Biology subjects

Shamipour, S.

Publications and source records attributed to Shamipour, S..

3 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↗

bioRxiv2022

Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes

Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect large-scale cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules upon germinal vesicle breakdown is achieved by the combined activities of yolk granule fusion and microtubule aster formation and translocation. We find that cortical granules are moved towards the oocyte surface through radially-outward cytoplasmic flows induced by yolk granules fusing within the oocyte center in response to GV breakdown. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with cortical granules at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GV breakdown, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of cortical granules by Rab11 at the oocyte surface is needed for cortical granule release and subsequent chorion elevation, a process central in oocyte activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in determining cytoplasmic organization during oocyte maturation.

developmental biology↗

bioRxiv2021

Multi-tier mechanics control stromal adaptations in swelling lymph nodes

Lymph nodes (LNs) comprise two main structural elements: Fibroblastic reticular cells (FRCs) that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. While LNs are fairly stable in size during homeostatic conditions, immunological challenge causes more than 10-fold increase in size within only a few days. How a solid organ can accommodate such extreme volumetric changes is poorly understood. Here, we characterize the biomechanics of LN swelling on the cellular and organ scale. We identify lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing FRCs and their associated conduits to stretch. After an initial phase of relaxation, FRCs sense the resulting strain via cell matrix adhesions, which coordinates local growth and remodeling of the stromal network. While the expanded FRC network adopts its typical configuration, a massive fibrotic reaction of the organ capsule sets in and counters further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multi-tier fashion.

immunology↗