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Copy number variation and selection during reprogramming to pluripotency

Abstract

The mechanisms underlying the low efficiency of reprogramming somatic cells into induced pluripotent stem (iPS) cells are poorly understood. There is a clear need to study whether the reprogramming process itself compromises genomic integrity and, through this, the efficiency of iPS cell establishment. Using a high-resolution single nucleotide polymorphism array, we compared copy number variations (CNVs) of different passages of human iPS cells with their fibroblast cell origins and with human embryonic stem (ES) cells. Here we show that significantly more CNVs are present in early-passage human iPS cells than intermediate passage human iPS cells, fibroblasts or human ES cells. Most CNVs are formed de novo and generate genetic mosaicism in early-passage human iPS cells. Most of these novel CNVs rendered the affected cells at a selective disadvantage. Remarkably, expansion of human iPS cells in culture selects rapidly against mutated cells, driving the lines towards a genetic state resembling human ES cells.

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Figure 1: High mutation level in human iPS cells is reduced through moderate culture.
Figure 2: Increased mosaicism in early-passage human iPS cells.
Figure 3: High selection pressure against de novo mutations suggests reprogramming as the source of novel CNVs.
Figure 4: Frequent mutations in fragile genomic regions influence selection during the expansion of human iPS cells.

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Gene Expression Omnibus

Data deposits

Affymetrix SNP array 6.0 data from each individual sample have been deposited with the NCBI Gene Expression Omnibus(http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE26173.

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Acknowledgements

This work was supported by funding for the ESTOOLS consortium under the Sixth RFP of the EU (S.M.H., T.O., R.L. and O.B.), the Academy of Finland (T.O. and R.A.), the Finnish Cancer Organizations (R.L.), the Research Funds of the Helsinki University Hospital (T.O.), the Sigrid Jusélius Foundation (T.O.), the Stem Cell Network Canada, GL2 and CIHR (A.N.). S.M.H. is a recipient of a McEwen Post-doctoral Fellowship from the McEwen Centre for Regenerative Medicine. N.N.B. is the recipient of a New Investigator Award from the Ontario Institute for Cancer Research, through the Ontario Ministry of Research and Innovation. A.N. is Tier 1 Canada Research Chair in Stem Cells and Regeneration. We are grateful to I. Rogers, M. Faiz and K. Nagy for critically reading and editing the manuscript, and J. Ustinov, H. Sariola and J. Palgi for skilled assistance in the characterization of human iPS cells. We thank N. Rahkonen for sample processing, as well as the Finnish Microarray and Sequencing Centre (http://www.btk.fi/), and the Institute of Human Genetics, University of Bonn, for array processing.

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Authors

Contributions

S.M.H. coordinated and performed most of the experiments in this project, analysed and interpreted the data, and prepared the manuscript. N.N.B. analysed and interpreted the data and prepared an early version of the manuscript. S.V. provided essential experimental assistance and performed some experiments in this study. R.W.C. performed, and advised on the planning of, FISH experiments. R.A. and E.N. analysed and interpreted the data and coordinated the sample processing of the arrays. O.B. and M.P. provided analysed data and samples from Illumina arrays for validation. M.S., S.N., R.H., R.T., M.M., C.O. and K.L. contributed experimentally. D.P.B-J. and K.A. provided essential experimental material and support. R.L. directed the SNP array data generation and analysis. T.O. directed, coordinated and supervised the first stage of the project and contributed to the preparation of the manuscript. A.N. prepared the manuscript, supervised the second stage of the project and helped to interpret the data. K.A. and R.L. contributed equally as co-authors. A.N. and T.O. contributed equally as senior authors.

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Correspondence to Andras Nagy or Timo Otonkoski.

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The authors declare no competing financial interests.

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Hussein, S., Batada, N., Vuoristo, S. et al. Copy number variation and selection during reprogramming to pluripotency. Nature 471, 58–62 (2011). https://doi.org/10.1038/nature09871

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