Biology subjects

Yildiz, E.

Publications and source records attributed to Yildiz, E..

10 recordsLinked to original sources

bioRxiv2026

An integrative cardio-informatics approach identifies positionally conserved ancestors of human lncRNA genes transcribed across vertebrate hearts

The poor conservation of lncRNA genes limits their comprehensive functional studies, as genetic engineering of relevant animal models presupposes the presence of corresponding defined orthologs. This limitation is prominently evident in cardiovascular research, where heart-related lncRNAs are rarely conserved between humans and other vertebrates, despite the highly conserved nature of cardiac function. Because lncRNAs frequently regulate neighboring protein-coding genes essential for cardomyocyte function (herein termed cardiomyocyte indispensable, CMIs), we hypothesized that they are under evolutionary pressure to retain their genomic position and transcriptional activity, irrespective of sequence similarities to prototypical human lncRNA genes. By integrating mouse cardiac knockout phenotypes with human single-cell transcriptomics data, we systematically identified heart-expressed CMIs and their neighboring. lncRNA genes. Cross-species synteny analyses revealed regions flanking 109 CMIs with conserved relative positions and transcriptional orientations across vertebrate genomes. As most of these loci reside within poorly annotated non-coding regions, we developed VertLncRNAchecker, a neural network-based web interface, that predicts lncRNA-like genes within these regions, which we termed positional ancestors. Finally, we validated in situ that these positional ancestors express mature lncRNA transcripts in the hearts of mice, pigs, and frogs, mirroring the expression of their human lncRNA counterparts. We present an accurate and retrainable computational platform for cross-species lncRNA discovery that prioritizes conserved genomic position over sequence conservation or existing genome annotations. This pipeline revealed putative ancestors of human heart-related lncRNAs hidden within the vertebrate non-coding dark genome, providing novel insights into lncRNA biology and evolution.

evolutionary biology↗

bioRxiv2026

METTL3 modulates cell viability and motility in HCC1143 and MDA-MB-231 triple-negative breast cancer cells

The m6A methyltransferase METTL3 functions as a critical oncogenic driver in triple-negative breast cancer (TNBC). However, its specific downstream targets and mechanistic functions in less metastatic TNBC subtypes remain poorly characterized. To address this, we evaluated METTL3 expression and the phenotypic effects of its siRNA-mediated knockdown in normal mammary epithelial (MCF10A), low-metastatic TNBC (HCC1143), and high-metastatic TNBC (MDA-MB-231) cell lines. We assessed global m6A levels, cell viability, cell cycle progression, and migration. To uncover specific downstream pathways, transcriptomic profiling was performed on HCC1143 cells, followed by RT-qPCR validation and m6A site prediction. METTL3 depletion reduced global m6A levels and cell viability across all cell lines. Notably, in low-metastatic HCC1143 cells, METTL3 knockdown induced a pronounced G2/M cell cycle arrest and dramatically impaired migratory capacity. Transcriptomic analysis of HCC1143 revealed altered expression of genes associated with the observed phenotypic changes. Specifically, critical transcripts harboring predicted m6A motifs, including LIMK1, CCNB2, and CDH1, were significantly dysregulated, pointing to potential alterations in pathways governing cytoskeletal remodeling, actin organization, and cell-cell adhesion. Taken together, we propose that METTL3 promotes cell viability and motility in low-metastatic TNBC by regulating key transcripts involved in cell cycle progression and actin dynamics. Significance StatementEpitranscriptomic studies on TNBC predominantly focus on highly metastatic models, leaving less aggressive subtypes poorly understood. This study uniquely addresses this gap by investigating the function of METTL3 in HCC1143, a low-metastatic TNBC cell line, alongside aggressive TNBC cell lines. We discovered that METTL3 depletion uniquely triggers a severe halt in cell division (G2/M arrest) in HCC1143 cells, while universally disrupting actin-associated cell motility across different backgrounds. These findings demonstrate that METTL3 acts as a context-dependent modulator of cell fate rather than a monolithic driver. Ultimately, highlighting these distinct cellular responses underscores the need to consider specific molecular backgrounds when evaluating epitranscriptomic targets in heterogeneous cancers, such as TNBC.

cancer biology↗

bioRxiv2026

In situ vaccine effect of radiotherapy is associated with intratumoural ERV reactivation and RNA virus sensing

Radiotherapy (RT) transforms tumour tissues into in situ vaccines that trigger antitumor immunity. Immunogenicity depends on how RT is delivered, since heterogeneous RT (spatially fractionated RT, SFRT) elicits more prominent responses than the conventional homogenous one. However, this phenomenon cannot be clinically harnessed, unless the relevant pathways are identified. To gain insights, we developed a hybrid dry-lab/wet-lab approach that integrates systems-level immune phenotypes established by homogenous or heterogenous RT (SFRT) with the transcriptomic profiling of irradiated tumors. By further combining feature extraction with machine-learning, including multilayer perceptron modelling, we ranked predictors of immune infiltration and patient survivability for each RT type. We found that conventional RT induces coordinated upregulation of cytosolic sensors of RNA viruses (OASes and RIG I-like receptors) along with ERV RNAs predominately 400-800 base-pairs long, which might serve as their ligands. For schemes establishing abscopal effects, a coordinated upregulation of the OAS sensors and shared ERV transcripts was observed in both irradiated and distant tumours. Compared to homogenous RT, SFRT triggered earlier and stronger activation of OAS signaling along with NK cell responses. Overall, we show a co-involvement of tumour cell-intrinsic ERVs and their cytosolic RNA sensors in RT-induced antitumor immunity. This key finding could guide mechanistic studies and future precision oncology.

cancer biology↗

bioRxiv2025

IFNAR1. Neutrophils Orchestrate Chronic Inflammatory Damage Through Mitochondrial Remodeling

Neutrophils are abundant innate effector cells that drive mucosal inflammation, yet the mechanisms by which they contribute to chronic inflammatory diseases across distinct tissues remain incompletely understood. Here, by reanalyzing single-cell RNA-seq datasets from patients with inflammatory bowel disease (IBD) and chronic obstructive pulmonary disease (COPD), we identify a shared neutrophil activation program enriched for type I interferon (IFN) signaling, nuclear factor-{kappa}B (NF-{kappa}B) and AP-1 transcriptional regulators, and effector pathways including NETosis, degranulation, and leukocyte trafficking. To interrogate these signatures, we established a CRISPR-compatible neutrophil differentiation platform from adult CD34 progenitors, which yielded cells closely resembling primary neutrophils at transcriptomic, proteomic, and functional levels. A targeted CRISPR-Cas9 screen revealed a central role for the mitochondrial iron transporter mitoferrin-1 (SLC25A37) in coordinating neutrophil oxidative phosphorylation, NET formation, and type I IFN production downstream of TLR9. Mechanistically, we show that NET-derived citrullinated histones activate an autocrine IFN-IFNAR1 loop, amplifying neutrophil inflammatory functions without impairing phagocytosis. Disruption of this loop, through IFNAR1 depletion or blockade, dampened neutrophil-driven tissue damage in human intestinal and alveolar organoid co-cultures as well as in murine models of colitis and cigarette smoke-induced lung inflammation. These findings uncover a conserved IFN-driven metabolic circuit in neutrophils that underpins pathology across chronic mucosal diseases and identify IFNAR1 as a therapeutic node to selectively disarm neutrophil-mediated tissue injury.

immunology↗

bioRxiv2024

A Novel Mouse Model Demonstrates In Vivo Replenishment of Central Nervous System Pericytes After Successful Acute Ablation

Central nervous system (CNS) pericytes play crucial roles in vascular development and blood-brain barrier maturation during prenatal development, as well as in regulating cerebral blood flow in adults. They have also been implicated in the pathogenesis of numerous neurological disorders. However, the behavior of pericytes in the adult brain after injury remains poorly understood, partly due to limitations in existing pericyte ablation models. To investigate pericyte responses following acute ablation, we developed a tamoxifen-inducible pericyte ablation model by crossing PDGFR{beta}-P2A-CreERT2 and Rosa26-DTA176 transgenic mouse lines. Using this model, we studied the effects of different tamoxifen doses and conducted histological examinations 15 and 60 days post-injection to assess both short- and long-term impacts of pericyte ablation. Our results demonstrate that a low dose of tamoxifen effectively ablates CNS pericytes in mice without reducing survival or causing significant systemic side effects, such as weight loss. Additionally, we found that the extent of pericyte depletion varies between the cortex and the spinal cords gray and white matter regions. Importantly, both pericyte coverage and numbers increased in the weeks following acute ablation, indicating the regenerative capacity of CNS pericytes in vivo. This model offers a valuable tool for future studies on the role of pericytes in neurological disorders, overcoming the limitations of constitutive pericyte ablation models.

neuroscience↗

bioRxiv2024

A novel pyridoindole improves the recovery of residual hearing following cochlear implantation after a single preoperative application

Sensorineural hearing loss (SNHL) is the most common sensory deficit worldwide. Due to the heterogeneity of causes for SNHL, effective treatment options remain scarce, creating an unmet need for novel drugs in the field of otology. Cochlear implantation (CI) currently is the only established method to restore hearing function in profound SNHL and deaf patients. The cochlear implant bypasses the non-functioning sensory hair cells (HCs) and electrically stimulates the neurons of the cochlear nerve. CI also benefits patients with residual hearing by combined electrical and auditory stimulation. However, the insertion of an electrode array into the cochlea induces an inflammatory response, characterized by the expression of pro-inflammatory cytokines, upregulation of reactive oxygen species, and apoptosis and necrosis of HCs, putting residual hearing at risk. Here, we characterize the effects of the small molecule AC102, a pyridoindole, for its protective effects on residual hearing in CI. We show that AC102 significantly preserves hearing thresholds across the whole cochlea and confines the cochlear trauma to the directly mechanically injured area. In addition, AC102 significantly preserves auditory nerve fibers and inner HC synapses throughout the whole cochlea. AC102s effects are likely elicited during the inflammatory phase of electrode insertion trauma (EIT) and mediated by anti-apoptotic and anti-inflammatory properties, as uncovered by an in vitro assay of ethanol induced apoptosis and evaluation of mRNA expression of pro-inflammatory cytokines in an organotypic ex vivo model of EIT. The results in this study highlight AC102 as a promising compound for the attenuation of EIT during CI. Moreover, as the inflammatory response in cochlear implantation shares similarities to other etiologies of SNHL, a beneficial effect of AC102 can be inferred for other inner ear conditions as well.

neuroscience↗

bioRxiv2023

Large-scale annotated dataset for cochlear hair cell detection and classification

Our sense of hearing is mediated by cochlear hair cells, localized within the sensory epithelium called the organ of Corti. There are two types of hair cells in the cochlea, which are organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains a few thousands of hair cells, and their survival is essential for our perception of sound because they are terminally differentiated and do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. However, the sheer number of cells along the cochlea makes manual quantification impractical. Machine learning can be used to overcome this challenge by automating the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, human, pig and guinea pig cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 90,000 hair cells, all of which have been manually identified and annotated as one of two cell types: inner hair cells and outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to supply other groups within the hearing research community with the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.

neuroscience↗

bioRxiv2022

Hepatic lipid overload potentiates biliary epithelial cell activation via E2Fs

During severe or chronic hepatic injury, biliary epithelial cells (BECs), also known as cholangiocytes, undergo rapid reprogramming and proliferation, a process known as ductular reaction (DR), and allow liver regeneration by differentiating into both functional cholangiocytes and hepatocytes. While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. Here, we demonstrate that BECs readily accumulate lipids upon fatty acid (FA) treatment in BEC-derived organoids, and during high-fat diet feeding in mice. Lipid overload induces a metabolic rewiring to support the conversion of adult cholangiocytes into active BECs. Mechanistically, we found that lipid overload unleashes the activation of the E2F transcription factors in BECs, which drives cell cycle progression while promoting glycolytic metabolism. These findings demonstrate that fat overload is sufficient to initiate a DR, without epithelial damage, and provide new insights into the mechanistic basis of BEC activation, revealing unexpected connections between lipid metabolism, stemness, and regeneration.

cell biology↗

bioRxiv2020

Microglial Associated Circadian Rhythms of Perineuronal Net Composition

Perineuronal Nets (PNNs) are extracellular matrix (ECM) structures that envelop neurons and regulate synaptic functions. Long thought to be stable structures, PNNs have been recently shown to respond dynamically during learning, potentially regulating the formation of new synapses. We postulated that PNNs vary during sleep, a period of active synaptic modification. Notably, PNN components are cleaved by matrix proteases such as the protease cathepsin-S. This protease is diurnally expressed in the mouse cortex, coinciding with dendritic spine density rhythms. Thus, cathepsin-S may contribute to PNN remodeling during sleep, mediating synaptic reorganization. These studies were designed to test the hypothesis that PNN numbers vary in a diurnal manner in the rodent and human brain, as well as in a circadian manner in the rodent brain, and that these rhythms are disrupted by sleep deprivation. In mice, we observed diurnal and circadian rhythms of PNNs labeled with the lectin wisteria floribunda agglutinin (WFA+PNNs) in several brain regions involved in emotional memory processing. Sleep deprivation prevented the daytime decrease of WFA+ PNNs and enhances fear memory extinction. Diurnal rhythms of cathepsin-S expression in microglia were observed in the same brain regions, opposite to PNN rhythms. Finally, incubation of mouse sections with cathepsin-S eliminated PNN labeling. In humans, WFA+PNNs showed a diurnal rhythm in the amygdala and thalamic reticular nucleus (TRN). Our results demonstrate that PNNs vary in a circadian manner and this is disrupted by sleep deprivation. We suggest that rhythmic modification of PNNs may contribute to memory consolidation during sleep.

neuroscience↗

bioRxiv2019

Mechano-modulatory synthetic niches for liver organoid derivation

The recent demonstration that primary cells from the liver can be expanded in vitro as organoids holds enormous promise for regenerative medicine and disease modeling1-5. The use of three-dimensional (3D) cultures based on ill-defined and potentially immunogenic matrices, however, hampers the translation of liver organoid technology into real-life applications6. We here used chemically defined hydrogels for the efficient derivation of both mouse and human hepatic organoids. Organoid growth was found to be highly stiffness-sensitive and dependent on yes-associated protein 1 (YAP) activity. However, in contrast to intestinal organoids7, YAP-mediated stiffness sensitivity was independent of acto-myosin contractility, requiring instead activation of the Src family of kinases (SFKs). Aberrant matrix stiffness on the other hand led to a shift in the progenitor phenotype, resulting in compromised proliferative capacity. Finally, we demonstrate the unprecedented establishment of biopsy-derived human liver organoids without the use of animal components at any step of the process. Our approach thus opens up exciting perspectives for the establishment of protocols for liver organoid-based regenerative medicine.

bioengineering↗