Biology subjects

Sagy, N.

Publications and source records attributed to Sagy, N..

8 recordsLinked to original sources

bioRxiv2026

Loss of cell-identity DNA methylation tracks division history, not DNA damage

One influential proposal holds that DNA damage drives aging by degrading the epigenome, so that a cell loses the information that specifies what it is. We test that specific proposed driver, not the broader idea that aging involves a loss of epigenetic information. Cell-type-unique CpGs are a direct place to test it. They are the sites where a cell's methylome differs most from every other cell type, so they are where its identity information can be accurately measured. We built such a panel for human skin fibroblasts against twenty primary cell types, and found that most of its 9,150 CpGs behave as a record of proliferation rather than identity. Their methylation state in fibroblasts is shared with continuously proliferating cell lines, consistent with the bulk hypomethylation of late-replicating chromatin that accumulates in culture, and this layer must be separated from identity marks before identity loss can be tested. We then expressed every perturbation as the fraction of the panel's identity information lost beyond baseline-matched background CpGs, using a Bernoulli cross-entropy between the fibroblast code and a generic comparator cell. In 24 matched fibroblast cultures, replicative exhaustion cost 24.3% of the identity information (95% CI 20.2 to 28.7) and RAS activation cost 5.4% (4.6 to 6.1), both at p = 1.2 X 10^-7;. A senescence-inducing dose of X-rays cost nothing: -0.5% (-0.7 to -0.2), with identity CpGs if anything moving slightly further from other cell types than matched background did. The design could detect a loss of 0.4%, about one sixtieth of the exhaustion effect, so the X-ray result is a bounded negative rather than an absence of power. Doxorubicin-induced and irradiation-induced senescence did not move the panel either. Clones that kept dividing after irradiation moved further from other cell types rather than collapsing toward them. In human fibroblasts, loss of identity information tracks prolonged division, not acute DNA damage.

molecular biology↗

bioRxiv2025

Colon-Specific Epigenetic Clocks from Minimal Features Reveal Disease-Driven Aging

Epigenetic clocks estimate chronological and biological age from DNA methylation patterns, but conventional models typically train on hundreds of thousands of CpG sites and large training cohorts. We previously demonstrated that tissue-unique methylation sites change in a predictable manner upon aging and disease. Here, we demonstrate that clocks built from tissue-unique methylation sites enable accurate age prediction in the human colon using a compact feature set and limited training data. We trained a machine learning model on healthy colon tissue, identifying CpG sites that capture both chronological age and anatomical location (proximal vs. distal). This clock maintains high predictive performance (r = 0.978; MAE 3.9 years) while using an order of magnitude fewer sites and samples than traditional approaches. Applying the model to tissues from individuals with HIV infection, inflammatory bowel disease (IBD), and colonic polyps reveals consistent patterns of accelerated aging, while aspirin treatment is associated with partial deceleration. Our findings establish tissue-unique CpGs as a powerful basis for efficient, interpretable clocks and offer new insights into how chronic inflammation and neoplasia shape the aging landscape of the colon.

molecular biology↗

bioRxiv2025

Reversible and Causal Epigenetic Information Loss in Liver Aging and Disease

The loss of epigenetic information has been proposed as a driver of aging and diseases, but the reversibility and causality of this process remain underexplored. Here we analyze liver-unique methylation sites - genomic loci that show distinct methylation patterns in the liver compared to other tissues. Upon disease progression, these sites overwhelmingly regress toward the pan-tissue average. In addition, we demonstrate that this regression also occurs in a majority of these sites during normal aging. Using Mendelian randomization analysis, we identify significant enrichment of liver-unique methylation sites in causal aging-associated loci, particularly sites that are highly methylated in healthy liver. Remarkably, repeated fasting, a metabolic intervention known to improve liver function, partially restores the liver-unique methylation patterns at these sites. This restoration also occurs in isolated hepatocytes subjected to fasting-mimicking conditions, suggesting the effect is cell-autonomous rather than due to changes in tissue composition. The liver-unique methylation sites are enriched for binding sites of key metabolic transcription factors and show significant overlap with genetic variants associated with liver disease risk, suggesting a mechanistic link between epigenetic information loss and liver dysfunction. Our findings establish epigenetic information loss as both a marker and mediator of liver aging and disease, while demonstrating its potential reversibility through metabolic interventions. Graphical abstract: Reversible information loss at liver-unique methylation sitesLiver-unique sites, showing higher (UH) or lower (UL) methylation levels, regress to the pan-tissue average upon aging and disease. UH are enriched for methylation sites causal to the aging process, while UL are enriched for liver-specific enhancers and PPAR- binding sites. Upon repeated fasting, both UL and UH diverge away from the pan-tissue average, partially restoring the more youthful and disease-free epigenetic state. O_FIG O_LINKSMALLFIG WIDTH=174 HEIGHT=200 SRC="FIGDIR/small/639802v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@6d9ce9org.highwire.dtl.DTLVardef@58a2f6org.highwire.dtl.DTLVardef@132ff20org.highwire.dtl.DTLVardef@10b9acc_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation

Characterization of DNA binding sites for specific proteins is of fundamental importance in molecular biology. It is commonly addressed experimentally by chromatin immunoprecipitation and sequencing (ChIP-seq) of bulk samples (103-107 cells). We have developed an alternative method that uses a Chromatin Antibody-mediated Methylating Protein (ChAMP) composed of a GpC methyltransferase fused to protein G. By tethering ChAMP to a primary antibody directed against the DNA-binding protein of interest, and selectively switching on its enzymatic activity in situ, we generated distinct and identifiable methylation patterns adjacent to the protein binding sites. This method is compatible with methods of single-cell methylation-detection and single molecule methylation identification. Indeed, as every binding event generates multiple nearby methylations, we were able to confidently detect protein binding in long single molecules. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/567792v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@dac365org.highwire.dtl.DTLVardef@522ecaorg.highwire.dtl.DTLVardef@17ddb38org.highwire.dtl.DTLVardef@1c371b0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO (i) ChAMP is added to fix and permeabilized cells, where it binds (ii) any antibody, and upon the addition of SAM, methylates nearby GpC sites, to be detected by sequencing (iii-iv). C_FIG

molecular biology↗

bioRxiv2023

Immunorecognition of Streptococcus mutans secreted proteins protects against caries by limiting tooth adhesion

Childhood caries, a chronic disease affecting 60-90% of children in industrialized countries, results in lesions in primary and permanent dentition, leading to hospitalizations, emergency room visits, high treatment costs, and loss of school days. It diminishes the childs ability to learn and increases the risk of caries in adulthood. Despite multiple risk factors for caries, significant interpersonal variability unaccounted for by these factors exists. The immune system generates a personal antibody repertoire that helps maintain a balanced and healthy oral microbiome. Streptococcus mutans is a key bacterium in caries development. Utilizing mass-spectrometry, we examined which S. mutans proteins are identified by antibodies of children with and without caries and identified a core set of proteins recognizable by the immune system of most individuals. This set was enriched with proteins enabling bacterial adhesion. To study the physiological relevance of these findings, we tested the ability of saliva to prevent S. mutans adherence to tooth surfaces. Saliva from caries-free individuals, but not children with caries, was found to hinder the binding of S. mutans to teeth. These findings delineate the S. mutans proteome targeted by the immune system and suggest that the inhibition of bacterial adherence to teeth is a primary mechanism employed by the immune system to maintain oral balance and prevent caries formation. These discoveries offer fresh insights into the immune systems role in preserving oral health and preventing caries development. Targeting S. mutans proteins implicated in bacterial adhesion could be a promising strategy for preventing childhood caries.

microbiology↗

bioRxiv2023

Epigenetic information loss is a common feature of multiple diseases and aging

Aging is a major risk factor for a plethora of diseases. The information theory of aging posits that epigenetic information loss is a principal driver of the aging process. Despite this, the connection between epigenetic information loss and disease has not been thoroughly investigated. Here, we analyzed tissue-unique methylation patterns in healthy and diseased organs, revealing that for several diseases these patterns degrade, regressing to a mean form. We interpret this as epigenetic information loss, where tissue-unique patterns erode. Information loss is not limited to diseases. Age-related erosion of unique methylation patterns was observed in some tissues and cells, while other tissues and cells diverged away from the mean. Our findings demonstrate that analyzing methylation patterns in tissue-unique sites can effectively distinguish between patients and healthy controls across a range of diseases, and underscore the role of epigenetic information loss as a common feature in various pathological conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/539727v3_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@12049e0org.highwire.dtl.DTLVardef@d214c7org.highwire.dtl.DTLVardef@52425forg.highwire.dtl.DTLVardef@839011_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Tissue unique methylation pattern regress toward the mean upon disease. A single methylation site, showing low methylation in the liver and high in every other tissue, becomes more methylated in diseased livers. C_FIG

molecular biology↗

bioRxiv2022

Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression

Chronological and biological age correlate with DNA methylation levels at specific sites in the genome. Linear combinations of multiple methylation sites, termed epigenetic clocks, can inform us of the chronological age and predict multiple health-related outcomes. However, why some sites correlate with lifespan, healthspan, or specific medical conditions remains poorly understood. Kidney fibrosis is the common pathway for Chronic Kidney Disease, which affects 10% of Europe and USA population. Here we identify epigenetic clocks and methylation sites that correlate with kidney function. Moreover, we identify methylation sites that have a unique methylation signature in the kidney. Methylation levels in the majority of these sites correlates with kidney state and function. When kidney function deteriorates, all of these sites regress towards the common methylation pattern observed in other tissues. Interestingly, while the majority of sites are less methylated in the kidney and become more methylated with loss of function, a fraction of the sites are highly methylated in the kidney and become less methylated when kidney function declines. These methylation sites are enriched for specific transcription-factor binding sites. In a large subset of sites, changes in methylation pattern are accompanied by changes in gene expression in kidneys of chronic kidney disease patients. These results support the information theory of aging, and the hypothesis that the unique tissue identity, as captured by methylation patterns, is lost as tissue function declines. However, this information loss is not random, but guided towards a baseline that is dependent on the genomic loci.

bioinformatics↗

bioRxiv2018

Prediction and control of symmetry breaking in embryoid bodies by environment and signal integration

During early embryogenesis, mechanical signals, localized biochemical signals and neighboring cell layers interaction coordinate around anteroposterior axis determination and symmetry breaking. Deciphering their relative roles, which are hard to tease apart in vivo, will enhance our understanding of how these processes are driven. In recent years, in vitro 3D models of early mammalian development, such as embryoid bodies (EBs) and gastruloids, were successful in mimicking various aspects of the early embryo, providing high throughput accessible systems for studying the basic rules shaping cell fate and morphology during embryogenesis. Using Brachyury (Bry), a primitive streak and mesendoderm marker in EBs, we study how contact, biochemical and neighboring cell cues affect the positioning of a primitive streak-like locus, determining the AP axis. We show that a Bry-competent layer must be formed in the EB before Bry expression initiates, and that Bry onset locus selection depends on contact points of the EB with its surrounding. We can maneuver Bry onset to occur at a specific locus, a few loci, or in an isotropic peripheral pattern. By spatially separating contact and biochemical signal sources, we show these two modalities can be integrated by the EB to generate a single Bry locus. Finally, we show Foxa2+ cells are predictive of the future location of Bry onset, demonstrating an earlier symmetry-breaking event. By delineating the temporal signaling pathway dependencies of Bry and Foxa2, we were able to selectively abolish either, or spatially decouple the two cell types during EB differentiation. These findings demonstrate multiple inputs integration during an early developmental process, and may prove valuable in directing in vitro differentiation.

developmental biology↗