Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut

Cell Syst. 2018 Jan 24;6(1):37-51.e9. doi: 10.1016/j.cels.2017.10.012. Epub 2017 Nov 15.


Modern single-cell technologies allow multiplexed sampling of cellular states within a tissue. However, computational tools that can infer developmental cell-state transitions reproducibly from such single-cell data are lacking. Here, we introduce p-Creode, an unsupervised algorithm that produces multi-branching graphs from single-cell data, compares graphs with differing topologies, and infers a statistically robust hierarchy of cell-state transitions that define developmental trajectories. We have applied p-Creode to mass cytometry, multiplex immunofluorescence, and single-cell RNA-seq data. As a test case, we validate cell-state-transition trajectories predicted by p-Creode for intestinal tuft cells, a rare, chemosensory cell type. We clarify that tuft cells are specified outside of the Atoh1-dependent secretory lineage in the small intestine. However, p-Creode also predicts, and we confirm, that tuft cells arise from an alternative, Atoh1-driven developmental program in the colon. These studies introduce p-Creode as a reliable method for analyzing large datasets that depict branching transition trajectories.

Keywords: cell-state transitions; differentiation hierachies; graph theory; intestine and colon; mass cytometry; pseudo-time analysis; single-cell RNA-seq; single-cell biology; trajectories; tuft cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Cell Differentiation
  • Cell Lineage / genetics
  • Humans
  • Image Cytometry / methods*
  • Intestinal Mucosa / metabolism
  • Intestine, Small / metabolism
  • K562 Cells
  • Mice
  • Mice, Inbred C57BL
  • RNA / metabolism
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis / methods*


  • ATOH1 protein, human
  • Basic Helix-Loop-Helix Transcription Factors
  • RNA