Biology subjects

Ambrosio, F.

Publications and source records attributed to Ambrosio, F..

11 recordsLinked to original sources

bioRxiv2025

Decay in transcriptional information flow is a hallmark of cellular aging

Aging is marked by the progressive loss of cellular function, yet the organizing principles underlying this decline remain unclear. Although molecular fingerprints of aging are diverse, many converge on disruption of the interrelated and overlapping communication networks that coordinate molecular activity. Here, we apply information theory to quantify age-related corruption in gene regulation by modeling regulatory interactions between transcription factors (TFs) and their target genes (TGs) as a multi-input multi-output communication channel. Using an analytically tractable probabilistic model and single-cell RNA-sequencing data from multiple tissues, we find that the mutual information (a measure of information transfer) between TFs and TGs declines with age across all ten tissues analyzed, establishing loss of regulatory information transmission as a hallmark of aging. Structural analysis of the regulatory network reveals that aging degrades communication primarily through input distribution mismatch, reflecting a loss of coordinated TF activity, rather than channel corruption, or the inability of TFs to reliably activate or inhibit their targets. This mismatch is caused by increased network centralization and loss of stabilizing feedback motifs, leading to reduced robustness to random perturbations. Notably, in silico upregulation of a small set of TFs restores youthful information transfer and gene expression levels, suggesting that targeted reinforcement of key regulatory nodes may rejuvenate aged networks.

systems biology↗

bioRxiv2025

Decoding menopause-induced tissue fibrosis using pan-tissue network inference

Menopause drives fibrotic remodeling and consequent tissue dysfunction across multiple organs, yet the tissue-conserved versus tissue-specific mechanisms underlying this phenomenon remain poorly defined. Here, we employed a network inference framework to uncover how menopause triggers coordinated shifts in intercellular signaling cascades that promote fibrosis. We leveraged publicly archived single-cell RNA-sequencing data from the liver, lung, pancreas, and skeletal muscle of ovariectomized and control mice. Given the central role of immune cells in orchestrating inflammation and fibrosis, we focused our analysis on immune cell populations. Using canonical markers of immune cells, we annotated major cell types and reconstructed cell-cell interaction networks to map transcriptional responses to hormonal shifts. Network analysis revealed pervasive reshaping of intercellular signaling common to all tissues evaluated in the setting of menopause. Within this immune-centered framework, we found that estrogen-responsive macrophages consistently function as major signaling hubs across all tissues evaluated, exhibiting extensive interactions with myofibroblasts--key drivers of extracellular matrix production and fibrotic remodeling. Notably, these shared signaling patterns were not detectable using conventional differential gene expression analysis, which revealed minimal overlap in gene-level responses in macrophages across tissues. In addition to conserved patterns, we identified tissue-specific interaction networks that reflect unique immune adaptations to hormonal loss. As an example, natural killer cells acted as a signaling hub in muscle-specific patterns, suggesting their direct contribution to menopausal skeletal muscle adaptation. Tissue-specific patterning was also evident in the liver, lung, and pancreas, where other immune cell types, such as CD8+ T cells and endothelial cells, functioned as prominent signaling hubs, indicating diverse remodeling of the immune microenvironment. The network approach introduced here represents a systems-level framework for mapping multicellular network rewiring following hormonal depletion and highlights conserved immune-stromal modules as potential therapeutic targets to prevent menopause-associated dysfunction.

systems biology↗

bioRxiv2023

Mapping the landscape of magnetic field effects on neural regeneration and repair: a systematic review, mathematical model, and meta-analysis

Although magnetic field exposure is a well-established diagnostic tool, its use as a therapeutic in regenerative medicine is relatively new. Our goal here was to evaluate how magnetic fields affect neural repair in vitro by performing a systematic review of the literature, mathematical modeling, and meta-analyses. The 38 included articles presented with high heterogeneity, representing 13 cell types, magnitudes ranging from 0.0002-10,000 mT, frequencies from 0-150 Hz, and exposure times lasting from one hour to several weeks. Mathematical modeling revealed that increasing magnetic field magnitude increases neural progenitor cell (NPC) viability. For regenerative processes that were not influenced by magnitude, frequency, and time, we integrated data with meta-analyses. Results revealed that magnetic field exposure increases NPC proliferation while decreasing astrocytic differentiation. Collectively, our work identifies neural repair processes that may be most responsive to magnetic field exposure and provides a framework for novel hypothesis and technology development.

neuroscience↗

bioRxiv2023

A network medicine approach to elucidate mechanisms underlying menopause-induced knee osteoarthritis

Post-menopausal women present with the highest incidence and morbidity of knee osteoarthritis (KOA), but no disease-modifying therapies are available. This treatment gap may be driven by the absence of menopause in preclinical studies, as rodents do not naturally maintain a menopausal phenotype. Here, we employed a chemically-induced menopause model to map the trajectory of KOA at the tissue and proteome levels and test therapeutics in silico. Middle-aged female mice were randomized to sesame oil (non-menopause) or 4-vinycyclohexene diepoxide (menopause) injections. Following comprehensive validation of our model, knees were collected across perimenopause and menopause for histology, and cartilage samples were micro-dissected for mass spectrometry proteomics. Menopause mice displayed aggravated cartilage degeneration and synovitis relative to non-menopause mice. An unbiased pathway analysis revealed progesterone as a predominant driver of pathological signaling cascades within the cartilage proteome. Network medicine-based analyses suggested that menopause induction amplifies chondrocyte senescence, actin cytoskeleton-based stress, and extracellular matrix disassembly. We then used in silico drug testing to evaluate how restoration of sex hormones impacted the cartilage network. The greatest restoration was observed with combined estradiol/progesterone treatment (i.e., hormone therapy), although in silico treatment with a senolytic drug also partially recovered the cartilage proteome. Taken together, our findings using a translatable female aging model demonstrate that menopausal aging induces progressive cartilage degeneration and amplifies age-related synovitis. These changes may be driven by a previously unappreciated role of progesterone loss and menopause-induced cellular senescence. Lastly, in silico treatment suggests an estradiol/progesterone cocktail or senolytics may attenuate menopause-induced cartilage pathology. One Sentence SummaryMenopause induces cartilage degradation, senescence, and extracellular matrix disassembly, while hormone therapy restores the cartilage proteome.

pathology↗

bioRxiv2023

Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate

Loss of muscle stem cell (MuSC) self-renewal with aging reflects a combination of influences from the intracellular (e.g., post-transcriptional modifications) and extracellular (e.g., matrix stiffness) environment. Whereas conventional single cell analyses have revealed valuable insights into factors contributing to impaired self-renewal with age, most are limited by static measurements that fail to capture nonlinear dynamics. Using bioengineered matrices mimicking the stiffness of young and old muscle, we showed that while young MuSCs were unaffected by aged matrices, old MuSCs were phenotypically rejuvenated by young matrices. Dynamical modeling of RNA velocity vector fields in silico revealed that soft matrices promoted a self-renewing state in old MuSCs by attenuating RNA decay. Vector field perturbations demonstrated that the effects of matrix stiffness on MuSC self-renewal could be circumvented by fine-tuning the expression of the RNA decay machinery. These results demonstrate that post-transcriptional dynamics dictate the negative effect of aged matrices on MuSC self-renewal. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/529950v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1a840corg.highwire.dtl.DTLVardef@d354cforg.highwire.dtl.DTLVardef@650556org.highwire.dtl.DTLVardef@41587c_HPS_FORMAT_FIGEXP M_FIG Graphical abstract description: The balance of self-renewal and differentiation in young muscle stem cells (MuSCs) is robust to perturbations of the biophysical microenvironment. In contrast, aged MuSCs are highly sensitive to extrinsic perturbations, and exposure to a youthful microenvironment rejuvenates the self-renewing potential of aged MuSCs by modulating post-transcriptional RNA dynamics. C_FIG

cell biology↗

bioRxiv2023

Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals

Accumulated fat in skeletal muscle, common in sedentary older individuals, compromises skeletal muscle health and function. Mechanistic understanding of how physical activity levels dictate fat accumulation represents a critical step towards establishment of therapies that promote healthy aging. Using a network paradigm that characterized the transcriptomic response of aged muscle to exercise versus immobilization protocols, this study uncovered a novel molecular cascade that regulates the fate of fibro-adipogenic progenitors (FAPs), the cell population primarily responsible for the fat accumulation. Specifically, gene set enrichment analyses (GSEA) with network propagation revealed Pgc1 as a functional hub of a large gene regulatory network underlying the regulation of FAPs by physical activity. Integrated in silico and in situ approaches to induce Pgc-1 overexpression promoted mitochondrial fatty acid oxidation and inhibited FAPs adipogenesis. These findings suggest that Pgc1 is a master regulator by which physical activity regulates fat accumulation in aged skeletal muscle. GRAPHICAL ABSTRUCT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/527478v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@5c4780org.highwire.dtl.DTLVardef@5a55ecorg.highwire.dtl.DTLVardef@bf1f16org.highwire.dtl.DTLVardef@192172e_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Network-based cytokine inference implicates Oncostatin M as a driver of knee osteoarthritis

Inflammatory cytokines released by the synovium after trauma disturb the gene regulatory network and have been implicated in the pathophysiology of osteoarthritis. A mechanistic understanding of how aging perturbs this process can help identify novel interventions. Here, we introduced network paradigms to simulate cytokine-mediated pathological communication between the synovium and cartilage. Cartilage-specific network analysis of injured young and aged murine knees revealed aberrant matrix remodeling as a transcriptomic response unique to aged knees displaying accelerated cartilage degradation. Next, network-based cytokine inference with pharmacological manipulation uncovered IL6 family member, Oncostatin M, as a driver for the aberrant matrix remodeling. By implementing a phenotypic drug discovery approach, we identified that the activation of Oncostatin M recapitulated "inflammation" phenotype of knee osteoarthritis and highlighted high-value targets for drug development and repurposing. These findings offer translational opportunities targeting the inflammation-driven osteoarthritis phenotype. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/525463v3_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@21b702org.highwire.dtl.DTLVardef@1761dd1org.highwire.dtl.DTLVardef@19f9fc2org.highwire.dtl.DTLVardef@b1a993_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2022

The fidelity of genetic information transfer with aging segregates according to biological processes

Maintenance of organismal function requires tightly regulated biomolecular communication. However, with aging, communication deteriorates, thereby disrupting effective information flow. Using information theory applied to skeletal muscle single cell RNA-seq data from young, middle-aged, and aged animals, we quantified the loss of communication efficiency over time. We considered communication channels between transcription factors (TF; input message) and corresponding target genes (TG; output message). Mutual information (MI), defined as the information effectively transmitted between TFs and TGs, declined with age. This decline was attributed to escalating biological noise and loss of precision with which TFs regulate TGs (i.e., channel capacity). When we ranked TF:TG pairs by MI, pairs associated with fatty acid oxidation displayed the greatest loss of communication with aging, while the system preserved communication between pairs related to RNA synthesis. These data suggest ineffective communication with aging against a backdrop of resource reallocation to support essential cellular functions.

bioengineering↗

bioRxiv2021

Meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related knee osteoarthritis

Increased mechanistic insight into the pathogenesis of knee osteoarthritis (KOA) is needed to develop efficacious disease-modifying treatments. Though age-related pathogenic mechanisms are most relevant to the great majority of KOA seen clinically, the bulk of our mechanistic understanding of KOA has been derived using surgically induced post-traumatic OA (PTOA) models. Here, we took an integrated approach of meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related KOA in murine model. Protein-level data together with transcriptomic profiling revealed inflammation, autophagy, and cellular senescence as primary hallmarks of age-related KOA. Importantly, the molecular profiles of aged cartilage were unique from those in PTOA, with only 1% overlap between the two. At the nexus of aging hallmarks, Advanced Glycation End-Product (AGE)/Receptor for AGE emerged as intrinsically linked to age-related KOA. This pathway was further validated by mass spectrometry. Collectively, these findings implicate dysregulation of AGE-RAGE signaling as a key driver of age-related KOA.

molecular biology↗

bioRxiv2021

Age-related increase in matrix stiffness downregulates α-Klotho in chondrocytes and induces cartilage degeneration

Enhanced mechanistic insight into age-related knee osteoarthritis (KOA) is an essential step to promote successful translation of animal research to bedside interventions. To this end, the goal of these studies was to interrogate molecular mechanisms driving age-related KOA in a mouse model and correspond findings to human knee cartilage. Unbiased mass spectrometry proteomics of cartilage tissue revealed PI3K/Akt signaling was the predominant pathway disrupted over time in male, but not female, mice. This finding was consistent with a significantly accelerated KOA progression in males when compared to female counterparts. In probing for upstream regulators of these age-dependent alterations, we found that -Klotho, a suppressor of PI3K/Akt signaling and potent longevity protein, significantly decreased with aging in both mouse and human knee cartilage. Upstream of these alterations, we found that age-related increases in matrix stiffness initiated a cascade of altered nuclear morphology and downregulated -Klotho expression, ultimately impairing chondrocyte health. Conversely, reducing matrix stiffness increased -Klotho expression in chondrocytes, thus enhancing their chondrogencity and cartilage integrity. Collectively, our findings establish a novel mechanistic link between age-related alterations in ECM biophysical properties and regulation of cartilage health by -Klotho.

molecular biology↗

bioRxiv2020

The biphasic and age-dependent impact of Klotho on hallmarks of aging and skeletal muscle function

Aging is accompanied by a disrupted information flow, which results from accumulation of molecular mistakes. These mistakes ultimately give rise to debilitating disorders such as skeletal muscle wasting, or sarcopenia. To estimate the growing "disorderliness" of the aging muscle system, we employed a statistical physics approach to estimate the state parameter, entropy, as a function of genes associated with hallmarks of aging. Although the most prominent structural and functional alterations were observed in the oldest old mice (27-29 months), we found that the escalating network entropy reached an inflection point at old age (22-24 months). To probe the potential for restoration of molecular "order" and reversal of the sarcopenic phenotype, we overexpressed the longevity protein, -Klotho. Klotho overexpression modulated genes representing all hallmarks of aging in both old and oldest-old mice. However, whereas Klotho improved strength in old mice, intervention failed to induce a benefit beyond the entropic tipping point.

physiology↗