Biology subjects

Chrysostomou, E.

Publications and source records attributed to Chrysostomou, E..

9 recordsLinked to original sources

bioRxiv2025

Muscle stem cells produce a protective Fibrillin-1 matrix to prevent precocious activation.

Multiple biological mechanisms have been uncovered to regulate muscle stem cell quiescence, including inhibition of differentiation, adhesion-dependent anchoring, and translational control, which can be broadly classified as intrinsic or extrinsic properties. Here, we identify the matrix glycoprotein Fibrillin-1 (FBN1) as a Notch-regulated, cell-autonomous effector, essential for maintaining quiescence in muscle stem cells. Known for its causal role in Marfan syndrome (MFS), a connective tissue disorder that also presents with skeletal muscle atrophy, our work positions FBN1 as a critical niche component that protects stem cells from aberrant growth factor signalling. We demonstrate that targeted deletion of Fbn1 in muscle stem cells leads to dose-dependent quiescence defects, characterized by loss of cellular projections, depletion of the stem cell pool, and progressive decline in muscle function. Consistently, human MFS muscle biopsies show abnormally activated satellite cells, implicating stem cell imbalance in the development of MFS-associated myopathy. Mechanistically, the loss of FBN1 upregulates TGF{beta} signalling, and pharmacological inhibition of this pathway using the Angiotensin Receptor blocker losartan restores the cellular and physiological defects of mutant muscles. These findings reveal a new quiescence-preserving mechanism through extracellular matrix-mediated shielding from mitogenic signals, and position stem cell dysfunction as a driver of MFS myopathy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/666604v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1895e71org.highwire.dtl.DTLVardef@1974e87org.highwire.dtl.DTLVardef@a49979org.highwire.dtl.DTLVardef@5813c9_HPS_FORMAT_FIGEXP M_FIG C_FIG Model of Fibrillin-1 protective barrier in quiescent satellite cells.Satellite cells produce Fibrillin-1 (FBN1) to establish a localized extracellular matrix barrier that limits exposure to mitogenic signals. Mechanistically, FBN1 expression is induced by Notch signalling and serves to sequester latent TGF{beta} complexes in an inactive form, thereby preventing their activation within the immediate niche. This barrier is spatially restricted beneath the basal lamina and remains functionally independent from the abundant interstitial FBN1 produced by fibro-adipogenic progenitors (FAPs). The model describes a self-contained, satellite cell-derived ECM system that maintains quiescence by insulating the cells from activating cues.

cell biology↗

bioRxiv2025

The Notch ligand Jagged1 plays a dual role in cochlear hair cell regeneration.

Hair cells (HCs) within the inner ear cochlea are specialized mechanoreceptors required for hearing. Cochlear HCs are not regenerated in mammals, and their loss is a leading cause of deafness in humans. Cochlear supporting cells (SCs) in newborn mice have the capacity to regenerate HCs, but persistent Notch signaling, presumably activated by SC-specific Notch ligand Jagged1 (JAG1), prevents SCs from converting into HCs. Here, employing an organoid platform, we show that while JAG1 participates in HC-fate repression, JAG1s primary function is to preserve the "progenitor-like characteristics" of cochlear SCs. Transcriptomic and mechanistic studies reveal that JAG1/Notch signaling maintains the expression of progenitor and metabolic genes in cochlear SCs and sustains pro-growth pathways, including PI3K-Akt-mTOR signaling, a function that is mediated by Notch1 and Notch2. Finally, we show that JAG1/Notch signaling stimulation with JAG1-Fc peptide enhances the HC-forming capacity of cochlear SCs undergoing maturation in cochlear explants and in vivo.

developmental biology↗

bioRxiv2025

Differential Roles of Broadly Expressed Transcription Factors in Early Cardiac Cell Specification

Early embryogenesis is governed by intricate gene regulatory networks that orchestrate cell fate specification across all three germ layers. While the role of transcription factors (TFs) and pioneer factors (PFs) in shaping chromatin accessibility is well established, the mechanisms coordinating spatiotemporal gene expression before gastrulation remain poorly understood. Here, we investigate how a coordinated network of early-acting regulators, including the pioneer factors Zelda (Zld), GAGA factor (GAF), and the pioneer-like timing factor Odd-paired (Opa/ZIC3), along with Dorsal (Dl), Twist (Twi), the Polycomb subunit Enhancer of Zeste (E(z)), and the co-activator CBP, govern early transcriptional events in the Drosophila embryo. Using integrated chromatin accessibility, histone modification, TF binding, and transcriptomic data (bulk and single-cell), we identify two distinct classes of regulatory elements that govern early gene expression. The first class includes distal, PF-dependent enhancers that are inaccessible early and require PFs such as Opa and Zld to overcome Su(H) activities and H3K27me3-mediated repression and initiate transcription. The second class, enriched for PcG domains, comprises proximal enhancers that are accessible from the earliest nuclear cycles, despite being marked by H3K27me3 and bound by E(z). These regions are preloaded with RNA Polymerase II and positioned near promoters, suggesting a regulatory state primed for activation. While bound by multiple early TFs, these enhancers maintain accessibility independently of PF activity, functioning instead as autoregulatory elements that rely on PFs for maintenance rather than initiation. This study expands our understanding of how early TFs and PFs coordinate to balance transcriptional precision and developmental plasticity across germ layers, and redefines the role of PFs as both activators and stabilizers of gene regulatory architecture. Within this framework, Opa regulates key mesodermal and neuroectodermal genes such as slp1 and odd, and its activity is modulated by Suppressor of Hairless (Su(H)). At earlier stages, Su(H) represses Opa target genes, but rising Opa levels at later timepoints override this repression, enabling activation. Together, these findings support a dual-mode enhancer logic: one mode driven by PF-mediated chromatin opening at distal, repressed enhancers, and another where proximal, pre-accessible enhancers within PcG-marked regions are reinforced by PF binding. This study redefines the role of PFs in early development, emphasizing their maintenance and stabilizing roles at poised enhancers, and provides a framework for how embryos balance transcriptional plasticity with spatial precision across all germ layers.

developmental biology↗

bioRxiv2024

An Open-Source Deep Learning-Based GUI Toolbox For Automated Auditory Brainstem Response Analyses (ABRA)

Hearing loss is a pervasive global health challenge with profound impacts on communication, cognitive function, and quality of life. Recent studies have established age-related hearing loss as a significant risk factor for dementia, highlighting the importance of hearing loss research. Auditory brainstem responses (ABRs), which are electrophysiological recordings of acoustically evoked synchronized neural activity from the auditory nerve and brainstem, serve as in vivo correlates for sensory hair cell and synaptic function, hearing sensitivity, and other critical readouts of auditory pathway physiology, making them highly valuable for both basic neuroscience and clinical research. Despite their utility, traditional ABR analyses rely heavily on subjective manual interpretation, which may introduce variability and pose challenges for reproducibility across studies. Here, we introduce Auditory Brainstem Response Analyzer (ABRA), a novel suite of open-source ABR analysis tools powered by deep learning, which automates and standardizes ABR waveform analysis. ABRA employs convolutional neural networks trained on diverse datasets collected from multiple experimental settings, achieving rapid and unbiased extraction of key ABR metrics, including peak amplitude, latency, and auditory threshold estimates. We demonstrate that ABRAs deep learning models provide performance comparable to expert human annotators while dramatically reducing analysis time and enhancing reproducibility across datasets from different laboratories. By bridging hearing research, sensory neuroscience, and advanced computational techniques, ABRA facilitates broader interdisciplinary insights into auditory function. An online version of the tool is available for use at no cost at https://abra.ucsd.edu.

neuroscience↗

bioRxiv2022

A pan-cnidarian microRNA is an ancient biogenesis regulator of stinging cells

An ancient evolutionary innovation of a novel cell-type, the stinging cell (cnidocyte), appeared >600 million years ago in the phylum Cnidaria (sea anemones, corals, hydroids, and jellyfish). A complex bursting nano-injector of venom, the cnidocyst, is embedded in cnidocytes and enables cnidarians paralyzing prey and predators, contributing to this phylums evolutionary success. In this work, we show that post-transcriptional regulation by a pan-cnidarian microRNA, miR-2022, is essential for biogenesis of these cells. By manipulation of miR-2022 levels in a transgenic reporter line of cnidocytes in the sea anemone Nematostella vectensis, followed by transcriptomics, single-cell data analysis, prey paralysis assays, and cell sorting of transgenic cnidocytes, we reveal that miR-2022 enables cnidocyte biogenesis, while exhibiting a conserved expression domain with its targets in cnidocytes of other cnidarian species. Thus, here we reveal one of natures most ancient microRNA-regulated processes by studying the functional basis for its conservation.

evolutionary biology↗

bioRxiv2022

The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain

Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these technologies at unprecedented scale to map the cell types in the mammalian brain. In an effort to increase data FAIRness (Findable, Accessible, Interoperable, Reusable), the NIH has established repositories to make data generated by the BICCN and related BRAIN Initiative projects accessible to the broader research community. Here, we describe the Neuroscience Multi-Omic Archive (NeMO Archive; nemoarchive.org), which serves as the primary repository for genomics data from the BRAIN Initiative. Working closely with other BRAIN Initiative researchers, we have organized these data into a continually expanding, curated repository, which contains transcriptomic and epigenomic data from over 50 million brain cells, including single-cell genomic data from all of the major regions of the adult and prenatal human and mouse brains, as well as substantial single-cell genomic data from non-human primates. We make available several tools for accessing these data, including a searchable web portal, a cloud-computing interface for large-scale data processing (implemented on Terra, terra.bio), and a visualization and analysis platform, NeMO Analytics (nemoanalytics.org). KEY POINTSO_LIThe Neuroscience Multi-Omic Archive serves as the genomics data repository for the BRAIN Initiative. C_LIO_LIGenomic data from >50 million cells span all the major regions of the brains of humans and mice. C_LIO_LIWe provide a searchable web portal, a cloud-computing interface, and a data visualization platform. C_LI

genomics↗

bioRxiv2022

A cellular and molecular analysis of SoxB-driven neurogenesis in a cnidarian

Neurogenesis is the generation of neurons from stem cells, a process that is regulated by SoxB transcription factors (TFs) in many animals. Although the roles of these TFs are well understood in bilaterians, how their neural function evolved is unclear. Here, we use Hydractinia symbiolongicarpus, a member of the early-branching phylum Cnidaria, to provide insight into this question. Using a combination of mRNA in situ hybridization, transgenesis, gene knockdown, transcriptomics, and in-vivo imaging, we provide a comprehensive molecular and cellular analysis of neurogenesis during embryogenesis, homeostasis, and regeneration in this animal. We show that SoxB genes act sequentially. Stem cells expressing Piwi1 and Soxb1, which have a broad developmental potential, become neural progenitors that express Soxb2 before differentiating into mature neural cells. Knockdown of SoxB genes resulted in complex defects in embryonic neurogenesis. Hydractinia neural cells differentiate while migrating from the aboral to the oral end of the animal, but it is unclear whether migration per se or exposure to different microenvironments is the main driver of their fate determination. Our data constitute a rich resource for studies aiming at addressing this question, which is at the heart of understanding neurological disorders in all animals, including humans.

developmental biology↗

bioRxiv2020

gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration

The gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data types (bulk, sorted, single cell/nucleus) and epigenomics data, from multiple species, time points and tissues in a single-page, user-friendly browsable format. An integrated scRNA-seq workbench provides access to raw data of scRNA-seq datasets for de novo analysis, as well as marker-gene and cluster comparisons of pre-assigned clusters. Users can upload, view, analyze and privately share their own data in the context of previously published datasets. Short, permanent URLs can be generated for dissemination of individual or collections of datasets in published manuscripts. While the gEAR is currently curated for auditory research with over 90 high-value datasets organized in thematic profiles, the gEAR also supports the BRAIN initiative (via nemoanalytics.org) and is easily adaptable for other research domains.

bioinformatics↗

bioRxiv2020

The Notch Ligand Jagged1 is Required for the Formation, Maintenance, and Survival of Hensen Cells in the Mouse Cochlea

During cochlear development, the Notch ligand JAGGED 1 (JAG1) plays an important role in the specification of the prosensory region, which gives rise to sound-sensing hair cells and neighboring supporting cells (SCs). While JAG1s expression is maintained in SCs through adulthood, the function of JAG1 in SC development is unknown. Here, we demonstrate that JAG1 is essential for the formation and maintenance of Hensen cells (HeCs), a highly specialized SC-subtype located at the edge of the auditory epithelium. Deletion of Jag1 at the onset of differentiation, at stage E14.5, disrupted HeC formation. Similar loss of HeCs was observed when Jag1 was deleted at P0/P1 and fate-mapping analysis revealed that in the absence of Jag1 some HeCs die, but others convert into neighboring Claudius cells. In support of a role for JAG1 in cell survival, genes involved in mitochondrial function and protein synthesis were downregulated in P0 cochlea lacking Jag1.

developmental biology↗