Biology subjects

Ceisel, A.

Publications and source records attributed to Ceisel, A..

4 recordsLinked to original sources

bioRxiv2026

Mechanochemical cues control the coupling of metabolic and migratory patterns in cancer

Confined migration is essential for metastasis, yet how cells adapt their migratory and metabolic programs across stiffness-varying microenvironments remains unclear. We uncover a stiffness-dependent mechano-metabolic switch governing migration. In stiff microchannels, cells utilize the osmotic engine model (OEM), relying on NHE1 activity, front-polarization, and glycolysis. In soft microchannels, migration is OEM-independent and requires pyruvate-fueled oxidative phosphorylation (OxPHOS). This OxPHOS-driven motility depends on Arp3, {beta}1-integrin and integrin-linked kinase, which increase membrane tension in confinement that in turn triggers TRPM7-mediated calcium influx and RhoA-/myosin-II contractility. Activating and polarizing NHE1, via overexpression, hypoxia or elevated viscosity, restore OEM- and glycolysis-dependent migration in soft microchannels, bypassing the need for actin polymerization in vitro and in chick embryos. Mitochondria addition reinstates Arp3 polarization and enhances migration in NHE1-overexpressing cells, enabling engagement of both mechanisms in vitro and in zebrafish. These findings uncover a previously unrecognized mechano-metabolic link, revealing that intracellular rewiring overrides stiffness-dependent metabolic demands.

cell biology↗

bioRxiv2026

Fluorescently-labeled split-QF hemidrivers: simplifying and enhancing methods enabling intersectional targeting of discrete cell types

Single cell transcriptomics data predict greater cell type diversity than previously appreciated, defined by combinatorial gene expression "codes". These codes can enable intersectional targeting strategies for selectively labeling and manipulating predicted cell types, thereby facilitating functional tests to resolve cell-specific roles and refine cell-type definitions. One such approach cleaves driver components of binary expression systems (e.g., Gal4/UAS and QF/QUAS) into two co-dependent halves, an Activation Domain (AD) and a DNA Binding Domain (DBD). The transcriptional activity of these "split-drivers" (aka, hemidrivers) is only reconstituted in cells that co-express them. While widely used in invertebrates, these systems have yet to be systematically deployed in vertebrates. Here, we developed a series of fluorescently labeled split-QF and QF2 hemidrivers via direct reporter fusions or the 2A viral peptide co-expression system. Fluorescent labeling serves to 1) simplify hemidriver transgenic line creation and maintenance, 2) allow AD and DBD intersects to be visualized directly, and 3) enable robust quality control assessments of on-target efficacy and off-target activity. These resources can enhance transgenic targeting specificity, enabling functional dissections of cell types revealed by single cell transcriptomics. SUMMARYWe engineered fluorescently labeled split-QF and -QF2 hemidrivers in zebrafish to simplify intersectional targeting tool generation and enable robust quality control assessments of split-driver function.

genetics↗

bioRxiv2025

Developing a zebrafish xenograft model of diffuse midline glioma

Diffuse midline glioma (DMG) is a highly aggressive brain tumor that predominantly affects children. Conventional treatments such as radiation therapy can control progression for a time, but DMG kills nearly 100 percent of patients. Although murine models have provided critical insights into the biology of DMG and in assessing new therapeutic strategies, they are not suitable for high-throughput screening to identify and profile novel therapies due to technical challenges, ethical considerations and high cost. Zebrafish (Danio rerio) is an established vertebrate model for large-scale drug screening, and zebrafish have demonstrated the ability to replicate the key biological and pathlogical aspects of human malignancies. Here, we developed a novel method for transplanting human DMG cells into large numbers of zebrafish embyros to speed the assessment of anti-tumor drug efficacy in vivo and thereby facilitate the development of novel therapeutics for clinical translation. We transplanted red fluorescent protein (RFP)-labeled, patient-derived DMG cell lines into zebrafish blastulas. Remarkably, many DMG cells migrate into the developing brain and are present in the midline of the brain 24 hours after blastula injection. Tumor cell burden was monitored by measuring RFP fluorescence intensity changes over time. Time-course images of transplanted tumor cell volumes were acquired, and the interactions between transplanted DMG cells and microglial cells were further analyzed using Imaris software. We have developed a simple and rapid transplantation protocol to establish a zebrafish xenograft model of DMG. Our method involves transplanting DMG cells into the blastula stage (1000 cell stage) of zebrafish embryos, which does not require complex surgical techniques. This approach allows for the transplantation of hundreds of embryos per hour, significantly increasing the efficiency of creating DMG zebrafish xenografts that are suitable for high-throughput drug and gene discovery screens.

cancer biology↗

bioRxiv2023

Molecular regulation of retinal regeneration is context specific

Many genes are known to regulate retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited retinal cell loss, akin to disease conditions, are undefined. Combining a novel retinal ganglion cell (RGC) ablation-based glaucoma model, single cell omics, and rapid CRISPR/Cas9-based knockout methods to screen 100 genes, we identified 18 effectors of RGC regeneration kinetics. Surprisingly, 32 of 33 previously known/implicated regulators of retinal tissue regeneration were not required for RGC replacement; 7 knockouts accelerated regeneration, including sox2, olig2, and ascl1a. Mechanistic analyses revealed loss of ascl1a increased "fate bias", the propensity of progenitors to produce RGCs. These data demonstrate plasticity and context-specificity in how genes function to control regeneration, insights that could help to advance disease-tailored therapeutics for replacing lost retinal cells. One sentence summaryWe discovered eighteen genes that regulate the regeneration of retinal ganglion cells in zebrafish.

neuroscience↗