Passage number is a major contributor to genomic structural variations in mouse iPSCs

Stem Cells. 2014 Oct;32(10):2657-67. doi: 10.1002/stem.1779.


Emergence of genomic instability is a practical issue in preparing neural stem cells (NSCs) and induced pluripotent stem cells (iPSCs). However, it is still not fully understood what the origins and mechanisms for formation are for the genomic alternations observed. Here, we studied the extent of genomic variation on the scale of individual cells originating from the same animal. We used mouse NSCs grown from embryonic cells and iPSCs generated from embryonic brain cells, B cells or fibroblasts, and performed comparative analysis with cultures of fibroblasts from the same mouse. In the first passage of these cell lines, aneuploidies were only observed for chromosomes 6, 11, 12, 19, and Y, which is overall at a rate lower than previously reported; de novo copy number variations (CNVs) were observed in 4.3% of neural iPSCs, 29% of B cell iPSCs, 10% of fibroblast iPSCs, and 1.3% of neurospheres. In contrast, propagation of these first passage cells to a later passage induced additional aneuploidies and CNVs. Breakpoint sequencing analysis suggested that the majority of the detected CNVs arose by replicative mechanisms. Interestingly, we detected identical de novo CNVs in different single cell colonies that appeared to have arisen independently from each other, which suggests a novel CNV formation mechanism in these cells. Our findings provide insights into mechanisms of CNV formation during reprogramming and suggest that replicative mechanisms for CNV formation accompany mitotic divisions.

Keywords: Chromosomal aberrations; DNA copy number variations; DNA replication; Induced pluripotent stem cells; Neural stem cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aneuploidy
  • Animals
  • Base Sequence
  • Cell Proliferation
  • Chromosome Breakage
  • Clone Cells
  • Comparative Genomic Hybridization
  • DNA Copy Number Variations / genetics
  • Genetic Loci
  • Genomic Instability
  • Genomic Structural Variation*
  • Induced Pluripotent Stem Cells / cytology*
  • Induced Pluripotent Stem Cells / metabolism*
  • Mice
  • Molecular Sequence Data
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism
  • Spheroids, Cellular / cytology
  • Spheroids, Cellular / metabolism