Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells
Kazim H. Narsinh, … , Robert C. Robbins, Joseph C. Wu
Kazim H. Narsinh, … , Robert C. Robbins, Joseph C. Wu
Published February 7, 2011
Citation Information: J Clin Invest. 2011;121(3):1217-1221. https://doi.org/10.1172/JCI44635.
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Brief Report

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.

Authors

Kazim H. Narsinh, Ning Sun, Veronica Sanchez-Freire, Andrew S. Lee, Patricia Almeida, Shijun Hu, Taha Jan, Kitchener D. Wilson, Denise Leong, Jarrett Rosenberg, Mylene Yao, Robert C. Robbins, Joseph C. Wu

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Figure 2

Immunophenotypic and positional variation in single cell gene expression.

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Immunophenotypic and positional variation in single cell gene expression...
(A) Gene expression profiling of single hiPSCs expressing the Tra-1-60+/SSEA-4+ immunophenotype. Heat map representations of gene expression levels in immunophenotyped hESCs and hiPSCs versus differentiated fibroblast cells (IMR90), with each column representing a single cell. Single hESCs (left) show minimal heterogeneity, while single hiPSCs (middle) show increased variability in comparison with 4 somatic IMR90 cells (right), with no segregation of cells according to cell line when subjected to a hierarchical clustering algorithm. A gradient of hiPSC expression is evident, with cells expressing low levels of pluripotency transcripts enriched to the right. (B and C) Positional variation in transcript expression levels within pluripotent stem cell colonies. (B) A positional gradient of expression is evident in both hESCs and hiPSCs, with lower expression of pluripotency transcripts observed in the periphery of the colony. (C) Expression levels of ectoderm (PAX6 and NES), early mesoderm (GATA4), and endoderm (SOX17) transcripts are uniform across hESC colonies. However, the periphery of hiPSC colonies has undergone relative downregulation of endoderm marker SOX17 and relative upregulation of ectoderm marker PAX6.