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

TitlePassage number is a major contributor to genomic structural variations in mouse iPSCs.
Publication TypeJournal Article
Year of Publication2014
AuthorsLiu, P, Kaplan, A, Yuan, B, Hanna, JH, Lupski, JR, Reiner, O
JournalStem Cells
Date Published2014 Oct
KeywordsAneuploidy, Animals, Base Sequence, Cell Proliferation, Chromosome Breakage, Clone Cells, Comparative Genomic Hybridization, DNA Copy Number Variations, Genetic Loci, Genomic Instability, Genomic Structural Variation, Induced Pluripotent Stem Cells, Mice, Molecular Sequence Data, Neural Stem Cells, Spheroids, Cellular

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.

Alternate JournalStem Cells
PubMed ID24965231
PubMed Central IDPMC4165691
Grant ListR01NS058529 / NS / NINDS NIH HHS / United States
P30 HD024064 / HD / NICHD NIH HHS / United States
P30HD024064 / HD / NICHD NIH HHS / United States
R01 NS058529 / NS / NINDS NIH HHS / United States
M01RR00188 / RR / NCRR NIH HHS / United States
M01 RR000188 / RR / NCRR NIH HHS / United States
U54 HD083092 / HD / NICHD NIH HHS / United States

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