowledge graph, whose identity model, schema and information-selection priorities are organized around the therapeutic intervention, and a graph built on this design. Each intervention has one identity, linked through relation types shared by all compounds, including target actions, indications, adverse effects, classifications, half-life and direct links to pathways, Gene Ontology concepts, cells and anatomy, and through modality-specific relation types describing small-molecule chemistry, antibody sequences and formats, protein-therapy sequences and antibody-drug conjugate components. Integrating 38 source resources, the graph contains 166,261 nodes of 27 types, 8,106,906 directed edges of 129 relation types and 18,429 compounds in eight therapeutic categories. Construction combines source-specific extraction, compound-identity resolution, language-model-assisted vocabulary and predicate mapping, confidence scoring and connectivity filtering; an expert-reviewed workflow adds investigational therapeutics without altering the base graph. The design offers a reusable template for representing interventions as structured, multimodal objects.

systems biology↗

bioRxiv2025

Vitamin D differentially modulates effector and regulatory T-cell migration across the blood-brain barrier

Multiple sclerosis (MS) is an inflammatory disease of the CNS influenced by a combination of genetic predisposition and environmental factors. Vitamin D (VitD) deficiency is considered a major risk factor for MS. While VitD is associated with immunomodulatory roles, the exact mechanisms by which VitD protects from disease are still largely unknown. CD4 T cells play a key role in MS pathogenesis with autoimmune effector T cells (Teff) infiltrating the CNS across the blood-brain barrier (BBB) and regulatory T cells (Treg) displaying impaired functions. Here we show that treatment of human CD4 T cells with the active form of VitD (1,25-Dihydroxyvitamin D3; 1,25(OH)2D3) decreased cell-surface expression of 4{beta}1- and L{beta}2-integrins on Teff but not Treg and reduced Teff adhesion to their endothelial ligands VCAM-1 and ICAM-1. By employing live cell imaging, we observed that VitD treatment reduced arrest of Teff but not Treg to the BBB as well as ICAM-1 and VCAM-1 under physiological flow in vitro and differentially affected post-arrest behaviour of Teff versus Treg on the BBB under physiological flow. Furthermore, VitD treatment favoured the migration of Treg over Teff across the BBB under static and flow conditions in vitro. In vivo live cell imaging showed that VitD reduced T cell arrest on the inflamed BBB during autoimmune neuroinflammation. Finally, VitD also reduced expression of integrins mediating CNS homing on pathogenic CD4 T cells isolated from the CSF of persons with MS (PwMS). As VitD treatment did not alter barrier properties or adhesion molecule profile of our BBB model we propose a beneficial effect of VitD supplementation in PwMS by reducing CNS trafficking of pro-inflammatory T cells while leaving CNS entry of Treg unaffected.

immunology↗

bioRxiv2024

Endothelial miR-34a deletion guards against aneurysm development despite endothelial dysfunction

ObjectivesOur previous study reported a reciprocal link between NRF2, a stress-responsive cytoprotective transcription factor, and aortic and endothelial cell (EC) ageing. We also found that NRF2 transcriptional knockout (tKO) mice are prone to abdominal aortic aneurysm (AAA) development. Given that miRNA-34a is a marker of ageing, in this study we explored its relationship with NRF2 and its role in vascular function and AAA formation. Approach and resultsThe experiments were performed in primary human aortic endothelial cells (HAECs) from young and aged donors and mice devoid of NRF2 transcriptional activity and endothelial miR-34a. The normolipidemic mice were challenged with angiotensin II (Ang II) to develop AAA. We show that premature NRF2-dependent aging of aortic endothelial cells (ECs) depends on miR-34a. Infusion of hypertensive Ang II in mice increases miR-34a in the aortic endothelial layer and serum, especially in mice which develop AAA. Mice deficient in endothelial miR-34a (miR-34a{Delta}EC) display severe EC dysfunction. Despite that, such mice are protected from AAA development, also on the NRF2 tKO background. Ang II infusion increases proliferation of intimal ECs in these mice. The protective effect of endothelial miR-34a deletion on AAA formation is reversed by rapamycin that suppresses EC proliferation. MTA2, but not SIRT1, is a direct target of miR-34a abrogating Ang II-induced EC proliferation. ConclusionsThese findings reveal that AAA development in NRF2 tKO mice relies on endothelial miR-34a overexpression. Deletion of endothelial miR-34a protects mice from AAA despite inducing endothelial cell dysfunction. The fine-tuning of EC proliferation may play a therapeutic role in the treatment of aneurysm.

pathology↗

bioRxiv2024

Quantification of beta cell carrying capacity in prediabetes

Prediabetes, a subclinical state of high glucose, carries a risk of transition to diabetes. One cause of prediabetes is insulin resistance, which impairs the ability of insulin to control blood glucose. However, many individuals with high insulin resistance retain normal glucose due to compensation by enhanced insulin secretion by beta cells. Individuals seem to differ in their maximum compensation level, termed beta cell carrying capacity, such that low carrying capacity is associated with a higher risk of prediabetes and diabetes. Carrying capacity has not been quantified using a mathematical model and cannot be estimated directly from measured glucose and insulin levels in patients, unlike insulin resistance and beta cell function which can be estimated using HOMA-IR and HOMA-B formula. Here we present a mathematical model of beta cell compensation and carrying capacity, and develop a new formula called HOMA-C to estimate it from glucose and insulin measurements. HOMA-C estimates the maximal potential beta cell function of an individual, rather than the current beta cell function. We test this approach using longitudinal cohorts of prediabetic people, finding 10-fold variation in carrying capacity. Low carrying capacity is associated with higher risk of transitioning to diabetes. We estimate the timescales of beta cell compensation and insulin resistance using large datasets, showing that, unlike previous mathematical models, the new model can explain the slow rise in glucose over decades. Our mathematical understanding of beta cell carrying capacity may help to assess the risk of prediabetes in each individual.

systems biology↗

bioRxiv2023

Unifying design principles of endocrine gland mass and its regulatory circuits

Hormones are regulatory molecules that impact physiological functions. Much is known about individual hormones, but general rules that connect the regulatory logic of different hormone systems are limited. In this study, we analyzed a range of human hormone systems using a mathematical approach to integrate knowledge on endocrine cells, target tissues and regulation, to uncover unifying principles and regulatory circuits. We find that the number of cells in an endocrine gland is proportional to the number of cells in its target tissues, as one single endocrine cell serves approximately 2000 target cells. We identified five classes of regulatory circuits, each has specific regulatory functions such as homeostasis or allostasis. The most complex class includes an intermediate gland, the pituitary, which can otherwise be considered redundant and exposes to fragilities. We suggest a tradeoff: with the price of fragilities comes advantages -amplification, buffering of hypersecreting tumors, and faster response times. By elucidating these unifying principles and circuits, this study deepens our understanding of the control of endocrine processes and builds the foundation for systems endocrinology.

physiology↗

bioRxiv2023

Pregnancy and postpartum dynamics revealed by an atlas of millions of lab tests

Pregnancy and delivery involve dynamic alterations in many physiological systems. However, the physiological dynamics during pregnancy and after delivery have not been systematically analyzed at high temporal resolution in a large human population. Here we present the dynamics of 76 lab tests based on a cross-sectional analysis of roughly 41 million measurements from over 300,000 pregnancies. We analyzed each test at weekly intervals from 20 weeks preconception to 80 weeks postpartum, providing detailed temporal profiles. About half of the tests take three months to a year to return to baseline during postpartum, highlighting the physiological load of childbirth. The precision of the data revealed effects of preconception supplements, overshoots after delivery and intricate temporal responses to changes in blood volume and renal filtration rate. Pregnancy complications - gestational diabetes, pre-eclampsia and postpartum hemorrhage - showed distinct dynamical changes. These results provide a comprehensive dynamic portrait of the systems physiology of pregnancy.

physiology↗

bioRxiv2023

Excitable dynamics of flares and relapses in autoimmune diseases

Many autoimmune diseases show flares in which symptoms erupt and then decline. A prominent example is multiple sclerosis (MS) in its relapsing-remitting phase. Mathematical models attempting to capture the flares in multiple sclerosis have often been oscillatory in nature, assuming a regular pattern of symptom flare-ups and remissions. However, this fails to account for the non-periodic nature of flares, which can appear at seemingly random intervals. Here we propose that flares resemble excitable dynamics triggered by stochastic events and show that a minimal mathematical model of autoimmune cells and inhibitory regulatory cells can provide such excitability. In our model, autoimmune response releases antigens that cause autoimmune cells to expand in a positive feedback loop, while regulatory cells inhibit the autoimmune cells in a negative feedback loop. The model can quantitatively explain the decline of MS relapses during pregnancy and their postpartum surge based on lymphocyte dynamics, as well as the decline in MS relapses with age. The model also points to potential therapeutic targets and predicts that even small modulation of regulatory T cell production, removal or activity can have a large effect on relapse rate. Excitable dynamics may underlie flares and relapses found across autoimmune diseases, thus providing an understanding that may help improve treatment strategies.

systems biology↗

bioRxiv2023

Ribosomal protein L24 modulates mammalian microRNA processing and transfer RNA fragment production

The evolutionary mechanism(s) underlying the expression of novel microRNAs (miRs) are still elusive. To explore this issue, we studied the expression of intronic primate-specific hsa-miR-608, located in the Semaphorin 4G (SEMA4G) gene. Engineered humanized mice carrying human miR-608 flanked by 250 bp in the murine Sema4g gene expressed miR-608 in several tissues. Moreover, miR-608 flanked by shortened fragments of its human genome region elevated miR-608 levels by 100-fold in murine and human-originated cells, identifying the 150 nucleotides 5 to pre-miR-608 as an active promoter. Surprisingly, pulldown of this 5 sequence revealed tight interaction with ribosomal protein L24 (RPL24), which inhibited miR-608 expression. Furthermore, RPL24 depletion altered the levels of 22 miRs, and we discovered that direct interaction of RPL24 with DDX5, a component of the large microprocessor complex, inhibits pri-miR processing. Moreover, RPL24 depletion resulted in Angiogenin (ANG)-mediated production of 5-half tRFs in human cells, and altered plant tRF profiles. Expanding previous reports that RPL24 regulates miR processing in Arabidopsis thaliana, we implicate RPL24 in an evolutionarily-conserved regulation of miR processing and tRF production. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/539194v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@4f2058org.highwire.dtl.DTLVardef@d4a2cdorg.highwire.dtl.DTLVardef@c7786org.highwire.dtl.DTLVardef@7b1608_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Human hormone seasonality

Hormones control the major biological functions of stress response, growth, metabolism and reproduction. In animals these hormones show pronounced seasonality, with different set-points for different seasons. In humans, the seasonality of these hormones remains unclear, due to a lack of datasets large enough to discern common patterns and cover all hormones. Here, we analyze an Israeli health record on 46 million person-years, including millions of hormone blood tests. We find clear seasonal patterns: the effector hormones peak in winter-spring, whereas most of their upstream regulating pituitary hormones peak only months later, in summer. This delay of months is unexpected because known delays in the hormone circuits last hours. We explain the precise delays and amplitudes by proposing and testing a mechanism for the circannual clock: the gland masses grow with a timescale of months due to trophic effects of the hormones, generating a feedback circuit with a natural frequency of about a year that can entrain to the seasons. Thus, humans may show coordinated seasonal set-points with a winter-spring peak in the growth, stress, metabolism and reproduction axes.

systems biology↗

bioRxiv2020

Hormonal dysregulation after prolonged HPA axis activation can be explained by changes of adrenal and corticotroph masses

Stress activates a complex network of hormones known as the Hypothalamic-Pituitary-Adrenal (HPA) axis. The HPA axis is dysregulated in chronic stress and psychiatric disorders, but the origin of this dysregulation is unclear and cannot be explained by current HPA models. To address this, we developed a new mathematical model for the HPA axis that incorporates changes in the total functional mass of the HPA hormone-secreting glands. The mass changes are caused by the HPA hormones which act as growth factors for the glands in the axis. We find that the HPA axis shows the property of dynamical compensation, where gland masses adjust over weeks to buffer variation in physiological parameters. These mass changes explain the experimental findings on dysregulation of cortisol and ACTH dynamics in alcoholism, anorexia and postpartum. Dysregulation occurs for a wide range of parameters, and is exacerbated by impaired glucocorticoid receptor (GR) feedback, providing an explanation for the implication of GR in mood disorders. These findings suggest that gland-mass dynamics may play an important role in the pathophysiology of stress-related disorders. Author SummaryThe HPA axis is a neuroendocrine axis that is activated in response to stressors. The classical description of this axis includes three hormones that act in a cascade, with the final hormone cortisol inhibiting the two upstream hormones, ACTH and CRH. This classical picture has timescales of hours due to hormone half-lives, and cannot explain phenomena on the scale of weeks to months associated with this axis, such as the dysregulation observed in depression, alcohol addiction, postpartum, and other conditions. Here, we use a minimal-model approach to add to the classical model two known interactions in which CRH and ACTH not only regulate downstream hormones, but also act as growth factors for the cells that secrete these hormones. This creates a physiological circuit that can maintain total cell mass and buffer parameter changes. It has a fragility in which after prolonged stress, the total cell functional masses grow and take weeks to return to baseline. This is sufficient to explain the specific dynamics of hormone dysregulation found in several contexts. It also quantifies the effect of the cortisol (glucocorticoid) receptor on resilience to prolonged stress. Our findings suggest that interactions between hormones and cell functional mass may play an important role in HPA axis regulation on the timescale of weeks to months. Synopsis O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY The HPA axis helps the body adapt to stress, but becomes dysregulated after prolonged activation, with clinical consequences. The origin of this dysregulation is unclear. We provide a mechanism for dysregulation based on the effect of the HPA hormones as growth factors for their downstream glands. O_LIA mathematical model that includes gland functional mass dynamics, introduces a new slow timescale of weeks to the HPA axis; previous models had only fast timescales of hours. C_LIO_LIThe gland masses grow during prolonged activation, providing dynamical compensation, and recover with overshoots over weeks after withdrawal of activation. C_LIO_LIThese overshoots are sufficient to explain the observed HPA dysregulation in pathological conditions, and clarify the role of glucocorticoid receptors in resilience to prolonged stress. C_LI

physiology↗