Biology subjects

Farag, N.

Publications and source records attributed to Farag, N..

3 recordsLinked to original sources

bioRxiv2024

Enzyme-Responsive DNA Condensates

Membrane-less compartments and organelles are widely acknowledged for their role in regulating cellular processes, and there is an urgent need to harness their full potential as both structural and functional elements of synthetic cells. Despite rapid progress, synthetically recapitulating the nonequilibrium, spatially distributed responses of natural membrane-less organelles remain elusive. Here we demonstrate that the activity of nucleic-acid cleaving enzymes can be localised within DNA-based membrane-less compartments by sequestering the respective DNA or RNA substrates. Reaction-diffusion processes lead to complex nonequilibrium patterns, dependent on enzyme concentration. By arresting similar dynamic patterns, we spatially organise different substrates in concentric sub-compartments, which can be then selectively addressed by different enzymes, demonstrating spatial distribution of enzymatic activity. Besides advancing our ability to engineer advanced biomimetic functions in synthetic membrane-less organelles, our results may facilitate the deployment of DNA-based condensates as microbioreactors or platforms for the detection and quantitation of enzymes and nucleic acids.

synthetic biology↗

bioRxiv2024

A high-throughput zebrafish screen identifies novel candidate treatments for Kaposiform Lymphangiomatosis (KLA)

Kaposiform Lymphangiomatosis (KLA) is a rare, aggressive, and incurable disease caused by a somatic activating NRAS mutation (p.Q61R) in lymphatic endothelial cells (LECs). The development of new therapeutic avenues is hampered by the lack of animal models faithfully replicating the clinical manifestations of KLA. Here, we established a novel zebrafish model of KLA by driving conditional expression of the human NRAS mutation in venous and lymphatic ECs. We find that mutant embryos recapitulated clinical features of KLA, including pericardial edema and a dilated thoracic duct, and that the phenotypes were reverted by Trametinib, a MEK inhibitor used for KLA treatment. We further leverage this model in combination with an AI-based high-throughput drug screening platform to search for small compounds selectively reverting the mutant phenotypes and identify Cabozantinib, an FDA-approved tyrosine kinase inhibitor, and GSK690693, a competitive pan-Akt kinase inhibitor, as leading hits. Finally, we test these drugs in cultured cells derived from KLA patient and demonstrate their ability to normalize LEC sprouting and block NRAS downstream pathways, underscoring the potential of GSK690693 and Cabozantinib as potential KLA treatments. Overall, our novel zebrafish model provides a valuable tool for research into the etiology of KLA and for identifying new therapeutic avenues.

developmental biology↗

bioRxiv2023

Coordination between endoderm progression and gastruloid elongation controls endodermal morphotype choice

Embryos mostly follow a single morphogenetic trajectory, where variability is largely quantitative with no qualitative differences. This robustness stands in contrast to in-vitro embryo-like models, which, like most organoids, display a high degree of variability. What makes embryonic morphogenesis so robust is unclear. We use the gastruloid model to study the morphogenetic progression of definitive endoderm (DE) and its divergence. We first catalog the different morphologies and characterize their statistics. We then learn predictive models for the lineage morphotype based on earlier expression and morphology measurements. Finally, we analyze these models to identify key drivers of morphotype variability, and devise personalized (gastruloid-specific) as well as global interventions that will lower this variability and steer morphotype choice. In the process we identify two types of coordination that are lacking in the in-vitro model but are required for robust gut tube formation. We expect the insights obtained here will improve the quality and usability of 3D embryo-like models, chart a methodology extendable to other organoids for controlling variability, and will also shed light on the factors that provide the embryo its morphogenetic robustness.

developmental biology↗