title: A continuum of cell states spans pluripotency and lineage commitment in human embryonic stem cells.
abstract: BACKGROUND
  Commitment in embryonic stem cells is often depicted as a binary choice between alternate cell states, pluripotency and specification to a particular germ layer or extraembryonic lineage. However, close examination of human ES cell cultures has revealed significant heterogeneity in the stem cell compartment.
  
  
  RESULTS
  We isolated subpopulations of embryonic stem cells using surface markers, then examined their expression of pluripotency genes and lineage specific transcription factors at the single cell level, and tested their ability to regenerate colonies of stem cells. Transcript analysis of single embryonic stem cells showed that there is a gradient and a hierarchy of expression of pluripotency genes in the population. Even cells at the top of the hierarchy generally express only a subset of the stem cell genes studied. Many cells co-express pluripotency and lineage specific genes. Cells along the continuum show a progressively decreasing likelihood of self renewal as their expression of stem cell surface markers and pluripotency genes wanes. Most cells that are positive for stem cell surface markers express Oct-4, but only those towards the top of the hierarchy express the nodal receptor TDGF-1 and the growth factor GDF3.
  
  
  CONCLUSIONS
  These findings on gene expression in single embryonic stem cells are in concert with recent studies of early mammalian development, which reveal molecular heterogeneity and a stochasticity of gene expression in blastomeres. Our work indicates that only a small fraction of the population resides at the top of the hierarchy, that lineage priming (co-expression of stem cell and lineage specific genes) characterizes pluripotent stem cell populations, and that extrinsic signaling pathways are upstream of transcription factor networks that control pluripotency.
authors.affiliation: Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America.
authors.forename: Shelley R
authors.initials: SR
authors.lastname: Hough
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Laslett
authors.forename: Sean B
authors.initials: SB
authors.lastname: Grimmond
authors.forename: Gabriel
authors.initials: G
authors.lastname: Kolle
authors.forename: Martin F
authors.initials: MF
authors.lastname: Pera
mesh_terms: D001757:Blastomeres / Q000166:cytology; D002454:Cell Differentiation; D019070:Cell Lineage; D029721:Drosophila Proteins; D053595:Embryonic Stem Cells / Q000166:cytology*; D004815:Epidermal Growth Factor / Q000378:metabolism; D005434:Flow Cytometry / Q000379:methods; D058851:GPI-Linked Proteins; D005786:Gene Expression Regulation; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins; D008562:Membrane Glycoproteins / Q000378:metabolism; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000378:metabolism; D050814:Octamer Transcription Factor-3 / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000166:cytology*; D013234:Stem Cells / Q000166:cytology; D014158:Transcription, Genetic
chemical_list: D029721:Drosophila Proteins; D058851:GPI-Linked Proteins; D036341:Intercellular Signaling Peptides and Proteins; D008562:Membrane Glycoproteins; D009363:Neoplasm Proteins; D050814:Octamer Transcription Factor-3; C070636:TDGF1 protein, human; D004815:Epidermal Growth Factor