Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5(+) Intestinal Stem Cells

Cell Rep. 2016 Aug 23;16(8):2053-2060. doi: 10.1016/j.celrep.2016.07.056. Epub 2016 Aug 11.


Lgr5(+) intestinal stem cells (ISCs) drive epithelial self-renewal, and their immediate progeny-intestinal bipotential progenitors-produce absorptive and secretory lineages via lateral inhibition. To define features of early transit from the ISC compartment, we used a microfluidics approach to measure selected stem- and lineage-specific transcripts in single Lgr5(+) cells. We identified two distinct cell populations, one that expresses known ISC markers and a second, abundant population that simultaneously expresses markers of stem and mature absorptive and secretory cells. Single-molecule mRNA in situ hybridization and immunofluorescence verified expression of lineage-restricted genes in a subset of Lgr5(+) cells in vivo. Transcriptional network analysis revealed that one group of Lgr5(+) cells arises from the other and displays characteristics expected of bipotential progenitors, including activation of Notch ligand and cell-cycle-inhibitor genes. These findings define the earliest steps in ISC differentiation and reveal multilineage gene priming as a fundamental property of the process.

MeSH terms

  • Animals
  • Apolipoproteins A / genetics
  • Apolipoproteins A / metabolism
  • Cell Differentiation
  • Cell Lineage / genetics*
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Genes, Reporter
  • Glycoproteins / genetics
  • Glycoproteins / metabolism
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • In Situ Hybridization
  • Intestinal Mucosa / metabolism*
  • Intestines / cytology
  • Mice
  • Mice, Transgenic
  • Microfluidic Analytical Techniques
  • Mucin-2 / genetics
  • Mucin-2 / metabolism
  • Real-Time Polymerase Chain Reaction
  • Receptors, G-Protein-Coupled / genetics
  • Receptors, G-Protein-Coupled / metabolism
  • Single-Cell Analysis
  • Stem Cells / cytology
  • Stem Cells / metabolism*
  • Transcriptome*


  • Apolipoproteins A
  • Glycoproteins
  • Lgr5 protein, mouse
  • Muc2 protein, mouse
  • Mucin-2
  • Receptors, G-Protein-Coupled
  • olfactomedin 4, mouse
  • Green Fluorescent Proteins