Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells

Abstract

Human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) are promising candidate cell sources for regenerative medicine. However, despite the common ability of hiPSCs and hESCs to differentiate into all 3 germ layers, their functional equivalence at the single cell level remains to be demonstrated. Moreover, single cell heterogeneity amongst stem cell populations may underlie important cell fate decisions. Here, we used single cell analysis to resolve the gene expression profiles of 362 hiPSCs and hESCs for an array of 42 genes that characterize the pluripotent and differentiated states. Comparison between single hESCs and single hiPSCs revealed markedly more heterogeneity in gene expression levels in the hiPSCs, suggesting that hiPSCs occupy an alternate, less stable pluripotent state. hiPSCs also displayed slower growth kinetics and impaired directed differentiation as compared with hESCs. Our results suggest that caution should be exercised before assuming that hiPSCs occupy a pluripotent state equivalent to that of hESCs, particularly when producing differentiated cells for regenerative medicine aims.

Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation

“…In mouse ESCs genes exist that are uniformly expressed in most cells and exhibiting a unimodal distribution ( Oct4 , Rest , Tcf3 , Sal4 ); other genes exhibit bimodal expression and are expressed in some populations but not in others ( Nanog , Rex1 , Tet1 , Esrrb ), and yet another group of genes display sporadic expression ( Neurod1 , Klf4 , Otx2 , Pax6 ) and are undetected in most cells but highly expressed in some specific subpopulations 3, 5. Similar results were obtained studying heterogeneity in human ESCs and induced PSCs, in which pluripotency regulators such as Nanog and Oct4 , exhibit similar expression patterns across different subpopulations to the expression patterns of their orthologous counterparts in mouse 2, 11. Gene expression heterogeneity has also been studied in hematopoietic stem cells (HSCs), in which gene expression uni‐ and bimodality have been observed for different genes in different hematopoietic progenitor cells 1, 12.…”

Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus

“…Our analysis of transcriptomes in progenitor populations showed that GATA1s mutations confer a strong bias toward myelo-megakaryocytic transcription. However, individual phenotypically matched stem and progenitor cells exhibit considerable heterogeneity in gene expression (32,33). Thus, subpopulations of cells within our iPSCderived progenitor pools could exhibit different fate biases.…”

Specific small nucleolar RNA expression profiles in acute leukemia

“…The Fluidigm high-throughput qPCR method (Biomark, Fluidigm, South San Francisco, CA, USA) was used as described previously 16 and developed in Supplementary Methods. Primers used for amplification are described in Supplementary Table 2.…”