TY - JOUR
T1 - Induced pluripotent stem cell differentiation and three-dimensional tissue formation attenuate clonal epigenetic differences in trichohyalin
AU - Petrova, Anastasia
AU - Capalbo, Antonio
AU - Jacquet, Laureen
AU - Hazelwood-Smith, Simon
AU - Dafou, Dimitra
AU - Hobbs, Carl
AU - Arno, Matthew
AU - Farcomeni, Alessio
AU - Devito, Liani
AU - Badraiq, Heba
AU - Simpson, Michael
AU - Mcgrath, John A.
AU - Di, Wei Li
AU - Cheng, Jeffrey B.
AU - Mauro, Theodora M.
AU - Ilic, Dusko
PY - 2016/9/1
Y1 - 2016/9/1
N2 - The epigenetic background of pluripotent stem cells can influence transcriptional and functional behavior. Most of these data have been obtained in standard monolayer cell culture systems. In this study, we used exome sequencing, array comparative genomic hybridization (CGH), miRNA array, DNA methylation array, three-dimensional (3D) tissue engineering, and immunostaining to conduct a comparative analysis of two induced pluripotent stem cell (iPSC) lines used in engineering of 3D human epidermal equivalent (HEE), which more closely approximates epidermis. Exome sequencing and array CGH suggested that their genome was stable following 3 months of feeder-free culture. While the miRNAome was also not affected, ≈7% of CpG sites were differently methylated between the two lines. Analysis of the epidermal differentiation complex, a region on chromosome 1 that contains multiple genes involved in skin barrier maturation (including trichohyalin, TCHH), found that in one of the iPSC clones (iKCL004), TCHH retained a DNA methylation signature characteristic of the original somatic cells, whereas in other iPSC line (iKCL011), the TCHH methylation signature matched that of the human embryonic stem cell line KCL034. The difference between the two iPSC clones in TCHH methylation did not have an obvious effect on its expression in 3D HEE, suggesting that differentiation and tissue formation may mitigate variations in the iPSC methylome.
AB - The epigenetic background of pluripotent stem cells can influence transcriptional and functional behavior. Most of these data have been obtained in standard monolayer cell culture systems. In this study, we used exome sequencing, array comparative genomic hybridization (CGH), miRNA array, DNA methylation array, three-dimensional (3D) tissue engineering, and immunostaining to conduct a comparative analysis of two induced pluripotent stem cell (iPSC) lines used in engineering of 3D human epidermal equivalent (HEE), which more closely approximates epidermis. Exome sequencing and array CGH suggested that their genome was stable following 3 months of feeder-free culture. While the miRNAome was also not affected, ≈7% of CpG sites were differently methylated between the two lines. Analysis of the epidermal differentiation complex, a region on chromosome 1 that contains multiple genes involved in skin barrier maturation (including trichohyalin, TCHH), found that in one of the iPSC clones (iKCL004), TCHH retained a DNA methylation signature characteristic of the original somatic cells, whereas in other iPSC line (iKCL011), the TCHH methylation signature matched that of the human embryonic stem cell line KCL034. The difference between the two iPSC clones in TCHH methylation did not have an obvious effect on its expression in 3D HEE, suggesting that differentiation and tissue formation may mitigate variations in the iPSC methylome.
UR - http://www.scopus.com/inward/record.url?scp=84987741171&partnerID=8YFLogxK
U2 - 10.1089/scd.2016.0156
DO - 10.1089/scd.2016.0156
M3 - Article
AN - SCOPUS:84987741171
SN - 1547-3287
VL - 25
SP - 1366
EP - 1375
JO - STEM CELLS AND DEVELOPMENT
JF - STEM CELLS AND DEVELOPMENT
IS - 18
ER -