title: Culture adaptation alters transcriptional hierarchies among single human embryonic stem cells reflecting altered patterns of differentiation.
abstract: We have used single cell transcriptome analysis to re-examine the substates of early passage, karyotypically Normal, and late passage, karyotypically Abnormal ('Culture Adapted') human embryonic stem cells characterized by differential expression of the cell surface marker antigen, SSEA3. The results confirmed that culture adaptation is associated with alterations to the dynamics of the SSEA3(+) and SSEA3(-) substates of these cells, with SSEA3(-) Adapted cells remaining within the stem cell compartment whereas the SSEA3(-) Normal cells appear to have differentiated. However, the single cell data reveal that these substates are characterized by further heterogeneity that changes on culture adaptation. Notably the Adapted population includes cells with a transcriptome substate suggestive of a shift to a more naïve-like phenotype in contrast to the cells of the Normal population. Further, a subset of the Normal SSEA3(+) cells expresses genes typical of endoderm differentiation, despite also expressing the undifferentiated stem cell genes, POU5F1 (OCT4) and NANOG, whereas such apparently lineage-primed cells are absent from the Adapted population. These results suggest that the selective growth advantage gained by genetically variant, culture adapted human embryonic stem cells may derive in part from a changed substate structure that influences their propensity for differentiation.
authors: Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom.
authors: Paul J
authors: PJ
authors: Gokhale
authors: ThermoFisher, Foster City, California, United States of America.
authors: Janice K
authors: JK
authors: Au-Young
authors: ThermoFisher, Foster City, California, United States of America.
authors: SriVidya
authors: S
authors: Dadi
authors: ThermoFisher, Foster City, California, United States of America.
authors: David N
authors: DN
authors: Keys
authors: Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom.
authors: Neil J
authors: NJ
authors: Harrison
authors: Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom.
authors: Mark
authors: M
authors: Jones
authors: Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
authors: Shamit
authors: S
authors: Soneji
authors: Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
authors: Tariq
authors: T
authors: Enver
authors: ThermoFisher, Foster City, California, United States of America.
authors: Jon K
authors: JK
authors: Sherlock
authors: Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom.
authors: Peter W
authors: PW
authors: Andrews
mesh_terms: D015295:Antigens, Tumor-Associated, Carbohydrate / Q000235:genetics* / Q000378:metabolism; D002454:Cell Differentiation; D002478:Cells, Cultured; D016000:Cluster Analysis; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D000066449:Human Embryonic Stem Cells; D006801:Humans; D000071317:Nanog Homeobox Protein; D050814:Octamer Transcription Factor-3 / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D055746:Stage-Specific Embryonic Antigens / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D015295:Antigens, Tumor-Associated, Carbohydrate; D018398:Homeodomain Proteins; C486780:NANOG protein, human; D000071317:Nanog Homeobox Protein; D050814:Octamer Transcription Factor-3; C494173:POU5F1 protein, human; D055746:Stage-Specific Embryonic Antigens; C052924:stage-specific embryonic antigen-3