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Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.

Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD, Batada NN - Cell Regen (Lond) (2014)

Bottom Line: Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs.Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs.These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

View Article: PubMed Central - PubMed

Affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Morphology, Piracicaba Dental School, University of Campinas, Piracicaba, SP Brazil.

ABSTRACT
The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

No MeSH data available.


Related in: MedlinePlus

Cancer versus Normal profile of Y-iPSCs and T-iPSCs aberrantly methylated regions. DNA methylation difference (delta beta value) between cancer patients and matched normal tissue of each CpG site identified as aberrantly methylated in Y-iPSCs (left panels) or T-iPSCs (right panels). The DNA methylation data was obtained from the TCGA depository (http://tcga-data.nci.nih.gov) for (A) Colon adenocarcinoma – COAD (258 tumor samples and 38 normal samples), (B) Head and neck squamous cell carcinoma – HNSC (310 tumor samples and 50 normal samples).
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Fig5: Cancer versus Normal profile of Y-iPSCs and T-iPSCs aberrantly methylated regions. DNA methylation difference (delta beta value) between cancer patients and matched normal tissue of each CpG site identified as aberrantly methylated in Y-iPSCs (left panels) or T-iPSCs (right panels). The DNA methylation data was obtained from the TCGA depository (http://tcga-data.nci.nih.gov) for (A) Colon adenocarcinoma – COAD (258 tumor samples and 38 normal samples), (B) Head and neck squamous cell carcinoma – HNSC (310 tumor samples and 50 normal samples).

Mentions: One major concern related to use iPSCs for regenerative medicine is the increased tumorigenicity of iPSCs. To gain further insight into the differences in the type of DNA methylation aberrations found in Y-iPSCs or T-iPSCs, we tested whether the differentially methylated CpGs are also aberrantly methylated in cancers. We obtained publicly available DNA methylation data generated by The Cancer Genome Atlas consortium [23]. We evaluated the DNA methylation difference (delta beta value) between cancer patients and matched normal tissue of each CpG site identified as aberrantly methylated in Y-iPSCs (Figure 5, left panels) or T-iPSCs (Figure 5, right panels). We analyzed 6 cancer types: bladder urothelial carcinoma (Additional file 1: Figure S7), breast invasive carcinoma (Additional file 1: Figure S7), colon adenocarcinoma (Figure 5A), head and neck squamous cell carcinoma (Figure 5B), lung adenocarcinoma (Additional file 1: figure S7), lung squamous cell carcinoma (Additional file 1: Figure S7). We observed that CpG sites that exhibited Class I aberrations in T-iPSCs were enriched (P < 0.05) among Class I aberrations in colon adenocarcinoma and head and neck squamous cell carcinoma (Figure 5). It is not obvious if genes present within the regions proximal to Class I aberrations shared between T-iPSCs and the 2 cancers play a functional role or have features that would make them susceptible to spurious methylation.Figure 5


Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.

Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD, Batada NN - Cell Regen (Lond) (2014)

Cancer versus Normal profile of Y-iPSCs and T-iPSCs aberrantly methylated regions. DNA methylation difference (delta beta value) between cancer patients and matched normal tissue of each CpG site identified as aberrantly methylated in Y-iPSCs (left panels) or T-iPSCs (right panels). The DNA methylation data was obtained from the TCGA depository (http://tcga-data.nci.nih.gov) for (A) Colon adenocarcinoma – COAD (258 tumor samples and 38 normal samples), (B) Head and neck squamous cell carcinoma – HNSC (310 tumor samples and 50 normal samples).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230737&req=5

Fig5: Cancer versus Normal profile of Y-iPSCs and T-iPSCs aberrantly methylated regions. DNA methylation difference (delta beta value) between cancer patients and matched normal tissue of each CpG site identified as aberrantly methylated in Y-iPSCs (left panels) or T-iPSCs (right panels). The DNA methylation data was obtained from the TCGA depository (http://tcga-data.nci.nih.gov) for (A) Colon adenocarcinoma – COAD (258 tumor samples and 38 normal samples), (B) Head and neck squamous cell carcinoma – HNSC (310 tumor samples and 50 normal samples).
Mentions: One major concern related to use iPSCs for regenerative medicine is the increased tumorigenicity of iPSCs. To gain further insight into the differences in the type of DNA methylation aberrations found in Y-iPSCs or T-iPSCs, we tested whether the differentially methylated CpGs are also aberrantly methylated in cancers. We obtained publicly available DNA methylation data generated by The Cancer Genome Atlas consortium [23]. We evaluated the DNA methylation difference (delta beta value) between cancer patients and matched normal tissue of each CpG site identified as aberrantly methylated in Y-iPSCs (Figure 5, left panels) or T-iPSCs (Figure 5, right panels). We analyzed 6 cancer types: bladder urothelial carcinoma (Additional file 1: Figure S7), breast invasive carcinoma (Additional file 1: Figure S7), colon adenocarcinoma (Figure 5A), head and neck squamous cell carcinoma (Figure 5B), lung adenocarcinoma (Additional file 1: figure S7), lung squamous cell carcinoma (Additional file 1: Figure S7). We observed that CpG sites that exhibited Class I aberrations in T-iPSCs were enriched (P < 0.05) among Class I aberrations in colon adenocarcinoma and head and neck squamous cell carcinoma (Figure 5). It is not obvious if genes present within the regions proximal to Class I aberrations shared between T-iPSCs and the 2 cancers play a functional role or have features that would make them susceptible to spurious methylation.Figure 5

Bottom Line: Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs.Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs.These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

View Article: PubMed Central - PubMed

Affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Morphology, Piracicaba Dental School, University of Campinas, Piracicaba, SP Brazil.

ABSTRACT
The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

No MeSH data available.


Related in: MedlinePlus