Biology subjects

Berrouayel, Y.

Publications and source records attributed to Berrouayel, Y..

4 recordsLinked to original sources

bioRxiv2025

Transcriptomic profile of embryoid bodies under hypoxia at single cell level

Oxygen availability is a key regulator of cellular physiology and hypoxia plays a central role driving vasculogenesis and angiogenesis during development. While bulk transcriptomics has revealed important oxygen-regulated gene networks, such approaches cannot resolve the cellular heterogeneity and lineage dynamics characteristic of early differentiation. To address this, we generated a single-cell transcriptomic dataset from murine embryoid bodies, a widely used in vitro model of early embryonic development, cultured 8 or 10 days under hypoxic (1% O2) or normoxic (21% O2) conditions for the final 16 or 48 hours of differentiation. This resource enables detailed exploration of how oxygen availability influences lineage specification, vascular and hematopoietic development, and cellular heterogeneity during early differentiation. Beyond developmental biology, the dataset provides a valuable reference for comparative studies of hypoxia responses, benchmarking of single-cell analysis methods, and integrative investigations into oxygen signaling across diverse biological systems.

cell biology↗

bioRxiv2025

Intermittent Hypoxia Drives Early Metabolic Dysfunction in Brown Adipose Tissue

BackgroundObstructive sleep apnea (OSA) is associated with metabolic dysfunction, yet the early impact of intermittent hypoxia (IH)--a defining feature of OSA--on brown adipose tissue (BAT) remains unclear. MethodsWe investigated the direct and early effects of IH on BAT using both in vitro and in vivo approaches. Differentiated mouse brown adipocytes were exposed to IH for 48 hours and analyzed for {beta}3-adrenergic signaling, lipolysis, and thermogenic activation. Complementary in vivo studies assessed transcriptomic, morphological, and functional changes in BAT, white adipose tissue (WAT), and liver after 1 or 4 weeks of IH exposure in mice. ResultsIH blunted {beta}3-adrenergic signaling in cultured brown adipocytes, leading to reduced phosphorylation of key signaling proteins, impaired lipolytic response, and decreased expression of UCP1. In vivo, BAT exhibited early and sustained transcriptomic rewiring characterized by downregulation of pathways related to fatty acid metabolism, oxidative phosphorylation, and peroxisomal function. These molecular changes were accompanied by abnormal lipid droplet enlargement and a reduced lipolytic response to adrenergic stimulation. In contrast, WAT showed transient gene expression changes, and the liver displayed a delayed and robust transcriptomic response evident only after four weeks of IH exposure. Despite these metabolic alterations, thermogenic responses to cold challenge remained intact in IH-treated mice. ConclusionsBAT is uniquely and rapidly affected by intermittent hypoxia, undergoing functional, molecular, and morphological changes within one week of exposure. These alterations precede systemic inflammation and metabolic dysfunction, positioning BAT dysfunction as an early event in the pathogenesis of OSA-associated metabolic disease.

pathology↗

bioRxiv2025

Enhancing TFEA.ChIP with ENCODE Regulatory Maps for Generalizable Transcription Factor Enrichment

Identifying transcription factors (TFs) responsible for gene expression changes remains a central challenge in functional genomics. TFEA.ChIP is a ChIP-seq-based TF enrichment analysis tool that addresses this by linking TF binding profiles to differentially expressed genes through experimentally supported cis-regulatory element (CRE)-gene associations. Unlike motif- or heuristic-based approaches, TFEA.ChIP adopts a biologically grounded strategy by intersecting TF binding data from ReMap2022 with regulatory maps from ENCODEs rE2G and CREdb. To overcome the high context-specificity of rE2G associations, we developed filtering strategies based on confidence scores and recurrence across biosamples. Benchmarking on 369 curated gene sets from the MSigDB C2 CGP collection showed that recurrence-based filtering significantly improved accuracy, outperforming the original GeneHancer-based implementation and leading tools including BARTv2.0, Lisa, ChEA3, and HOMER. A case study on hypoxia further validated the method, demonstrating accurate and pathway-specific enrichment of HIF-related TFs using both overrepresentation analysis and gene set enrichment analysis (GSEA). Additionally, the updated implementation of TFEA.ChIP in R/Bioconductor introduces several user-friendly features, including automated analysis workflows and expression-based filtering of candidate TFs. These additions streamline the integration of TFEA.ChIP into standard RNA-seq analysis pipelines, enabling more efficient and reproducible workflows. Together with its strong benchmarking performance and biologically grounded framework, the updated tool provides a robust and accessible solution for inferring transcriptional regulators from gene expression data.

bioinformatics↗

bioRxiv2024

Bhlhe40 limits proliferation and prevents excessive angiogenesis in mouse embryoid bodies under hypoxia

Knowledge of the molecular mechanisms that underlie the regulation of the major adaptive responses to an unbalanced oxygen tension is central to understanding tissue homeostasis and disease. Hypoxia-inducible transcription factors (HIFs) coordinate changes in the transcriptome that control these adaptive responses. Here, we focused on the functional role of the transcriptional repressor basic-helix-loop-helix family member e40 (Bhlhe40), which we previously identified in a meta-analysis as one of the most consistently up-regulated genes in response to hypoxia across various cell types. We investigated the role of Bhlhe40 in controlling proliferation and angiogenesis using a gene editing strategy in mouse embryonic stem cells (mESCs) that we differentiated in embryoid bodies (EBs). We observed that hypoxia-induced Bhlhe40 expression was compatible with the rapid proliferation of pluripotent mESCs under low oxygen tension. However, in EBs, hypoxia triggered a Bhlhe40-dependent cell cycle arrest in most progenitor cells and endothelial cells within vascular structures. Furthermore, Bhlhe40 knockout increased the basal vascularization of the EBs in normoxia and exacerbated the hypoxia-induced vascularization, supporting a novel role for Bhlhe40 as a negative regulator of blood vessel formation. Our findings implicate Bhlhe40 in mediating key functional adaptive responses to hypoxia, such as proliferation arrest and angiogenesis.

molecular biology↗