Limits...
Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells.

Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, Wu JC - PLoS ONE (2010)

Bottom Line: We further identify genes that have a similar mode of regulation in hiPSCs and their corresponding donor cells compared to hESCs, allowing us to specify core sets of donor genes that continue to be expressed in each hiPSC line.We report that residual gene expression of the donor cell type contributes significantly to the differences among hiPSCs and hESCs, and adds to the incompleteness in reprogramming.Specifically, our analysis reveals that fetal fibroblast-derived hiPSCs are closer to hESCs, followed by adipose, neonatal fibroblast, and keratinocyte-derived hiPSCs.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America.

ABSTRACT
Human induced pluripotent stem cells (hiPSCs) generated by de-differentiation of adult somatic cells offer potential solutions for the ethical issues surrounding human embryonic stem cells (hESCs), as well as their immunologic rejection after cellular transplantation. However, although hiPSCs have been described as "embryonic stem cell-like", these cells have a distinct gene expression pattern compared to hESCs, making incomplete reprogramming a potential pitfall. It is unclear to what degree the difference in tissue of origin may contribute to these gene expression differences. To answer these important questions, a careful transcriptional profiling analysis is necessary to investigate the exact reprogramming state of hiPSCs, as well as analysis of the impression, if any, of the tissue of origin on the resulting hiPSCs. In this study, we compare the gene profiles of hiPSCs derived from fetal fibroblasts, neonatal fibroblasts, adipose stem cells, and keratinocytes to their corresponding donor cells and hESCs. Our analysis elucidates the overall degree of reprogramming within each hiPSC line, as well as the "distance" between each hiPSC line and its donor cell. We further identify genes that have a similar mode of regulation in hiPSCs and their corresponding donor cells compared to hESCs, allowing us to specify core sets of donor genes that continue to be expressed in each hiPSC line. We report that residual gene expression of the donor cell type contributes significantly to the differences among hiPSCs and hESCs, and adds to the incompleteness in reprogramming. Specifically, our analysis reveals that fetal fibroblast-derived hiPSCs are closer to hESCs, followed by adipose, neonatal fibroblast, and keratinocyte-derived hiPSCs.

Show MeSH

Related in: MedlinePlus

Residual signatures of the donor cell specific genes (upregulated in both hiPSCs and donor cells compared to hESC) in hiPSCs.(A) Expression fold-change of fibroblast specific genes in iPS-hFFib, hFFib, iPS-hNFib, and hNFib. (B) Expression fold-change of adipose cell specific genes in iPS-hASC and hASC. (C) Expression fold-change of keratinocyte specific genes in iPS-hKT and hKT.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2813859&req=5

pone-0008975-g006: Residual signatures of the donor cell specific genes (upregulated in both hiPSCs and donor cells compared to hESC) in hiPSCs.(A) Expression fold-change of fibroblast specific genes in iPS-hFFib, hFFib, iPS-hNFib, and hNFib. (B) Expression fold-change of adipose cell specific genes in iPS-hASC and hASC. (C) Expression fold-change of keratinocyte specific genes in iPS-hKT and hKT.

Mentions: Unsupervised hierarchical clustering of upregulated genes in hiPSCs and donor cells with respect to hESCs further confirmed the proximity of hiPSCs to their corresponding cell of origin (Figure 5) as compared to other donor cell types. For each set of iPS-donor cell types, IPA analysis was performed for functional annotation of the set of upregulated genes (Supplementary Table S1-A to S1-D). We clarified the role of these genes in various basic processes (cellular growth and proliferation, tissue development, cellular function, lipid metabolism, connective tissue development, DNA repair, cellular maintenance, etc). Next, we examined the expression of fibroblast [32], fat [33], [34], [35], [36], and keratinocyte [37] specific genes within the upregulated gene sets. We found significant residual gene expression of fibroblast (Figure 6A), adipocyte (Figure 6B), and keratinocyte genes (Figure 6C) within their corresponding hiPSCs. Specifically, fibroblast genes in Figure 6A such as PLAT and PLAU [32], [38] play important roles in remodeling the extracellular matrix and other functions in the coagulation system. Other fibroblast genes include CXCL1, which is involved in cell migration [32], and FOXF1 and FOXP1, which are forkhead family transcription factors expressed in fibroblasts [39]. CXCL2 in Figure 6B, also known as MIP-2 or macrophage inflammatory protein-2, PALLD, and COL1A1 are proteins expressed in adipocytes [34]. Among the keratinocyte-specific genes showed in Figure 6C, we found various keratins, transcription factors, and proteolytic enzymes (and their inhibitors) that are active in protein turnover and remodeling in keratinocytes, and which are not common to other cell types [37]. Taken together, our results demonstrate persistent donor cell gene expression within hiPSCs, and suggest a failure of reprogramming to efficiently silence the expression of these somatic genes.


Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells.

Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, Wu JC - PLoS ONE (2010)

Residual signatures of the donor cell specific genes (upregulated in both hiPSCs and donor cells compared to hESC) in hiPSCs.(A) Expression fold-change of fibroblast specific genes in iPS-hFFib, hFFib, iPS-hNFib, and hNFib. (B) Expression fold-change of adipose cell specific genes in iPS-hASC and hASC. (C) Expression fold-change of keratinocyte specific genes in iPS-hKT and hKT.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2813859&req=5

pone-0008975-g006: Residual signatures of the donor cell specific genes (upregulated in both hiPSCs and donor cells compared to hESC) in hiPSCs.(A) Expression fold-change of fibroblast specific genes in iPS-hFFib, hFFib, iPS-hNFib, and hNFib. (B) Expression fold-change of adipose cell specific genes in iPS-hASC and hASC. (C) Expression fold-change of keratinocyte specific genes in iPS-hKT and hKT.
Mentions: Unsupervised hierarchical clustering of upregulated genes in hiPSCs and donor cells with respect to hESCs further confirmed the proximity of hiPSCs to their corresponding cell of origin (Figure 5) as compared to other donor cell types. For each set of iPS-donor cell types, IPA analysis was performed for functional annotation of the set of upregulated genes (Supplementary Table S1-A to S1-D). We clarified the role of these genes in various basic processes (cellular growth and proliferation, tissue development, cellular function, lipid metabolism, connective tissue development, DNA repair, cellular maintenance, etc). Next, we examined the expression of fibroblast [32], fat [33], [34], [35], [36], and keratinocyte [37] specific genes within the upregulated gene sets. We found significant residual gene expression of fibroblast (Figure 6A), adipocyte (Figure 6B), and keratinocyte genes (Figure 6C) within their corresponding hiPSCs. Specifically, fibroblast genes in Figure 6A such as PLAT and PLAU [32], [38] play important roles in remodeling the extracellular matrix and other functions in the coagulation system. Other fibroblast genes include CXCL1, which is involved in cell migration [32], and FOXF1 and FOXP1, which are forkhead family transcription factors expressed in fibroblasts [39]. CXCL2 in Figure 6B, also known as MIP-2 or macrophage inflammatory protein-2, PALLD, and COL1A1 are proteins expressed in adipocytes [34]. Among the keratinocyte-specific genes showed in Figure 6C, we found various keratins, transcription factors, and proteolytic enzymes (and their inhibitors) that are active in protein turnover and remodeling in keratinocytes, and which are not common to other cell types [37]. Taken together, our results demonstrate persistent donor cell gene expression within hiPSCs, and suggest a failure of reprogramming to efficiently silence the expression of these somatic genes.

Bottom Line: We further identify genes that have a similar mode of regulation in hiPSCs and their corresponding donor cells compared to hESCs, allowing us to specify core sets of donor genes that continue to be expressed in each hiPSC line.We report that residual gene expression of the donor cell type contributes significantly to the differences among hiPSCs and hESCs, and adds to the incompleteness in reprogramming.Specifically, our analysis reveals that fetal fibroblast-derived hiPSCs are closer to hESCs, followed by adipose, neonatal fibroblast, and keratinocyte-derived hiPSCs.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America.

ABSTRACT
Human induced pluripotent stem cells (hiPSCs) generated by de-differentiation of adult somatic cells offer potential solutions for the ethical issues surrounding human embryonic stem cells (hESCs), as well as their immunologic rejection after cellular transplantation. However, although hiPSCs have been described as "embryonic stem cell-like", these cells have a distinct gene expression pattern compared to hESCs, making incomplete reprogramming a potential pitfall. It is unclear to what degree the difference in tissue of origin may contribute to these gene expression differences. To answer these important questions, a careful transcriptional profiling analysis is necessary to investigate the exact reprogramming state of hiPSCs, as well as analysis of the impression, if any, of the tissue of origin on the resulting hiPSCs. In this study, we compare the gene profiles of hiPSCs derived from fetal fibroblasts, neonatal fibroblasts, adipose stem cells, and keratinocytes to their corresponding donor cells and hESCs. Our analysis elucidates the overall degree of reprogramming within each hiPSC line, as well as the "distance" between each hiPSC line and its donor cell. We further identify genes that have a similar mode of regulation in hiPSCs and their corresponding donor cells compared to hESCs, allowing us to specify core sets of donor genes that continue to be expressed in each hiPSC line. We report that residual gene expression of the donor cell type contributes significantly to the differences among hiPSCs and hESCs, and adds to the incompleteness in reprogramming. Specifically, our analysis reveals that fetal fibroblast-derived hiPSCs are closer to hESCs, followed by adipose, neonatal fibroblast, and keratinocyte-derived hiPSCs.

Show MeSH
Related in: MedlinePlus