Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods

ABSTRACT Many reprogramming methods can generate human induced pluripotent stem cells (hiPSCs) that closely resemble human embryonic stem cells (hESCs). This has led to assessments of how

similar hiPSCs are to hESCs, by evaluating differences in gene expression, epigenetic marks and differentiation potential. However, all previous studies were performed using hiPSCs acquired

from different laboratories, passage numbers, culturing conditions, genetic backgrounds and reprogramming methods, all of which may contribute to the reported differences. Here, by using

high-throughput sequencing under standardized cell culturing conditions and passage number, we compare the epigenetic signatures (H3K4me3, H3K27me3 and HDAC2 ChIP-seq profiles) and

transcriptome differences (by RNA-seq) of hiPSCs generated from the same primary fibroblast population by using six different reprogramming methods. We found that the reprogramming method

impacts the resulting transcriptome and that all hiPSC lines could terminally differentiate, regardless of the reprogramming method. Moreover, by comparing the differences between the hiPSC

and hESC lines, we observed a significant proportion of differentially expressed genes that could be attributed to polycomb repressive complex targets. Access through your institution Buy or

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  CAS  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS This study was funded by the Canadian Institute of Health Research 201210MFE-289547 (J.M.C.), National

Institutes of Health 1K99HL128906 (J.M.C.), PCBC_JS_2014/4_01 (J.M.C.), National Research Foundation of Korea 2012R1A6A3A03039821 (J.L.), the Burroughs Wellcome Foundation, National

Institutes of Health R01 HL123968, HL128170, R01 HL126527 (J.C.W.), and P01 GM099130 (M.P.S.). The authors would like to thank the Stanford Stem Cell Institute Genome Center for their

sequencing knowledge, V. Sebastiano for hESC culturing, and B. Huber for his help with the teratoma assay. We would also like to thank J. Brito and B. Wu for their help in editing the

manuscript. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA Jared M.

Churko, Jaecheol Lee, Mohamed Ameen, Mingxia Gu, Sebastian Diecke, Karim Sallam, Joseph D. Gold & Joseph C. Wu * Stanford Cardiovascular Institute, Stanford University School of

Medicine, Stanford, CA, 94305, USA Jared M. Churko, Jaecheol Lee, Mohamed Ameen, Mingxia Gu, Sebastian Diecke, Karim Sallam & Joseph C. Wu * Department of Medicine, Stanford University

School of Medicine, Stanford, CA, 94305, USA Jared M. Churko, Jaecheol Lee, Mohamed Ameen, Mingxia Gu, Sebastian Diecke, Karim Sallam & Joseph C. Wu * Division of Biomedical Informatics,

Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA Meenakshi Venkatasubramanian, Hogune Im & Nathan Salomonis * Department of Genetics, Stanford University School

of Medicine, Stanford, CA, 94305, USA Gavin Wang & Michael P. Snyder Authors * Jared M. Churko View author publications You can also search for this author inPubMed Google Scholar *

Jaecheol Lee View author publications You can also search for this author inPubMed Google Scholar * Mohamed Ameen View author publications You can also search for this author inPubMed Google

Scholar * Mingxia Gu View author publications You can also search for this author inPubMed Google Scholar * Meenakshi Venkatasubramanian View author publications You can also search for

this author inPubMed Google Scholar * Sebastian Diecke View author publications You can also search for this author inPubMed Google Scholar * Karim Sallam View author publications You can

also search for this author inPubMed Google Scholar * Hogune Im View author publications You can also search for this author inPubMed Google Scholar * Gavin Wang View author publications You

can also search for this author inPubMed Google Scholar * Joseph D. Gold View author publications You can also search for this author inPubMed Google Scholar * Nathan Salomonis View author

publications You can also search for this author inPubMed Google Scholar * Michael P. Snyder View author publications You can also search for this author inPubMed Google Scholar * Joseph C.

Wu View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS J.D.G., N.S., M.P.S. and J.C.W. supervised and planned the project. J.M.C. wrote the

manuscript, performed data analysis, generated and cultured hiPSC lines, and performed RNA-seq. N.S. and M.V. performed integration analysis. H.I. helped analyse RNA-seq. J.L. performed

ChIP-seq experiments. M.A. and M.G. performed FACS analysis on differentiated cardiomyocytes. G.W. and K.S. helped to culture hiPSC and hESC lines. S.D. generated minicircle hiPSC lines.

CORRESPONDING AUTHOR Correspondence to Joseph C. Wu. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE:

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Supplementary figures LIFE SCIENCES REPORTING SUMMARY SUPPLEMENTARY DATASET 1 Reads per kilobase of transcript per million mapped reads of each Ensembl ID, calculated via AltAnalyze.

SUPPLEMENTARY DATASET 2 Gene-expression differences, calculated via a Bayes moderated t-test p-value (unpaired), assuming unequal variance, and _p_ < 0.05 with two-fold difference.

SUPPLEMENTARY DATASET 3 Splicing events between hiPSCs and hESCs. SUPPLEMENTARY DATASET 4 Differential peaks unique to the hESCs and peaks unique to hiPSCs, corresponding to HDAC2

localization. SUPPLEMENTARY DATASET 5 Transcriptional-start-site peak-density differences within the H3K4me3 ChIP-seq set between hESCs and hiPSCs. SUPPLEMENTARY DATASET 6

Transcriptional-start-site peak-density differences in the H3K27me3 ChIP-seq profile between hESCs and hiPSCs. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS

ARTICLE Churko, J.M., Lee, J., Ameen, M. _et al._ Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods. _Nat Biomed Eng_

1, 826–837 (2017). https://doi.org/10.1038/s41551-017-0141-6 Download citation * Received: 24 October 2016 * Accepted: 04 September 2017 * Published: 03 October 2017 * Issue Date: October

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