Biology subjects

Wurtzel, O.

Publications and source records attributed to Wurtzel, O..

4 recordsLinked to original sources

bioRxiv2023

Methods for cell isolation and analysis of the highly regenerative tunicate Polycarpa mytiligera

Polycarpa mytiligera is the only molecularly characterized solitary ascidian capable of regenerating all organs and tissue types. The cellular basis for regeneration in P. mytiligera is largely unknown, and methods for isolating live cells from this species for functional analyses are unavailable. Here, we developed a method for isolating live cells from P. mytiligera, overcoming major experimental challenges, including the dissociation of its thick body wall and native cellular autofluorescence. We demonstrated the applicability of our approach for tissue dissociation and cell analysis using three flow cytometry platforms, and by using broadly used non-species-specific cell labeling reagents. In addition to live cell isolation, proof-of-concept experiments showed that this approach was compatible with gene expression analysis of RNA extracted from the isolated cells, and with ex vivo analysis of phagocytosis. The ability to purify live cells will promote future studies of cell function in P. mytiligera regeneration.

developmental biology↗

bioRxiv2022

PLANAtools - an interactive gene expression repository for the planarian Schmidtea mediterranea

MotivationPlanarians are a widespread model for studying regeneration. Major efforts for studying gene function in planarian regeneration produced massive datasets, including transcriptome-wide gene expression analyses from hundreds of conditions. However, the accessibility of gene expression datasets to investigators is limited because of the need for expertise in gene expression analysis in this model, the requirement for computational resources, and the lack of a curated planarian gene expression metadata resource associating samples and their controls. ResultsWe implemented a computational resource, PLANAtools, that is available online and provides a portal to the analysis of over 160 gene expression analyses. Planarian gene expression datasets from the last decade were processed using a standardized pipeline based on curated planarian metadata. PLANAtools generates plots, annotations, and analyses of gene expression data, based on user parameters. AvailabilityPLANAtools is implemented using the R/Shiny framework and is accessible from https://wurtzellab.org/planatools

developmental biology↗

bioRxiv2021

Stemness activity underlying whole brain regeneration in a basal chordate

Central nervous system (CNS) regeneration extent is highly diverse across the metazoans, with adult mammals demonstrating limited ability1,2. Understanding how neurons regenerate following injury remains a central challenge in regenerative medicine. Although conserved pathways associated with neural regeneration have been identified3,4, a study describing the stepwise morphogenetic changes that take place throughout a complete CNS regeneration is lacking. Utilizing the highly regenerative tunicate model Polycarpa mytiligera5, we characterized the morphological, cell proliferation, and transcriptomic dynamics that lead to entire CNS regeneration. The regenerated CNS of adult P. mytiligera expressed key neurodevelopmental markers that are not otherwise present in the adult CNS. Removal of the entire CNS resulted in high cell proliferation in the regenerated area. Transcriptome analysis revealed enhanced stem-cell related gene activity, with high expression of P53 and piRNA pathways preceding the activation of Notch, Wnt, and Nanos pathways. The CNS regeneration atlas created here depicts the transcriptomic landscape of the entire CNS regeneration process, revealing the core pathways that regulate neuronal response to injury, and the regeneration stage at which they are most pronounced. The molecular and cellular mechanisms controlling regenerative capacity that this atlas reveals could be used to develop approaches to enhancing neurogenesis in closely-related chordate species, including humans.

developmental biology↗

bioRxiv2021

m6A is required for resolving progenitor identity during planarian stem cell differentiation

Regeneration requires accurate production of missing cell lineages. Cell production is driven by changes to gene expression, which is shaped by multiple layers of regulation. Here, we find that the ubiquitous mRNA base-modification, m6A, is required for proper cell fate choice and cellular maturation in planarian stem cells (neoblasts). We mapped m6A-enriched regions in 7,600 planarian genes, and found that perturbation of the m6A pathway resulted in progressive deterioration of tissues and death. Using single cell RNA sequencing of >20,000 cells following perturbation of the pathway, we discovered that m6A negatively regulates transcription of histone variants, and that inhibition of the pathway resulted in accumulation of undifferentiated cells throughout the animal in an abnormal transcriptional state. Analysis of >1000 planarian gene expression datasets revealed that the inhibition of the chromatin modifying complex NuRD had almost indistinguishable consequences, unraveling an unappreciated link between m6A and chromatin modifications. Our findings reveal that m6A is critical for planarian stem cell homeostasis and gene regulation in regeneration.

developmental biology↗