Biology subjects

Wurtzel, O.

Publications and source records attributed to Wurtzel, O..

9 recordsLinked to original sources

bioRxiv2026

Sustained immune activation suppresses planarian regeneration

Tissue injury immediately triggers immune defenses to prevent infection, a process that can paradoxically interfere with repair. Yet, how some organisms resolve this tension to fully regenerate remains poorly understood. Planarians, flatworms capable of regenerating any body part, offer a unique model for studying how robust immunity coexists with extensive regenerative capacity. Here, we show that the planarian immediate injury response is dominated by the robust upregulation of immune and stress-related genes, demonstrating that defense mechanisms are intrinsically wired into wound sensing. By uncoupling immune activation from tissue injury using exposure to heat-inactivated bacteria, we found that immune stimulation alone induced a transcriptional program mirroring central aspects of the early injury response. Prolonged immune activation led to progressive, host-driven tissue lysis that was fully reversible upon removal of the stimulus. Single-cell profiling identified distinct epidermal and phagocytic subpopulations as the central mediators of this "defense-first" response. Furthermore, we identified foxF-1-regulated phagocytes as critical drivers of immune resolution, as suppressing foxF-1 markedly increased vulnerability to noninfectious immune challenge. Finally, we demonstrated that sustained immune hyperactivation delayed regenerative progression by approximately 50%. Together, our findings establish the resolution of immune activity as a critical prerequisite for regeneration and define sustained immune activation as a fundamental constraint on tissue repair.

developmental biology↗

bioRxiv2026

Trans-regenerational RNAi Memory in Planarians

How cells and organisms preserve molecular memory is a central question in biology. Chromatin states can maintain cellular memory in animals, yet DNA and histone modifications are typically reset in the germ line and early embryo. In Caenorhabditis elegans, RNA-dependent RNA polymerases (RdRPs) amplify small RNAs and enable transgenerational gene regulation. However, many organisms, including mammals, lack canonical RdRPs. Here we find that planarians, highly regenerative flatworms that lack canonical RdRPs and critical nuclear RNAi machinery, mount long-term heritable gene regulatory responses. We show that ingestion of double-stranded RNA induces potent, sequence-specific silencing that persists for months, withstands repeated cycles of whole-body regeneration, and can be transferred between animals. This long-term silencing, heritable during asexual reproduction, follows two phases: an early, transient response to exogenous RNA, and a stable, cell-autonomous memory phase that maintains repression long after the RNA trigger is gone. The memory phase is maintained post-transcriptionally, as transcription and chromatin accessibility remain unchanged while mature mRNA is depleted. This phase coincides with the emergence of A-tailed 21-23-nt antisense small RNAs and with silencing responses that act in trans and spread across the length of the target transcript. These results reveal a two-step, canonical RdRP-independent mechanism for persistent RNAi memory in a regenerating animal and establish planarians as a model for RNA-based inheritance, illuminating a novel mode by which RNA can encode durable gene-silencing states in metazoans.

developmental biology↗

bioRxiv2026

Single-cell and spatial transcriptomics unveils key regulators governing cell differentiation for Schistosoma sexual development

Schistosomiasis remains a major global health challenge, primarily due to the large number of egg production by sexually mature parasites. However, the cellular basis and regulatory programs governing sexual development and egg production are poorly characterized. Here, we constructed a dynamic single-cell atlas of Schistosoma japonicum (S. japonicum) covering key development stages of sexual maturation and egg production, and integrated it for the first time with spatial transcriptomics to map tissue-resolved cellular niches. Through bioinformatic analysis and experimental validation, we identified several critical cell populations and regulatory networks that drive parasite development and egg laying. By mapping de novo identified transcription factors (TFs) onto these atlases, we generated a comprehensive spatiotemporal expression profile of TFs and define the regulatory programs of several tissue-specific TFs including Zfp, Fbp3, and Lim. Integrated re-clustering further revealed and validated key regulators of germline stem-cell differentiation in S. japonicum. Finally, comparative analyses with S. mansoni single-cell datasets revealed both conserved and species-divergent cellular plasticity, providing unprecedented insights into their distinct biological traits. Collectively, our comprehensive study establishes a foundational resource for understanding schistosome biology, deciphers regulatory programs underlying cell differentiation and pathogenicity, and accelerates the identification of key molecules involved in sexual development against schistosomiasis.

microbiology↗

bioRxiv2025

Single-Nucleotide m6A Mapping Uncovers Redundant YTHDF Function in Planarian Progenitor Fate Selection

Cell fate decisions require tight regulation of gene expression. In planarians--highly regenerative flatworms--the mRNA modification N6-methyladenosine (m6A) modulates progenitor production and fate. However, the mechanisms governing m6A deposition in the planarian transcriptome--and the role of their expanded family of YTHDF m6A reader proteins in orchestrating biological functions--remain unclear. Here, we generated the first single-nucleotide resolution map of m6A in planarians, and revealed that simple sequence rules guide m6A deposition, facilitating the flexible evolutionary gain and loss of these marks. Functional analyses of the five planarian m6A readers revealed that while individual reader expression is dispensable, together, the planarian readers regulate the production of specific progenitor lineages and overall body size. Collectively, our findings uncover a robust, redundant regulatory architecture, characterized by multiple m6A sites per gene and coordinated m6A reader expression. This architecture is essential for proper lineage resolution and provides insights into the evolutionary dynamics of the m6A landscape.

developmental biology↗

bioRxiv2024

A quantitative model for in vivo stem cell decisions in planarians

Stem cells contribute to organismal homeostasis by balancing division, self-renewal and differentiation. Elucidating the strategies by which stem cells achieve this balance is critical for understanding homeostasis, and for addressing pathogenesis associated with the disruption of this balance (e.g., cancer). Planarians, highly regenerative flatworms, use pluripotent stem cells called neoblasts to maintain and regrow organs. A single neoblast can rescue an entire animal depleted from stem cells and regenerate all cell lineages. How neoblast differentiation and clonal expansion are governed to produce all the required cell types is unclear. Here, we integrated experimental and computational approaches to develop a quantitative model revealing basic principles of clonal growth of individual neoblasts. By experimentally suppressing differentiation to major lineages, we elucidated the interplay between colony growth and lineage decisions. Our findings suggest that neoblasts select their progenitor lineage based on a cell-intrinsic fate distribution. Arresting differentiation into specific lineages disrupts neoblast proliferative capacity without inducing compensatory expression of other lineages. Our analysis of neoblast colonies is consistent with a cell-intrinsic decision model that can operate without memory or communication between neoblasts. This simple cell fate decision process breaks down in homeostasis, likely because of the activity of feedback mechanisms. Our findings uncover essential principles of stem cell regulation in planarians, which are distinct from those observed in many vertebrate models. These mechanisms enable robust production of diverse cell types and facilitate regeneration of missing tissues.

developmental biology↗

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↗