Genetically tractable embryonic cell lines from sea urchins Lytechinus variegatus and Strongylocentrotus purpuratus

Sea urchins have been valuable research models for over a century, advancing our understanding of fundamental biological processes like cell cycle regulation and developmental gene regulatory networks. While an increasing number of functional genomic resources are being developed for sea urchins, in vitro cell culture tools and methods for scalable transgenesis have remained elusive. Here, we successfully established embryonic cell lines from sea urchins (Lytechinus variegatus and Strongylocentrotus purpuratus) which recapitulated aspects of the developmental program in vitro, generating 3D structures and diverse cell types representing all three germ layers. Single-cell transcriptomics revealed signatures of naive stem-like cells and distinct cell clusters expressing markers of neurons, myocytes, skeletogenic, endodermal, and pigment cells. Integration of the single-cell RNA sequencing data from L. variegatus cell cultures and the single-cell developmental atlas revealed that, while most cultured cells were notably distinct from cells in vivo, some cell-types were remarkably similar to their corresponding in vivo counterparts. The ability to genetically manipulate the cultured cells was demonstrated using a lentiviral vector, providing a scalable platform for mechanistic studies. These advances expand the utility of this classic model organism and provide a framework for developing similar tools for other non-model marine invertebrates.