Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

INTRODUCTION The cnidarian polyp Hydra undergoes continual self-renewal and is capable of whole-body regeneration from a small piece of tissue. The stem cell populations, morphological cell types, and lineage relationships of Hydra are well characterized, but the molecular definition of its cell states has remained elusive. Capturing the molecular diversity of Hydra cells and the transcriptional programs underlying homeostatic development would greatly advance the utility of this organism for tackling questions in developmental and regenerative biology as well as neurobiology, and would help to elucidate ancestral mechanisms by means of comparative approaches. RATIONALE Recent advances in single-cell RNA sequencing permit identification of the complete molecular diversity of cell states in an animal. This includes capturing the transcriptomes of cells in the process of differentiation. Ordering such cells into differentiation trajectories can uncover the genetic cascades that accompany cell fate specification. Here, we applied these approaches to Hydra to uncover the molecular cell complement, characterize the nervous system, and capture cell differentiation in the homeostatic adult. RESULTS We generated ~25,000 single-cell transcriptomes from Hydra using Drop-seq, clustered the cells, and annotated cell states. These data identified candidate molecular markers for elusive cell populations such as multipotent interstitial stem cells and germline stem cells. We then constructed differentiation trajectories for cells from each of the three cell lineages found in Hydra using the software URD. This revealed the dynamics of gene expression that occur during cell specification and differentiation in the adult Hydra, including the spatial and temporal expression of transcription factors and gene modules. To identify potential cell state regulators, we used ATAC-seq to reveal regulatory regions of coexpressed genes, identified enriched transcription factor binding motifs within these regulatory regions, and matched these motifs to coexpressed candidate transcriptional regulators. Our trajectory reconstruction also identified similarities between the neurogenesis and gland cell differentiation pathways that suggest a shared or similar progenitor state. We propose a model in which interstitial stem cells give rise to a bipotential progenitor in the ectodermal layer, which crosses the extracellular matrix to supply the endodermal layer with neurons and gland cells. Additionally, trajectory reconstructions of individual cell types (including gland cells and epithelial cells of the ectoderm and endoderm) uncovered gene expression changes that occur as they are translocated along the body column; these results suggest candidate genes and pathways involved in spatial patterning along the oral-aboral axis. Finally, we profiled neurons and neuronal progenitors that were enriched using fluorescence-activated cell sorting and used the data to build a molecular map of the nervous system. We found 12 distinct neuronal subtypes and determined their location using differential gene expression analysis, in situ hybridization, and transgenic approaches. Access to neuronal transcriptional signatures, including the first molecular markers specific to endodermal neurons, creates opportunities for precise manipulations of the nervous system. CONCLUSION We provide a molecular map of Hydra cell states, including differentiation trajectories for each lineage, identification of candidate regulators of cell states, and a spatial/molecular map of the nervous system. This resource identifies numerous candidates for functional testing, and we therefore anticipate that it will accelerate the discovery of developmental mechanisms in this highly regenerative animal. Hydra has diverse cell specification pathways that can be captured in one life stage by a relatively small number of sequenced single cells, which paves the way to study organism-wide changes at a single-cell level in response to perturbations.