Biology subjects

Sherwood, D.

Publications and source records attributed to Sherwood, D..

5 recordsLinked to original sources

bioRxiv2026

Scarless regeneration requires post-translational proteolytic regulation via macrophage-derived Legumain

Macrophages express proteolytic factors in response to injury but how proteases are deployed and regulated during regeneration are incompletely defined. Beyond their transcriptomic expression, activity of individual proteases is defined both by their unique substrate specificity and post-translational modifications of their active forms. Here we show a key role for the lysosomal protease Legumain in controlling ECM dynamics and post-translational processing of the regenerative proteome. Injury interface-targeted Ctsla localization and post-translational processing requires Lgmn in macrophages. Extracellular cues from physical remodeling control differentiation state and injury response of ligament resident fibroblasts. Loss of ECM turnover, including localized Fibronectin 1a/b remodeling, impairs dedifferentiation in legumain mutants and leads to fibrotic scarring. Taken together, we demonstrate a role for macrophage-derived lysosomal proteases as specialized tools required to fine-tune proteome composition and function in regeneration.

cell biology↗

bioRxiv2025

WormTagDB: A Systematic Survey of Endogenously Tagged Proteins in C. elegans and Roadmap Towards the Tagged Proteome

Endogenous protein tagging in Caenorhabditis elegans enables direct visualization and manipulation of proteins in vivo, providing native readouts of expression, localization, and dynamics. No coordinated effort currently exists to comprehensively tag proteins on a large scale, resulting in patchy coverage that limits comprehensive proteome analyses. We systematically reviewed 2,500 primary research articles, identifying 778 that report novel endogenous tags, and integrated these with the Caenorhabditis Genetics Center strain records to catalog >90% of all existing tagged alleles. In total, we found that 1,554 unique genes (~8% of the proteome) have been endogenously tagged. Gene Ontology enrichment analysis revealed that cytoskeletal proteins, transcription factors, and RNA-binding proteins dominate the tagged proteome, while membrane proteins, metabolic enzymes, and mitochondrial components remain largely untagged, reflecting both technical barriers and research priorities that have shaped the last decade of tagging efforts. We created WormTagDB (https://wormtagdb.rc.duke.edu), an interactive, community-updatable resource that consolidates all known endogenously tagged alleles and provides precomputed CRISPR guide and homology-arm primer designs for N- and C-terminal knock-ins across all protein-coding genes. This will enable researchers to easily identify existing alleles to prevent redundant strain generation and rapidly initiate new knock-in experiments. A systematic effort to tag every C. elegans gene would deliver the first complete metazoan visual proteome, providing comprehensive insights into protein localization, dynamics, and regulation, revealing new protein associations and molecular processes.

genetics↗

bioRxiv2024

Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration

Adult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using a combination of microCT, histological, live imaging, and single-cell RNA sequencing (scRNAseq) approaches after complete removal of all joint tissues, we find de novo regeneration of articular cartilage, ligament, and synovium into a functional joint. Clonal lineage tracing and scRNAseq implicate a multipotent, neural crest-derived population in the adult skeleton as a cell source for these regenerating tissues. Together, our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.

developmental biology↗

bioRxiv2023

Ligament injury in adult zebrafish triggers ECM remodeling and cell dedifferentiation for scar-free regeneration

After traumatic injury, healing of mammalian ligaments is typically associated with fibrotic scarring as opposed to scar-free regeneration. In contrast, here we show that the ligament supporting the jaw joint of adult zebrafish is capable of rapid and complete scar-free healing. Following surgical transection of the jaw joint ligament, we observe breakdown of ligament tissue adjacent to the cut sites, expansion of mesenchymal tissue within the wound site, and then remodeling of extracellular matrix (ECM) to a normal ligament morphology. Lineage tracing of mature ligamentocytes following transection shows that they dedifferentiate, undergo cell cycle re-entry, and contribute to the regenerated ligament. Single-cell RNA sequencing of the regenerating ligament reveals dynamic expression of ECM genes in neural-crest-derived mesenchymal cells, as well as diverse immune cells expressing the endopeptidase-encoding gene legumain. Analysis of legumain mutant zebrafish shows a requirement for early ECM remodeling and efficient ligament regeneration. Our study establishes a new model of adult scar-free ligament regeneration and highlights roles of immune-mesenchyme cross-talk in ECM remodeling that initiates regeneration. HighlightsO_LIRapid regeneration of the jaw joint ligament in adult zebrafish C_LIO_LIDedifferentiation of mature ligamentocytes contributes to regeneration C_LIO_LIscRNAseq reveals dynamic ECM remodeling and immune activation during regeneration C_LIO_LIRequirement of Legumain for ECM remodeling and ligament healing C_LI

molecular biology↗

bioRxiv2019

α-integrins dictate distinct modes of type IV collagen recruitment to basement membranes

Basement membranes (BMs) are cell-associated extracellular matrices that support tissue integrity, signaling, and barrier properties. Type IV collagen is critical for BM mechanical and signaling functions, yet how it is directed into BMs in vivo is unclear. Through live-cell imaging of endogenous localization, conditional knockdown, and misexpression experiments, we uncovered distinct mechanisms of integrin-mediated collagen recruitment to Caenorhabditis elegans gonadal and pharyngeal BMs. The putative laminin-binding INA-1/{beta}PAT-3 integrin was selectively activated in the gonad and recruited laminin, which directed moderate collagen incorporation. In contrast, the putative Arg-Gly-Asp (RGD)-binding PAT-2/{beta}PAT-3 integrin was activated in the pharynx and recruited high levels of collagen independent of laminin. Through an RNAi screen, we further identified the small GTPase RAP-3 (Rap1) as a pharyngeal-specific PAT-2/PAT-3 activator that modulates collagen levels. Together, these studies demonstrate that tissues can use distinct mechanisms to direct collagen incorporation into BMs to precisely control collagen levels and construct diverse BMs.

cell biology↗