Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements

CRISPR-based genome editing of pseudogene-associated disorders, such as p47phox-deficient chronic granulomatous disease (p47 CGD), is challenged by chromosomal rearrangements due to presence of multiple targets. We report that interactions between highly homologous sequences that are localized on the same chromosome contribute substantially to post-editing chromosomal rearrangements. We successfully employed editing approaches at the NCF1 gene and its pseudogenes, NCF1B and NCF1C, in a human cell line model of p47 CGD and in patient-derived human hematopoietic stem and progenitor cells. Upon genetic engineering, a droplet digital PCR-based method identified cells with altered copy numbers, spanning megabases from the edited loci. We attributed the high aberration frequency to the interaction between repetitive sequences and their predisposition to recombination events. Our findings emphasize the need for careful evaluation of the target-specific genomic context, such as the presence of homologous regions, whose instability can constitute a risk factor for chromosomal rearrangements upon genome editing.

Keywords

Subject (DDC)

600 - Technik, Medizin, angewandte Wissenschaften

Project

Event

Exhibition start date

Exhibition end date

Conference start date

Conference end date

Date of the last check

ISBN

ISSN

2399-3642

Language

English

Created during FHNW affiliation

Yes

Strategic action fields FHNW

Publication status

Published

Review

Peer review of the complete publication

Open access category

Gold

License

Citation

Raimondi, F., Siow, K. M., Wrona, D., Fuster-García, C., Pastukhov, O., Schmitz, M., Bargsten, K., Kissling, L., Swarts, D. C., Andrieux, G., Cathomen, T., Modlich, U., Jinek, M., Siler, U., & Reichenbach, J. (2024). Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements. Communications Biology, 7(1), 1291. https://doi.org/10.1038/s42003-024-06959-z

Full item page