Spontaneous ATM Gene Reversion in A-T iPSC to Produce an Isogenic Cell Line

Summary

A spontaneously reverted iPSC line was identified from an A-T subject with heterozygous ATM truncation mutations. The reverted iPSC line expressed ATM protein and was capable of radiation-induced phosphorylation of CHK2 and H2A.X. Genome-wide SNP analysis confirmed a match to source T cells and also to a distinct, non-reverted iPSC line from the same subject. Rearranged T cell receptor sequences predict that the iPSC culture originated as several independently reprogrammed cells that resolved into a single major clone, suggesting that gene correction likely occurred early in the reprogramming process. Gene expression analysis comparing ATM ^−/− iPSC lines to unrelated ATM ^+/− cells identifies a large number of differences, but comparing only the isogenic pair of A-T iPSC lines reveals that the primary pathway affected by loss of ATM is a diminished expression of p53-related mRNAs. Gene reversion in culture, although likely a rare event, provided a novel, reverted cell line for studying ATM function.

Highlights

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  Spontaneous reversion of an ATM mutation was found in A-T iPSC

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  Reversion was due to gene correction, based on LOH of a nearby SNP

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  Gene expression changes between individuals overwhelm those from single mutations

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  Loss of ATM in unstimulated cells primarily reduced the p53 pathway

Abstract

Hart and colleagues identify an isogenic iPSC line resulting from spontaneous gene reversion of the ATM gene. Gene expression studies find that an isogenic pair of cell lines reveals a more focused pattern of ATM-responding mRNAs, highlighting the p53 pathway.