Biology subjects

Eroglu, A.

Publications and source records attributed to Eroglu, A..

8 recordsLinked to original sources

bioRxiv2025

Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures

The human immune system undergoes continuous remodeling from infancy through old age, yet the timing and trajectory of these changes across the lifespan remain poorly defined. To address this, we profiled peripheral blood mononuclear cells from 95 healthy individuals (ages 2 months to 88 years), including infants (n=27), children (n=23), adults (n=18), and older adults (n=27) using scRNA-seq and snATAC-seq. MAIT and {gamma}{delta} T cells showed a "Rise and fall" pattern, which rise in childhood, peak in young adulthood, and decline with age. CD8+ T cells were the most affected by aging with decreasing naive T cells and increasing GzK+ CD8+ T cells and TEMRA cells. Infants had lower myeloid/lymphoid ratio, with a distinct composition marked by increased frequencies of CD16+ monocytes and plasmacytoid dendritic cells and reduced frequencies of CD14+ monocytes and conventional DCs. Their adaptive immune compartment also displayed unique features, including constitutive interferon-stimulated gene expression in T and B cells, and an expanded SOX4+ populations in naive CD4+, naive CD8+ and {gamma}{delta} T cells, comprising [~]30% of the naive T cell pool. SOX4+ naive CD4+ T cells displayed a Th2 epigenetic signature. This map provides critical insights into human immune system dynamics across the lifespan, emphasizing unique features of the infant immune system.

immunology↗

bioRxiv2025

High-Throughput Evaluation of Cryoprotective Agents for Mixture Effects That Reduce Toxicity

Vitrification is a promising approach for cryopreserving complex biological structures such as organs. However, to prevent ice formation, high concentrations of cell-permeable cryoprotective agents (CPAs) are required, which can be highly toxic. The current reliance on a small number of CPAs limits optimization of low-toxicity compositions for vitrification. To address this, there is growing interest in uncovering novel chemicals with analogous protective qualities. This may not only enhance vitrification efficacy but also mitigate toxic effects. In the current study, we employed a high throughput method to assess the toxicity of 21 compounds at room temperature, both individually and in binary combinations. Our analysis revealed that toxicity increases with both exposure duration and concentration, and that several CPA combinations result in reduced overall toxicity. Notably, among all tested mixtures, four binary combinations--formamide/glycerol, dimethyl sulfoxide/1,3-propanediol, 1,2-propanediol/diethylene glycol, and 1,3-propanediol/diethylene glycol--produced a statistically significant decrease in toxicity, resulting in significantly higher viability for the 6 mol/kg mixture than both corresponding 6 mol/kg single CPA solutions. The high-throughput approach presented here will aid in building a comprehensive CPA toxicity database, which will improve our understanding of toxicity mechanisms and support the development of predictive models for identifying novel CPA mixtures with low toxicity.

pharmacology and toxicology↗

bioRxiv2025

Multi-cellular phenotypic dynamics during the progression of breast tumors

In cancer, improving diagnostics and therapeutic interventions can benefit from understanding the cellular and phenotypic heterogeneity of the tumor microenvironment (TME). In recent years, the TME has been profiled at an unprecedented level of detail by performing single-cell RNA sequencing (scRNAseq) on patient samples. However, from patient samples, studying the temporal dynamics of the TME using patient samples has been challenging. Interrogating the temporal dynamics of the TME is critical to understand how inter-tumor heterogeneity is organized into a temporally ordered sequence of causes and consequences in cellular events. Here we survey the temporal dynamics of the TME by performing longitudinal scRNAseq on mouse breast tumors at different progression time points of tumor progression. We reveal multi-cellular phenotypic dynamics that follow one out of three possible temporal patterns: stable colonization, wave-like, or progressive increase. In particular, IFN-responsive cancer cells, GzmB + cytotoxic T cells, as well as C1q macrophages, progressively increase in parallel with tumors progression. These findings establish the single-cell types and phenotypes in a progressing breast tumor, and determine when these cellular players enter and leave the TME.

cancer biology↗

bioRxiv2024

The Biochemical Effects of Carotenoids in Orange Carrots on the Colonic Proteome in a Mouse Model of Diet-induced Obesity

Carotenoids are naturally occurring pigments in plants and are responsible for the orange, yellow, and red color of fruits and vegetables. Carrots are one of the primary dietary sources of carotenoids. The biological activities of carotenoids in higher organisms are well documented in most tissues but not the large intestine. The gastrointestinal barrier acts as a line of defense against the systemic invasion of pathogenic bacteria, especially at the colonic level. Proteins involved in tight junction assembly between epithelial cells and mucus secretion from goblet cells are essential for maintaining intestinal barrier homeostasis. A high-fat diet can cause gut impairment by inducing barrier permeability, leading to low-grade chronic inflammation via metabolic endotoxemia. Our hypothesis for this study is that the dietary intake of carotenoid-rich foods can alleviate obesity-associated gut inflammation and strengthen the intestinal barrier function. Male C57BL/6J mice were randomized to one of four experimental diets for 20 weeks (n = 20 animals/group): Low-fat diet (LFD, 10% calories from fat), high-fat diet (HFD, 45% calories from fat), HFD with white carrot powder (HFD + WC), or HFD with orange carrot powder (HFD + OC). Colon tissues were harvested to analyze the biochemical effects of carotenoids in carrots. The distal sections were subjected to isobaric labeling-based quantitative proteomics in which tryptic peptides were labeled with tandem mass tags, followed by fractionation and LC-MS/MS analysis in an Orbitrap Eclipse Tribrid instrument. High-performance liquid chromatography results revealed that the HFD+WC pellets were carotenoid-deficient, and the HFD+OC pellets contained high concentrations of provitamin A carotenoids, specifically -carotene and {beta}-carotene. As a result of the quantitative proteomics, a total of 4410 differentially expressed proteins were identified. Intestinal barrier-associated proteins were highly upregulated in the HFD+OC group, particularly mucin-2 (MUC-2). Upon closer investigation into mucosal activity, other proteins related to MUC-2 functionality and tight junction management were upregulated by the HFD+OC dietary intervention. Collectively, our findings suggest that carotenoid-rich foods can prevent high-fat diet-induced intestinal barrier disruption by promoting colonic mucus synthesis and secretion in mammalian organisms. Data are available via ProteomeXchange with identifier PXD054150.

biochemistry↗

bioRxiv2024

High throughput method for simultaneous screening of membrane permeability and toxicity for discovery of new cryoprotective agents

Vitrification is the most promising method for cryopreservation of complex structures such as organs and tissue constructs. However, this method requires multimolar concentrations of cell-permeant cryoprotective agents (CPAs), which can be toxic at such elevated levels. The selection of CPAs for organ vitrification has been limited to a few chemicals; however, there are numerous chemicals with properties similar to commonly used CPAs. In this study, we developed a high-throughput method that significantly increases the speed of cell membrane permeability measurement, enabling ~100 times faster permeability measurement than previous methods. The method also allows assessment of CPA toxicity using the same 96-well plate. We tested five commonly used CPAs and 22 less common ones at both 4 {degrees}C and room temperature, with 23 of them passing the screening process based on their favorable toxicity and permeability properties. Considering its advantages such as high throughput measurement of membrane permeability along with simultaneous toxicity assessment, the presented method holds promise as an effective initial screening tool to identify new CPAs for cryopreservation. SignificanceCryoprotective agent (CPA) toxicity is the most limiting factor impeding cryopreservation of critically needed tissues and organs for transplantation and medical research. This limitation is in part due to the challenge of rapidly screening compounds to identify candidate molecules that are highly membrane permeable and non-toxic at high concentrations. Such a combination would facilitate rapid CPA permeation throughout the sample, enabling ice-free cryopreservation with minimal toxicity. This study presents a method for rapidly assessing the cell membrane permeability and toxicity of candidate CPAs, identifies several novel high-permeability low-toxicity CPAs for further testing, and lays the groundwork for additional high throughput screening to discover novel CPAs with the potential to improve cryopreservation of complex tissues and organs.

bioengineering↗

bioRxiv2024

Top-Down Modulation of Visual Action Perception: Distinct Task Effects in the Action Observation Network

Perceiving others actions is essential for survival and social interaction. Cognitive neuroscience research has identified a network of brain regions crucial to visual action perception, known as the Action Observation Network (AON), comprising the posterior superior temporal cortex (pSTS), posterior parietal cortex, and premotor cortex. Recent research highlights the importance of integrating top-down processes, such as attention, to gain a deeper understanding of action perception. This study investigates how attention modulates the AON during human action perception. We conducted a two-session fMRI experiment with 27 participants. They viewed eight videos of pushing actions, varying in actor (female vs. male), effector (hand vs. foot), and target (human vs. object). In the first session, participants focused on specific features of the videos (actor, effector, or target). In the second, they passively viewed the videos. From the passive viewing session data, we defined regions of interest (ROIs) in the pSTS, parietal, and premotor cortices for each hemisphere. We then performed model-based representational similarity analysis (RSA) and decoding analysis. RSA results showed that only the task model, among all tested models, exhibited a significant correlation with neural representational similarity matrices (RDMs) across all ROIs, indicating a specific alignment between AON nodes and the ongoing task. Decoding analysis further showed that different task types uniquely affected each AON node, indicating feature- and region-specific interactions. These findings underscore that top-down attentional processes significantly alter neural representations within the AON, highlighting the dynamic interplay between attention and action perception in the brain.

neuroscience↗

bioRxiv2021

A read count-based method to detect multiplets and their cellular origins from snATAC-seq data

Similar to other droplet-based single cell assays, single nucleus ATAC-seq (snATAC-seq) data harbor multiplets that confound downstream analyses. Detecting multiplets in snATAC-seq data is particularly challenging due to its sparsity and trinary nature (0 reads: closed chromatin, 1: open in one allele, 2: open in both alleles), yet offers a unique opportunity to infer multiplets when >2 uniquely aligned reads are observed at multiple loci. Here, we implemented the first read count-based multiplet detection method, ATAC-DoubletDetector, that detects multiplets independently of cell-type. Using PBMC and pancreatic islet datasets, ATAC-DoubletDetector captured simulated heterotypic multiplets (different cell-types) with [~]0.60 recall, showing [~]24% improvement over state of the art. ATAC-DoubletDetector detected homotypic multiplets with [~]0.61 recall, representing the first method to detect multiplets originating from the same cell type. Using our novel clustering-based algorithm, multiplets were annotated to their cellular origins with [~]85% accuracy. Application of ATAC-DoubletDetector will improve downstream analysis of snATAC-seq.

bioinformatics↗

bioRxiv2020

CoRE-ATAC: A Deep Learning model for the functional Classification of Regulatory Elements from single cell and bulk ATAC-seq data

Cis-Regulatory elements (cis-REs) include promoters, enhancers, and insulators that regulate gene expression programs via binding of transcription factors. ATAC-seq technology effectively identifies active cis-REs in a given cell type (including from single cells) by mapping accessible chromatin at base-pair resolution. However, these maps are not immediately useful for inferring specific functions of cis-REs. For this purpose, we developed a deep learning framework (CoRE-ATAC) with novel data encoders that integrate DNA sequence (reference or personal genotypes) with ATAC-seq cut sites and read pileups. CoRE-ATAC was trained on 4 cell types (n=6 samples/replicates) and accurately predicted known cis-RE functions from 7 cell types (n=40 samples) that were not used in model training (mean average precision=0.80). CoRE-ATAC enhancer predictions from 19 human islet samples coincided with genetically modulated gain/loss of enhancer activity, which was confirmed by massively parallel reporter assays (MPRAs). Finally, CoRE-ATAC effectively inferred cis-RE function from aggregate single nucleus ATAC-seq (snATAC) data from human blood-derived immune cells that overlapped with known functional annotations in sorted immune cells, which established the efficacy of these models to study cis-RE functions of rare cells without the need for cell sorting. ATAC-seq maps from primary human cells reveal individual- and cell-specific variation in cis-RE activity. CoRE-ATAC increases the functional resolution of these maps, a critical step for studying regulatory disruptions behind diseases.Author Summary Non-coding DNA sequences serve different functional roles to regulate gene expression. For these sequences to be active, they must be accessible for proteins and other factors to bind in order to carry out a specific regulatory function. Even so, mutations within these sequences or other regulatory events may modulate their activity or regulatory function. It is therefore critical that we identify these non-coding sequences and their specific regulatory function to fully understand how specific genes are regulated. Current sequencing technologies allow us to identify accessible sequences via chromatin accessibility maps from low cell numbers, enabling the study of clinical samples. However, determining the functional role associated with these sequences remains a challenge. Towards this goal, we harnessed the power of deep learning to unravel the intricacies of chromatin accessibility maps to infer their associated gene regulatory functions. We demonstrate that our method, CoRE-ATAC, can infer regulatory functions in diverse cell types, captures activity differences modulated by genetic mutations, and can be applied to accessibility maps of single cell clusters to infer regulatory functions of rare cell populations. These inferences will further our understanding of how genes are regulated and enable the study of these mechanisms as they relate to disease.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗