title: In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians.
abstract: BACKGROUND
  The planarian Schmidtea mediterranea is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal has hindered the study of lineage progression and has made understanding the mechanisms of tissue regeneration a challenge. However, recent advances in single-cell transcriptomics and analysis methods allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell.
  
  
  RESULTS
  Here we apply pseudotime analysis and single-cell transcriptomics to identify adult stem cells belonging to specific cellular lineages and identify novel candidate genes for future in vivo lineage studies. We purify 168 single stem and progeny cells from the planarian head, which were subjected to single-cell RNA sequencing (scRNAseq). Pseudotime analysis with Waterfall and gene set enrichment analysis predicts a molecularly distinct neoblast sub-population with neural character (νNeoblasts) as well as a novel alternative lineage. Using the predicted νNeoblast markers, we demonstrate that a novel proliferative stem cell population exists adjacent to the brain.
  
  
  CONCLUSIONS
  scRNAseq coupled with in silico lineage analysis offers a new approach for studying lineage progression in planarians. The lineages identified here are extracted from a highly heterogeneous dataset with minimal prior knowledge of planarian lineages, demonstrating that lineage purification by transgenic labeling is not a prerequisite for this approach. The identification of the νNeoblast lineage demonstrates the usefulness of the planarian system for computationally predicting cellular lineages in an adult context coupled with in vivo verification.
authors.affiliation: Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada.|Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
authors.forename: Alyssa M
authors.initials: AM
authors.lastname: Molinaro
authors.affiliation: Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada. bret.pearson@utoronto.ca.|Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. bret.pearson@utoronto.ca.|Ontario Institute for Cancer Research, Toronto, ON, M5G0A4, Canada. bret.pearson@utoronto.ca.
authors.forename: Bret J
authors.initials: BJ
authors.lastname: Pearson
mesh_terms: D000818:Animals; D019070:Cell Lineage; D003198:Computer Simulation; D058953:Neural Stem Cells / Q000166:cytology / Q000378:metabolism*; D010932:Planarians / Q000166:cytology* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D059467:Transcriptome
keywords: Neural stem cells; Planarians; Schmidtea mediterranea; Single cell RNAseq; Waterfall; in silico lineage tracing; νNeoblasts