The advent of induced pluripotent stem cells (iPSCs) revolutionized human genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We find a remarkably small number of differences in DNA methylation and gene expression levels between iPSCs derived from different somatic precursors. Instead, we demonstrate genetic variation is associated with the majority of identifiable variation in DNA methylation and gene expression levels. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs, and that genetic variation is the main driver of regulatory differences between iPSCs of different donors. Our findings suggest that studies using iPSCs should focus on additional individuals rather than clones from the same individual.
References
[1]
Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, et al. (2007) Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors. Cell 131: 861–872. pmid:18035408 doi: 10.1016/j.cell.2007.11.019
[2]
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, et al. (2007) Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. Science 318: 1917–1920. pmid:18029452 doi: 10.1126/science.1151526
[3]
Yamanaka S, Takahashi K (2006) Induction of pluripotent stem cells from mouse fibroblast cultures. Tanpakushitsu Kakusan Koso 51: 2346–2351. pmid:17154061
[4]
Okita K, Ichisaka T, Yamanaka S (2007) Generation of germline-competent induced pluripotent stem cells. Nature 448: 313–317. pmid:17554338 doi: 10.1038/nature05934
[5]
Park I-H, Arora N, Huo H, Maherali N, Ahfeldt T, et al. (2008) Disease-specific induced pluripotent stem cells. Cell 134: 877–886. doi: 10.1016/j.cell.2008.07.041. pmid:18691744
[6]
Narsinh K, Narsinh KH, Wu JC (2011) Derivation of Induced Pluripotent Stem Cells for Human Disease Modeling. Circ Res 108: 1146–1156. doi: 10.1161/CIRCRESAHA.111.240374. pmid:21527744
[7]
Josowitz R, Carvajal-Vergara X, Lemischka IR, Gelb BD (2011) Induced pluripotent stem cell-derived cardiomyocytes as models for genetic cardiovascular disorders. Curr Opin Cardiol 26: 223–229. doi: 10.1097/HCO.0b013e32834598ad. pmid:21451408
[8]
Chang WY, Garcha K, Manias JL, Stanford WL (2012) Deciphering the complexities of human diseases and disorders by coupling induced-pluripotent stem cells and systems genetics. Wiley Interdisciplinary Reviews Systems Biology and Medicine 4: 339–350. doi: 10.1002/wsbm.1170. pmid:22492636
[9]
Chin MH, Mason MJ, Xie W, Volinia S, Singer M, et al. (2009) Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 5: 111–123. doi: 10.1016/j.stem.2009.06.008. pmid:19570518
[10]
Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, et al. (2010) Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. PLoS One 5: e8975. doi: 10.1371/journal.pone.0008975. pmid:20126639
[11]
Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, et al. (2010) Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 7: 249–257. doi: 10.1016/j.stem.2010.06.015. pmid:20682450
[12]
Kim K, Doi A, Wen B, Ng K, Zhao R, et al. (2010) Epigenetic memory in induced pluripotent stem cells. Nature 467: 285–290. doi: 10.1038/nature09342. pmid:20644535
[13]
Bar-Nur O, Russ HA, Efrat S, Benvenisty N (2011) Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell 9: 17–23. doi: 10.1016/j.stem.2011.06.007. pmid:21726830
[14]
Polo JM, Liu S, Figueroa ME, Kulalert W, Eminli S, et al. (2010) Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol 28: 848–855. doi: 10.1038/nbt.1667. pmid:20644536
[15]
Ohi Y, Qin H, Hong C, Blouin L, Polo JM, et al. (2011) Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 13: 541–549. doi: 10.1038/ncb2239. pmid:21499256
[16]
Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, et al. (2011) Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 29: 1117–1119. doi: 10.1038/nbt.2052. pmid:22119740
[17]
Cahan P, Daley GQ (2013) Origins and implications of pluripotent stem cell variability and heterogeneity. Nat Rev Mol Cell Biol 14: 357–368. doi: 10.1038/nrm3584. pmid:23673969
[18]
Ma H, Morey R, O'Neil RC, Yupeng H, Brittany D, et al. (2014) Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature. doi: 10.1038/nature13551
[19]
Kvaratskhelia M, Sharma A, Larue RC, Serrao E, Engelman A (2014) Molecular mechanisms of retroviral integration site selection. Nucleic Acids Research. doi: 10.1093/nar/gku769
[20]
LaFave MC, Varshney GK, Gildea DE, Wolfsberg TG, Baxevanis AD, et al. (2014) MLV integration site selection is driven by strong enhancers and active promoters. Nucleic Acids Research. doi: 10.1093/nar/gkt1399
[21]
Okita K, Matsumura Y, Sato Y, Okada A, Morizane A, et al. (2011) A more efficient method to generate integration-free human iPS cells. Nat Meth 8: 409–412. doi: 10.1038/nmeth.1591
[22]
Cheng L, Hansen NF, Zhao L, Du Y, Zou C, et al. (2012) Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by nonintegrating plasmid expression. Cell Stem Cell 10: 337–344. doi: 10.1016/j.stem.2012.01.005. pmid:22385660
[23]
Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L, et al. (2014) Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells. PLoS Genet 10: e1004432. doi: 10.1371/journal.pgen.1004432. pmid:24901476
[24]
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, et al. (2014) Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30: 1363–1369. doi: 10.1093/bioinformatics/btu049. pmid:24478339
[25]
Maksimovic J, Gordon L, Oshlack A (2012) SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips. Genome Biology 13: R44. doi: 10.1186/gb-2012-13-6-r44. pmid:22703947
[26]
Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3. doi: 10.2202/1544-6115.1027
[27]
Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Banovich NE, Kagan CL, et al. (2014) Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics. doi: 10.1101/008862
[28]
Chen G, Gulbranson DR, Hou Z, Bolin JM, Ruotti V, et al. (2011) Chemically defined conditions for human iPSC derivation and culture. Nat Meth 8: 424–429. doi: 10.1038/nmeth.1593
[29]
Howden SE, Wardan H, Voullaire L, McLenachan S, Williamson R, et al. (2006) Chromatin-binding regions of EBNA1 protein facilitate the enhanced transfection of Epstein-Barr virus-based vectors. Hum Gene Ther 17: 833–844. pmid:16942443 doi: 10.1089/hum.2006.17.833
[30]
Müller F-J, Schuldt BM, Williams R, Mason D, Altun G, et al. (2011) A bioinformatic assay for pluripotency in human cells. Nature Methods 8: 315–317. doi: 10.1038/nmeth.1580. pmid:21378979
[31]
Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571–1572. doi: 10.1093/bioinformatics/btr167. pmid:21493656
[32]
Du P, Kibbe WA, Lin SM (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24: 1547–1548. doi: 10.1093/bioinformatics/btn224. pmid:18467348
[33]
WJ K , CW S , TS F , KM R , TH P , et al. (2002) The human genome browser at UCSC. Genome Res 12: 996–1006. pmid:12045153 doi: 10.1101/gr.229102.
[34]
Kasprzyk A (2011) BioMart: driving a paradigm change in biological data management. Database (Oxford) 2011: bar049. doi: 10.1093/database/bar049
Kim K- Y, Hysolli E, Tanaka Y, Wang B, Jung Y-W, et al. (2014) X Chromosome of Female Cells Shows Dynamic Changes in Status during Human Somatic Cell Reprogramming. Stem Cell Reports 2: 896–909. doi: 10.1016/j.stemcr.2014.04.003. pmid:24936474
[37]
Ernst J, Pouya K, Tarjei SM, Noam S, Lucas DW, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43–49. doi: 10.1038/nature09906. pmid:21441907
[38]
Lappalainen T, Sammeth M, Friedlander MR, t Hoen PAC, Monlong J, et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506–511. doi: 10.1038/nature12531. pmid:24037378
[39]
Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, et al. (2014) Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels. PLoS Genet 10: e1004663. doi: 10.1371/journal.pgen.1004663. pmid:25233095
