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Series GSE119079 Query DataSets for GSE119079
Status Public on Jan 24, 2019
Title Tracking of epigenetic changes during hematopoietic differentiation of induced pluripotent stem cells
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Differentiation of induced pluripotent stem cells (iPSCs) toward hematopoietic progenitor cells (HPCs) raises high hopes for disease modelling, drug screening, and cellular therapy. Various differentiation protocols have been established to generate iPSC-derived HPCs (iHPCs) that resemble their primary counterparts in morphology and immunophenotype, whereas a systematic epigenetic comparison was yet elusive. In this study, we compared genome wide DNA methylation (DNAm) patterns of iHPCs with various different hematopoietic subsets. Furthermore, we analyzed if additional co-culture for two weeks with syngenic primary mesenchymal stromal cells (MSCs) or iPSC-derived MSCs (iMSCs) further supports epigenetic maturation toward hematopoietic lineage. After 20 days of in vitro differentiation cells revealed typical hematopoietic morphology, CD45 expression and colony forming unit (CFU) potential. DNAm changes were particularly observed in genes that are associated with hematopoietic differentiation. On the other hand, the epigenetic profiles of iHPCs remained overall very distinct from normal hematopoiesis. Co-culture with MSCs or iMSCs enhanced proliferation of iHPCs and maintenance of CFU potential. However, morphology, immunophenotype, and DNAm profiles did not indicate that additional culture expansion with stromal support increases hematopoietic differentiation. In conclusion, differentiation of iPSCs towards hematopoietic lineage remains epigenetically incomplete. These results substantiate the need to elaborate advanced differentiation regimen while DNAm profiles provide a suitable measure to track this process.
 
Overall design DNA from iPSC-derived hematopoietic progenitor cells was isolated after 20 days of differentiation or after additional 14 days of culture expansion on either tissue culture plastic or in co-culture with bone marrow derived MSCs or iPSC-derived MSCs. DNA was bisulfite converted and hybridized to the Illumina Infinium MethylationEPIC BeadChip.
 
Contributor(s) Cypris O, Frobel J, Rai S, Franzen J, Sontag S, Goetzke R, Szymanski de Toledo MA, Zenke M, Wagner W
Citation(s) 30717806
Submission date Aug 27, 2018
Last update date Feb 07, 2019
Contact name Wolfgang Wagner
E-mail(s) wwagner@ukaachen.de
Phone +49 241 8088611
Organization name RWTH Aachen University
Department Helmholtz Institute for Biomedical Engineering
Lab Stem Cell Biology and Cellular Engineering
Street address Pauwelsstrasse 20
City Aachen
ZIP/Postal code 52074
Country Germany
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (8)
GSM3357561 iHPC_donor1_d20
GSM3357562 iHPC_donor1_d34_TCP
GSM3357563 iHPC_donor1_d34_MSC
Relations
BioProject PRJNA488066

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119079_RAW.tar 274.0 Mb (http)(custom) TAR (of IDAT)
GSE119079_signal_intensities.txt.gz 32.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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