title: Induced Pluripotent Stem Cell Differentiation and Three-Dimensional Tissue Formation Attenuate Clonal Epigenetic Differences in Trichohyalin.
abstract: 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.
authors.affiliation: 1 Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London , London, United Kingdom .|2 St John's Institute of Dermatology , King's College London, London, United Kingdom .|3 Immunobiology Unit, Institute of Child Health, University College London , London, United Kingdom .
authors.forename: Anastasia
authors.initials: A
authors.lastname: Petrova
authors.affiliation: 4 GENERA, Centers for Reproductive Medicine , Rome, Italy .
authors.forename: Antonio
authors.initials: A
authors.lastname: Capalbo
authors.affiliation: 1 Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London , London, United Kingdom .
authors.forename: Laureen
authors.initials: L
authors.lastname: Jacquet
authors.affiliation: 5 Division of Genetics and Molecular Medicine, King's College London , London, United Kingdom .
authors.forename: Simon
authors.initials: S
authors.lastname: Hazelwood-Smith
authors.affiliation: 5 Division of Genetics and Molecular Medicine, King's College London , London, United Kingdom .
authors.forename: Dimitra
authors.initials: D
authors.lastname: Dafou
authors.affiliation: 6 Histology Laboratory, Wolfson Centre for Age-Related Diseases, King's College London , London, United Kingdom .
authors.forename: Carl
authors.initials: C
authors.lastname: Hobbs
authors.affiliation: 7 Genomics Centre, King's College London , London, United Kingdom .
authors.forename: Matthew
authors.initials: M
authors.lastname: Arno
authors.affiliation: 8 Statistics Section, Department of Public Health and Infectious Diseases, Sapienza-University of Rome , Rome, Italy .
authors.forename: Alessio
authors.initials: A
authors.lastname: Farcomeni
authors.affiliation: 1 Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London , London, United Kingdom .
authors.forename: Liani
authors.initials: L
authors.lastname: Devito
authors.affiliation: 1 Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London , London, United Kingdom .
authors.forename: Heba
authors.initials: H
authors.lastname: Badraiq
authors.affiliation: 5 Division of Genetics and Molecular Medicine, King's College London , London, United Kingdom .
authors.forename: Michael
authors.initials: M
authors.lastname: Simpson
authors.affiliation: 2 St John's Institute of Dermatology , King's College London, London, United Kingdom .
authors.forename: John A
authors.initials: JA
authors.lastname: McGrath
authors.affiliation: 3 Immunobiology Unit, Institute of Child Health, University College London , London, United Kingdom .
authors.forename: Wei-Li
authors.initials: WL
authors.lastname: Di
authors.affiliation: 9 Department of Dermatology, Veteran Affairs Medical Center, University of California San Francisco , San Francisco, California.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Cheng
authors.affiliation: 9 Department of Dermatology, Veteran Affairs Medical Center, University of California San Francisco , San Francisco, California.
authors.forename: Theodora M
authors.initials: TM
authors.lastname: Mauro
authors.affiliation: 1 Assisted Conception Unit, Stem Cell Laboratory, Division of Women's Health, Women's Health Academic Centre, King's College London , London, United Kingdom .
authors.forename: Dusko
authors.initials: D
authors.lastname: Ilic
mesh_terms: D000328:Adult; D002454:Cell Differentiation / Q000235:genetics*; D002460:Cell Line; D065150:Cellular Reprogramming / Q000235:genetics; D002999:Clone Cells; D019175:DNA Methylation / Q000235:genetics; D004817:Epidermis / Q000378:metabolism; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D042822:Genomic Instability; D000066449:Human Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism; D007231:Infant, Newborn; D007381:Intermediate Filament Proteins / Q000235:genetics* / Q000378:metabolism; D015603:Keratinocytes / Q000166:cytology / Q000378:metabolism; D008297:Male; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D059645:Mutation Rate; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D023822:Tissue Engineering / Q000379:methods*
chemical_list: D007381:Intermediate Filament Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; C016159:trichohyalin