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A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

Abstract

The equivalence of human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) remains controversial. Here we use genetically matched hESC and hiPSC lines to assess the contribution of cellular origin (hESC vs. hiPSC), the Sendai virus (SeV) reprogramming method and genetic background to transcriptional and DNA methylation patterns while controlling for cell line clonality and sex. We find that transcriptional and epigenetic variation originating from genetic background dominates over variation due to cellular origin or SeV infection. Moreover, the 49 differentially expressed genes we detect between genetically matched hESCs and hiPSCs neither predict functional outcome nor distinguish an independently derived, larger set of unmatched hESC and hiPSC lines. We conclude that hESCs and hiPSCs are molecularly and functionally equivalent and cannot be distinguished by a consistent gene expression signature. Our data further imply that genetic background variation is a major confounding factor for transcriptional and epigenetic comparisons of pluripotent cell lines, explaining some of the previously observed differences between genetically unmatched hESCs and hiPSCs.

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Figure 1: Generation of genetically matched hESCs and hiPSCs.
Figure 2: Influence of viral infection and genetic background on transcriptional and epigenetic patterns in hESCs and hiPSCs.
Figure 3: Genes differentially expressed between genetically matched hESC and hiPSC lines.
Figure 4: Dysregulation of genes in a subset of hiPSC lines.
Figure 5: Analysis of previously reported gene expression differences and role of genetic background.

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Acknowledgements

We thank members of the Hochedlinger and Park laboratories for productive discussions and a critical reading of the manuscript. We also thank M. Stadtfeld for his helpful discussions and D. Melton for his generous donation of HUES2 and HUES3 lines. We are grateful to K. Folz-Donahue, M. Weglarz and L. Prickett at the Massachusetts General Hospital (MGH)/Harvard Stem Cell Institute (HSCI) flow cytometry core for their constant assistance and support. We are also thankful to the members of the Tufts Genomics Core for performing RNA-seq. Work in the Lee laboratory was supported by grants from the Robertson Investigator Award of the New York Stem Cell Foundation and from the Maryland Stem Cell Research Fund (TEDCO). A.M. and J.L.R. are supported by US National Institutes of Health (NIH) grant P01GM099117. A.M. is a New York Stem Cell Foundation Robertson Investigator. Parts of this work were supported by the Howard Hughes Medical Institute (HHMI), MGH startup funds, the Gerald and Darlene Jordan Endowed Chair for Regenerative Medicine (to K.H.) and a pilot grant from the NIH (P01GM099117 to K.H.). J.C. was supported by the Vranos Family Graduate Research Fellowship in Developmental & Regenerative Biology.

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Authors and Affiliations

Authors

Contributions

J.C., S.L., P.J.P. and K.H. conceived the experiments, interpreted results and wrote the manuscript. J.C. generated all HUES2- and HUES3-derived in vitro-differentiated fibroblasts and hiPSCs. A.M. and J.L.R. provided RNA-seq data from hESCs and hiPSCs generated with retroviral vectors. J.C. performed AP staining, immunostaining, lactate production and glucose uptake assays, western blot analysis, RT-PCR and qPCR analyses. S.L., W.M., G.M.T., F.F. and P.J.P. performed bioinformatics analysis of RNA-seq data. H.L., I.Y.C. and G.L. performed neural differentiation experiments and marker analyses of differentiated cells. R.P. conducted the ScoreCard assay, which was bioinformatically analyzed by A.M.T., and K.C. performed bioinformatics analysis of reduced representation bisulfite sequencing data.

Corresponding authors

Correspondence to Peter J Park or Konrad Hochedlinger.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Reprogramming of fibroblast-like cells in vitro- differentiated from hESCs.

A) Representative AP staining for parental fibroblasts of each genetic background (top panels) and control hESC GFP lines from corresponding background (bottom panels) that were cultured in hESC media. Parental fibroblast failed to form any pluripotent colonies whereas hESC lines formed multiple pluripotent colonies. Insets show magnification of AP staining (B) PCA analysis of isogenic cell lines based on global gene expression levels. (C) The hiPSC1 line was stained with DAPI and α-SeV antibody at passage 7 (top panels) and 15 (bottom panels). Representative images are shown. (D) Transgene-specific primers were used to detect the expression of Oct4 and Klf4 at passage 15. hiPSC1 at passage 7 was used as a positive control. (E) Heatmap and dendrogram separating all genetically matched hESC lines based on the 63 DEGs from Fig. 2B. HUES lines, dark blue; hESC GFP lines, light blue. (F) Gene ontology enrichment analysis for the 63 DEGs from Fig. 2B. Gene count for each term is shown.

Supplementary Figure 2 Effects of genetic background on global gene expression and DNA methylation patterns.

(A) Heatmap and dendrogram for isogenic hESC subclones, in vitro- differentiated fibroblasts, derivative hiPSCs, and dermal fibroblast based on pairwise Pearson correlation (r) on global gene expression levels. hiPSC lines, red; hESC lines, blue; fibroblasts, black. (B) Dendrogram for hESCs, in vitro-differentiated fibroblasts and derivative hiPSCs based on global DNA methylation levels as determined by RRBS analysis. (C) Bar plots showing mean absolute deviation (MAD) in global gene expression levels of hiPSC lines relative to matched hESC GFP (i.e., HUES2-derived hiPSCs vs HUES2-derived hESC GFPs and HUES3-derived hiPSCs vs HUES3-derived hESC GFPs; top bar) or unmatched hESC GFP (i.e., HUES2-derived hiPSCs vs HUES3-derived hESC GFPs and HUES3-derived hiPSCs vs HUES2-derived hESC GFPs; bottom bar) (also see Methods). Blue rectangles and error bars represent mean values and s.d. of six hiPSC lines. (D) Bar plots showing MAD in global gene expression levels of hiPSC lines relative to either hESC GFP lines (1st bar) or hiPSC lines (2nd bar) and of hESC GFP lines relative to either hiPSC lines (3rd bar) or hESC GFP lines (4th bar) independent of genetic background. Blue rectangles and error bars represent mean values and s.d. of either six hiPSC lines or six hESC GFP lines. (E) Total number of mapped reads for individual RNA-seq samples with technical replicates merged. Red dotted line indicates average.

Supplementary Figure 3 Western blot for LDHA levels in hESC GFP and hiPSC lines

(A) Full blot for Fig. 3g.

Supplementary Figure 4 Comparison of differentiated cells derived from isogenic hESC GFP and hiPSC lines.

(A) Venn diagram showing the number of up- and down-regulated genes in 3 biological replicate hiPSC fibroblasts relative to 3 biological replicate hESC GFP fibroblasts within each genetic background. (B) Box plot of 12 in vitro- differentiated fibroblast-like cell lines and primary dermal fibroblasts (cross) based on the 2 DEGs (identified in A) between hiPSC fibroblasts (red) and hESC GFP fibroblasts (blue). (C) Schematic for identifying “inconsistently differentially expressed genes (iDEGs)” that were dysregulated in only a subset of hiPSC lines when compared to hESC GFP lines. Red and green boxes stand for 6 discrete grouping patterns of samples for differential expression analysis, where one or two hiPSC lines are pretended to be a replicate of the hESC lines of the same genetic background. Differentially expressed genes for each pattern were identified and merged within each genetic background and the intersection was taken for the two genetic backgrounds (Venn diagram, grey: HUES2, green: HUES3). 8 iDEGs that were common between the two backgrounds are indicated. (D) hESC GFP and hiPSC lines were differentiated into neuroectodermal cells and Western blot analysis was used to detect neural differentiation by PAX6 expression at day 6 in each cell line. GAPDH was used as a control.

Supplementary Figure 5 Analyses of differentially expressed genes between hESC and hiPSC lines using independent reprogramming data sets.

(A) 16 genes were identified as differentially expressed between unmatched hESC and hiPSC lines described in this study. (FDR<0.15 and fold change >2 or <0.5, see details in the Methods). (B) Definition and number of significantly differentially expressed genes (DEGs) between hESCs and hiPSCs. (C) Dendrogram for all isogenic hESC (blue) and hiPSC (red) lines from Choi et al. based on expression levels of the 16 DEGs identified in A. (D-F) Dendrograms for non-isogenic hESC (blue) and hiPSC (red) lines (Choi et al.) based on DEGs defined in other studies (see Supplementary Fig. 5B). (G-I) Dendrograms for non-isogenic hESC (blue) and hiPSC (red) lines (Phanstiel et al.10) based on DEGs defined in other studies (see Supplementary Fig. 5B). (J) Genes were ranked by the sum of –log10(p-value) of differential expression between HUES2 and HUES3 lines (see Methods for details), and the frequency (top) and placement (bottom) of Phanstiel et al.’s DEGs10 (red circles) within the ranking were determined. (K) Left panel: distribution of Dunn-index-based scores of random gene sets, which measures how well a gene set separates our isogenic samples by genetic background. Larger values indicate better separation. Zero indicates the samples are not separated by genetic background. Each of the 10,000 random gene sets was size- and expression-matched to Phanstiel’s DEGs10. Red vertical line indicates the value for Phantiel’s DEGs10, suggesting a significantly better separation by Phanstiel’s DEGs10 than a random set of genes (p-value = 0.0236). Right panel: distribution of expression levels of the random gene sets computed as the sum of log(TPM+1). Gene sets were stratified according to whether they separate our isogenic samples by genetic background (red) or not (green), showing the separation is not affected by expression levels. Dotted line indicates Phanstiel’s DEGs10.

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Choi, J., Lee, S., Mallard, W. et al. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol 33, 1173–1181 (2015). https://doi.org/10.1038/nbt.3388

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