Biology subjects

Bedzhov, I.

Publications and source records attributed to Bedzhov, I..

4 recordsLinked to original sources

bioRxiv2026

Shield-4i: A Whole-mount Multiplexed Imaging Platform for Studying Multiscale Information Flow in 3D Multicellular Systems

Self-organization in multicellular systems emerges from reciprocal interactions across spatiotemporal scales. Understanding how subcellular organization, tissue remodeling and developmental outcome are coordinated, thus requires simultaneous profiling of biological processes spanning orders of magnitudes in space and time. Yet, a unified experimental and computational framework for capturing these multiscale properties across in vivo and stem cell-derived systems has been lacking. Here, we introduce Shield-4i, a high-throughput, versatile, and accessible method for automated in toto iterative immunofluorescence imaging of whole-mount structures at subcellular resolution. Through polyepoxide-mediated inter- and intramolecular crosslinking, Shield-4i preserves sample integrity during repeated SDS-based elution cycles. We benchmark this method in gastrulating zebrafish and post-implantation mouse embryos and demonstrate its applicability to stem cell-derived 3D gastruloids, achieving up to 30-plex measurements of proteins and their post-translational modifications across hundreds of samples. To enable scalable analysis, we developed a dedicated 3D workflow supporting OME-Zarr-based and FAIR-compliant data storage, standardized processing, and multiscale feature extraction. Applying this framework to investigate gastruloid self-organization, we quantify how cellular physicochemical state and signaling properties encode cell position along embryonic axes and connect molecular patterning and fate decisions to morphological symmetry breaking at the multicellular scale. Together, Shield-4i provides a high-content in toto spatial proteomics platform for dissecting multiscale information flow and self-organization in multicellular systems.

systems biology↗

bioRxiv2023

Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse embryos

During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 activate the pluripotency-related genes through the putative OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory towards the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.

developmental biology↗

bioRxiv2023

Tissue-intrinsic Wnt signals antagonize Nodal-driven AVE differentiation

The anterior-posterior axis of the mammalian embryo is laid down by the anterior visceral endoderm (AVE), an extraembryonic signaling center that is specified within the visceral endoderm. Current models posit that AVE differentiation is promoted globally by epiblast-derived Nodal signals, and spatially restricted by a BMP gradient established by the extraembryonic ectoderm. Here, we report spatially restricted AVE differentiation in bilayered embryo-like aggregates made from mouse embryonic stem cells that lack an extraembryonic ectoderm. Notably, clusters of AVE cells also form in pure visceral endoderm cultures upon activation of Nodal signaling, indicating that tissue-intrinsic factors restrict AVE differentiation. We identify Wnt signaling as a tissue-intrinsic factor that antagonizes AVE-inducing Nodal signals. Together, our results suggest that interactions between epiblast and visceral endoderm alone enable local AVE differentiation in the absence of graded BMP signals. This may be a flexible solution for axis patterning in a wide range of embryo geometries.

developmental biology↗

bioRxiv2021

Hypoxia induces a transcriptional early primitive streak signature in pluripotent cells enhancing spontaneous elongation and lineage representation in gastruloids

The cellular microenvironment together with intrinsic regulators shapes stem cell identity and differentiation capacity. Mammalian early embryos are exposed to hypoxia in vivo and appear to benefit from hypoxic culture in vitro. Yet, components of the hypoxia response and how their interplay impacts stem cell transcriptional networks and lineage choices remain poorly understood. Here we investigated the molecular effects of acute and prolonged hypoxia on distinct embryonic and extraembryonic stem cell types as well as the functional impact on differentiation potential. We find a temporal and cell type-specific transcriptional response including an early primitive streak signature in hypoxic embryonic stem (ES) cells. Using a 3D gastruloid differentiation model, we show that hypoxia-induced T expression enables symmetry breaking and axial elongation in the absence of exogenous WNT activation. Importantly, hypoxia also modulates T levels in conventional gastruloids and enhances representation of endodermal and neural markers. Mechanistically, we identify Hif1 as a central factor that mediates the transcriptional response to hypoxia in balance with epigenetic and metabolic rewiring. Our findings directly link the microenvironment to stem cell function and provide a rationale supportive of applying physiological conditions in models of embryo development

developmental biology↗