Biology subjects

Sahin, A.

Publications and source records attributed to Sahin, A..

11 recordsLinked to original sources

bioRxiv2026

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome

Mechanistic and functional analysis of omics data largely relies on the incorporation of prior knowledge; however, connecting metabolomics data and knowledge is a major methodological challenge. This is largely driven by the diverse prior knowledge being fragmented across many databases requiring the merging of different database records across chemical structures, identifiers, and varying levels of structural specificity. Hence, this limits mechanistic interpretation and functional characterisation of the metabolome. Here, we present OmniPath Metabo, a comprehensive, harmonized, metabolome-centric database covering metabolites, lipids, food-derived compounds, and small molecule drugs, along with their associated receptors, transporters, enzymes, reactions, allosteric regulators, and disease associations. OmniPath Metabo harmonizes attributes using controlled vocabularies and ontologies, structures and built-in cheminformatics to map identifiers and track ambiguity. OmniPath Metabo is built directly from 40+ original resources and is freely accessible via an interactive web app and API at metabo.omnipathdb.org. OmniPath Metabo enables dynamic, context-specific construction of subnetworks to serve dedicated purposes, such as cell-cell communication or integrated multi-omics metabolite-driven regulation, connecting reactions, allosteric regulation, metabolite-receptor and metabolite-transporter interactions. Combining it with the over 170 other resources in OmniPath, it can be used for integrated networks of signaling, gene regulation, and metabolism. We showcase the application of OmniPath Metabo by analysing publicly available metabolomics data of lung cancer cell lines and metabolic footprints to mutational patterns. In summary, OmniPath Metabo transforms fragmented resources into a harmonised prior knowledge framework for a mechanistic and functional analysis of the metabolome.

bioinformatics↗

bioRxiv2024

Effects of Primed Adipose Mesenchymal Stem Cell-Derived Exosomes on Immunomodulation in Behcet Uveitis

PurposeThis study sought to investigate the potential role of exosomes of interferon-gamma (IFN-{gamma}) primed (IFN+Exo) and non-primed (IFN-Exo) adipose-derived mesenchymal stem cells (AdMSCs) for the treatment of Behcet Disease (BD) uveitis (BU). MethodsAdMSCs were isolated from adipose tissue. Characterization and multipotency analyses were performed. Exosomes were isolated from the media of AdMSCs and then characterized. Peripheral blood mononuclear cells (PBMC) were isolated from patients with BU and healthy individuals. AdMSCs were preincubated with or without IFN-{gamma} for 48 h. PBMC of patients with BU and healthy controls separately cultured with exosomes for 72 h. After the culture period, lymphocyte proliferation, viability, and apoptosis were carried out via flow cytometry. The expression of interleukin (IL)-10, IL-17, transforming growth factor (TGF)-{beta}, and interferon (IFN)-{gamma} levels were measured by real-time polymerase chain reaction (RT-PCR). ResultsIFN+Exo promoted lymphocyte apoptosis in patients with BU. IFN+Exo suppressed cell viability of T lymphocytes of BU. Exosomes alone did not affect on T lymphocyte proliferation. Additionally, exosomes increased anti-inflammatory cytokine levels and reduced pro-inflammatory cytokine levels of T lymphocytes in patients with BU. ConclusionThis studys findings can open a new pathway in MSCs/exosome therapy in BU.

immunology↗

bioRxiv2024

Aberrant expression of CD14 in breast tumor cells is associated with poor outcome

Emerging evidence suggests that cancer cells can mimic features of immune cells during oncogenic transformation to drive disease progression. We assessed the occurrence of immunological markers in breast cancer cells to determine their expression pattern. We initially analyzed 18 immune protein markers (CCR4, CCR6, CCR7, CD11, CD123, CD14, CD16, CD19, CD24, CD25, CD27, CD3, CD38, CD4, CD45, CD56, CD8 and CXCR3) expressed on the surface of 28 breast cancer cell lines using mass spectrometry. CD14 protein expression in tumor cells and its association with clinical outcomes was subsequently evaluated by tissue microarray (TMA) analysis of 346 breast tumors. Single-cell RNA sequencing data from breast cancer tumors and bulk transcriptomic data of breast cancer cell lines were interrogated for molecular signatures associated with CD14 tumor cell expression. Among the markers interrogated, CD14 protein was aberrantly expressed on the surface of 13 out of 15 triple-negative breast cancer (TNBC), one of six hormone receptor positive (HR+), one of five hormone receptors negative (HR-)/Her2+ cell lines. Likewise, RNA expression revealed higher levels of CD14 in TNBC cell lines compared to other subtypes. Tumor tissue microarray analysis revealed elevated levels of CD14 membrane expression predominantly in TNBC and was associated with higher tumor grade and increased incidence of disease recurrence compared to CD14-negative tumors. The CD14-positive subgroup exhibited Nuclear Factor Kappa Beta (NFkB) and TGF-{beta} centric networks at both the protein and Single-cell RNA levels. We have uncovered a novel subset of breast cancers characterized by aberrant surface expression of CD14 associated with aggressive disease. CD14 identifies a subset of breast cancers with poor outcome and is a potential therapeutic target.

cancer biology↗

bioRxiv2024

Distinct effects of acute and chronic blood loss anemia on vascular function after acute myocardial infarction

BackgroundAnemia is frequently observed in patients with cardiovascular diseases (CVD). Anemia alone or in combination with other morbid conditions leads to poor prognosis in acute myocardial infarction (AMI). We recently showed that moderate blood loss anemia is associated with red blood cell (RBC) dysfunction and a compensatory increase in flow-mediated dilation (FMD) responses which are compromised in chronic blood loss anemia However, the effects of acute anemia (AA) and chronic anemia (CA) on endothelial function after AMI are unclear. In this study, we evaluated systemic endothelial function following AMI in established murine models of blood loss acute and chronic anemia. We hypothesize that both AA and CA aggravate systemic endothelial dysfunction (ED) after AMI. Methods and resultsAA or CA was induced in male C57BL/6J mice by repeated blood withdrawal for three consecutive days or six weeks, respectively. Separate groups of anemic and non-anemic mice underwent AMI via left anterior descending artery (LAD) ligation (45 min), followed by reperfusion. Endothelial function was assessed using both in vivo and in vitro methods 24 h post-AMI. Impaired flow-mediated dilation (FMD, in vivo) and endothelium-dependent relaxation (EDR) responses were observed in the aorta, femoral, and saphenous arteries of AA mice compared to their respective control groups 24 h post AMI. The aorta and saphenous arteries from CA mice showed significantly reduced vascular smooth muscle (VSM) contractile responses after AMI. Analysis of oxidative products of nitric oxide (NO) in plasma revealed reduced nitrite and nitrate levels in both AA and CA mice compared to controls 24 h post-AMI. Immunohistochemistry of aortic tissues from both anemic groups showed increased reactive oxygen species (ROS) product 4-Hydroxynonenal (4-HNE). Co-incubation of RBCs from anemic mice or anemic ST-elevation myocardial infarction (STEMI) patients with aortic rings from wild type mice demonstrated attenuated VSM contractile and EDR responses. Supplementation with the ROS scavenger N-acetyl cysteine (NAC) for four weeks improved both in vivo and ex vivo EDR in AA and CA mice 24 h post-AMI. ConclusionAfter AMI, both AA and CA are associated with severe ED, while VSM contractile responses specifically reduced in CA mice. These effects are accompanied by increased ROS and partly mediated by RBCs. Antioxidant supplementation with NAC is a potential therapeutic option to reverse the severe vascular dysfunction in anemia following AMI. Graphical AbstractDistinct effects of acute and chronic anemia on vascular function 24 h post-AMI. After acute myocardial infarction, acute and chronic anemia are associated with increased reactive oxygen species (ROS) and inflammation in endothelial cells (EC), leading to the inhibition of endothelial nitric oxide synthase (eNOS) and subsequent endothelial dysfunction by limiting NO bioavailability. Chronic anemia is additionally associated with decreased vascular smooth muscle cell (VSMC) function due to increased oxidative stress, leading to SMC dysfunction. After N-Acetyl-L-Cysteine (NAC) treatment, vascular function is improved in both anemic groups. O_FIG O_LINKSMALLFIG WIDTH=98 HEIGHT=200 SRC="FIGDIR/small/614629v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@136583aorg.highwire.dtl.DTLVardef@da8708org.highwire.dtl.DTLVardef@d73539org.highwire.dtl.DTLVardef@e7516a_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

TYK2 as a novel therapeutic target in Alzheimer Disease

Neuroinflammation is a pathological feature of many neurodegenerative diseases, including Alzheimers disease (AD)1,2 and amyotrophic lateral sclerosis (ALS)3, raising the possibility of common therapeutic targets. We previously established that cytoplasmic double-stranded RNA (cdsRNA) is spatially coincident with cytoplasmic pTDP-43 inclusions in neurons of patients with C9ORF72-mediated ALS4. CdsRNA triggers a type-I interferon (IFN-I)-based innate immune response in human neural cells, resulting in their death 4. Here, we report that cdsRNA is also spatially coincident with pTDP-43 cytoplasmic inclusions in brain cells of patients with AD pathology and that type-I interferon response genes are significantly upregulated in brain regions affected by AD. We updated our machine-learning pipeline DRIAD-SP (Drug Repurposing In Alzheimers Disease with Systems Pharmacology) to incorporate cryptic exon (CE) detection as a proxy of pTDP-43 inclusions and demonstrated that the FDA-approved JAK inhibitors baricitinib and ruxolitinib that block interferon signaling show a protective signal only in cortical brain regions expressing multiple CEs. Furthermore, the JAK family member TYK2 was a top hit in a CRISPR screen of cdsRNA-mediated death in differentiated human neural cells. The selective TYK2 inhibitor deucravacitinib, an FDA-approved drug for psoriasis, rescued toxicity elicited by cdsRNA. Finally, we identified CCL2, CXCL10, and IL-6 as candidate predictive biomarkers for cdsRNA-related neurodegenerative diseases. Together, we find parallel neuroinflammatory mechanisms between TDP-43 associated-AD and ALS and nominate TYK2 as a possible disease-modifying target of these incurable neurodegenerative diseases.

neuroscience↗

bioRxiv2024

A unique and biocompatible approach for corneal collagen crosslinking in vivo

Corneal crosslinking (CXL) is a widely applied technique to halt the progression of ectatic diseases by increasing the thickness and mechanical stiffness of the cornea. This study investigated the biocompatibility and efficiency of a novel CXL procedure using ruthenium and blue light in rat corneas and evaluated factors important for clinical application. To perform the CXL procedure, the corneal epithelium of rats was removed under anesthesia, followed by the application of a solution containing ruthenium and sodium persulfate (SPS). The corneas were then exposed to blue light at 430 nm at 3 mW/cm2 for 5 minutes. Rat corneas were examined and evaluated for corneal opacity, corneal and limbal neovascularization, and corneal epithelial regeneration at days 0, 1, 3, 6, 8, and 14. On day 28, the corneas were isolated for subsequent tissue follow-up and analysis. CXL with ruthenium and blue light showed rapid epithelial healing, with 100% regeneration of the corneal epithelium and no corneal opacity by day 6. The ruthenium group also exhibited significantly reduced corneal (p<0.01) and limbal neovascularization (p<0.001). Histological analysis revealed no signs of cellular damage or apoptosis, which further confirms the biocompatibility and nontoxicity of our method. Confocal and scanning electron microscopy (SEM) images showed a greater density of collagen fibrils, indicating efficient crosslinking and enhanced structural integrity. This study confirmed the in vivo safety, biocompatibility, and functionality of ruthenium and blue light CXL. This method can prevent toxicity caused by UV-A light and can be a rapid alternative treatment to standard crosslinking procedures. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/585574v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@c05147org.highwire.dtl.DTLVardef@18244borg.highwire.dtl.DTLVardef@f6e30eorg.highwire.dtl.DTLVardef@b4ec3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

A constraint-based framework to reconstruct interaction networks in microbial communities

Microbial communities live in diverse habitats and significantly impact our health and the environment. However, the principles that govern their formation and evolution remain poorly understood. A crucial step in studying microbial communities is to identify the potential metabolic interactions between the community members, such as competition for nutrients or cross-feeding. Due to the size and complexity of the metabolic network of each organism, there may be a variety of connections between each pair of organisms, which poses a challenge to unraveling the metabolic interactions. Here, we present ReMIND, a computational framework to reconstruct the interaction networks in microbial communities based on the metabolic capabilities of individual organisms. We applied ReMIND to a well-studied uranium-reducing community and the honeybee gut microbiome. Our results provide new perspectives on the evolutionary forces that shape these ecosystems and the trade-off between metabolite exchange and biomass yield. By enumerating alternative interaction networks, we systematically identified the most likely metabolites to be exchanged and highlighted metabolites that could mediate competitive interactions. We envision that ReMIND will help characterize the metabolic capacity of individual members and elucidate metabolic interactions in diverse communities, thus holds the potential to guide many applications in precision medicine and synthetic ecology.

systems biology↗

bioRxiv2023

Variable and reversible opacification process on IOLs for cataract simulation

Understanding vision through mild and dense cataracts is important for vision scientists and IOL developers. There have been virtual simulators using VR headsets for subjective evaluation of cataractous vision. However, a physical intraocular lens with variable cataracts for objective evaluation is not available. In this study, we developed a reversible process that can be selectively applied to the whole or parts of an IOL to affect the opacification level. We used our eye model and developed a cataractous lens simulator for progressive levels of opacification, which is achieved by applying a reversible chemical procedure on the intraocular lens surfaces. After the lens is fully or partially immersed in acetone, subsequent testing of the lens in distilled water results in a progressive change in opacification level within minutes. We measured the quality of vision by obtaining modulation transfer function curves, transmission, and spectroscopic measurements at different opacification levels. By simulating variable opacification across the IOLs, we tested how vision changes from less dense to more dense cataractous regions in a holographic display system with programmable small exit pupils. All results were consistent with the expected vision degradation caused by natural opacification.

bioengineering↗

bioRxiv2022

Optimal enzyme utilization suggests concentrations and thermodynamics favor condition-specific saturations and binding mechanisms

Understanding the dynamic responses of living cells upon genetic and environmental perturbations is crucial to decipher the metabolic functions of organisms. The rates of enzymatic reactions and their evolution are key to this understanding, as metabolic fluxes are limited by enzymatic activity. In this work, we investigate the optimal modes of operations for enzymes with regard that the evolutionary pressure drives enzyme kinetics toward increased catalytic efficiency. We use an efficient mixed-integer formulation to decipher the principles of optimal catalytic properties at various operating points. Our framework allows assessing the distribution of the thermodynamic forces and enzyme states, providing detailed insight into the mode of operation. Our results confirm earlier theoretical studies on the optimal kinetic design using a reversible Michaelis-Menten mechanism. The results further explored the optimal modes of operation for random-ordered multi-substrate mechanisms. We show that optimal enzyme utilization is achieved by unique or alternative modes of operations depending on the reactants concentrations. Our novel formulation allows investigating the optimal catalytic properties of all enzyme mechanisms with known elementary reactions. We propose that our novel framework provides the means to guide and evaluate directed evolution studies and estimate the limits of the direct evolution of enzymes.

systems biology↗

bioRxiv2018

Circuit dysfunction in SOD1-ALS model first detected in sensory feedback prior to motor neuron degeneration is alleviated by BMP signaling

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease whose origin and underlying cellular defects are still not fully understood. While motor neuron degeneration is the signature feature of ALS, it is not yet clear if motor neurons, or other cells of the motor circuit, are the site of disease initiation. To better understand the contribution of multiple cell types in ALS, we made use of a Drosophila Sod1G85R knock-in model, in which all cells harbor the disease allele. End-stage dSod1G85R animals exhibit severe motor deficits with clear degeneration of motor neurons. Interestingly, earlier in dSod1G85R larvae motor function is also compromised, but their motor neurons exhibit only subtle morphological and electrophysiological changes, that are unlikely to cause the observed decrease in locomotion. We analyzed the intact motor circuit and identified a defect in sensory feedback that likely accounts for the altered motor activity of dSod1G85R. Furthermore, we found that the cell-autonomous activation of BMP signaling in proprioceptor sensory neurons that relay the contractile status of muscles back to the central nerve cord, is able to completely rescue early stage motor defects and partially rescue late stage motor function to extend lifespan. Identifying a defect in sensory feedback as a potential initiating event in ALS motor dysfunction, coupled with the ability of modified proprioceptors to alleviate such motor deficits, underscores the critical role that non-motor neurons play in disease progression and highlights their potential as a site to identify early-stage ALS biomarkers and for therapeutic intervention.\n\nSignificance StatementAt diagnosis, many cellular processes are already disrupted in the ALS patient. Identifying the initiating cellular events is critical for achieving an earlier diagnosis in order to slow or prevent disease progression. Our findings indicate that neurons relaying sensory information underlie early stage motor deficits in a Drosophila knock-in model of ALS that best replicates gene dosage in familial ALS (fALS). Importantly, studies on intact motor circuits revealed defects in sensory feedback before evidence of motor neuron degeneration. These findings strengthen our understanding of how neural circuit dysfunctions lead to neurodegeneration and coupled with our demonstration that activation of BMP signaling in proprioceptors alleviates both early and late motor dysfunction, underscores the importance of considering non-motor neurons as therapeutic targets.

neuroscience↗

bioRxiv2018

Genome-encoded Cytoplasmic Double-Stranded RNAs, Found in C9ORF72 ALS-FTD Brain, Provoke Propagated Neuronal Death

Innate immune signaling activation and DNA damage are pathological hallmarks of aging that may herald multiple adult-onset neurodegenerative diseases. Here, we report that both cell autonomous and non-autonomous neuronal death are triggered by the production of cytoplasmic double-stranded RNA (cdsRNA) from a regulated, disarticulated transgene in the setting of type I interferon (IFN-I) signaling. CdsRNA is a pathogen associated molecular pattern that induces IFN-I in many cell types. Transfection of a dsRNA mimetic into cultured human neurons also induces IFN-I signaling and cell death in a dose-dependent manner. Direct relevance to human disease is found in neurons of ALS-FTD patients carrying C9ORF72 intronic hexanucleotide expansions; cdsRNA isolated from these tissues is comprised of repeat sequences. Together, these findings implicate cdsRNA generated from genomic sequences in neurons as a trigger for sterile, viral-mimetic IFN-I induction and propagated neuronal death within in a neural circuit in the aging nervous system.

neuroscience↗