A large CRISPR-induced bystander mutation causes immune dysregulation

Dimitre R Simeonov; Alexander J Brandt; Alice Y Chan; Jessica T Cortez; Zhongmei Li; Jonathan M Woo; Youjin Lee; Claudia M B Carvalho; Alyssa C Indart; Theodore L Roth; James Zou; Andrew P May; James R Lupski; Mark S Anderson; F William Buaas; Daniel S Rokhsar; Alexander Marson

doi:10.1038/s42003-019-0321-x

A large CRISPR-induced bystander mutation causes immune dysregulation

Commun Biol. 2019 Feb 18:2:70. doi: 10.1038/s42003-019-0321-x. eCollection 2019.

Authors

Dimitre R Simeonov^{1

2

3

4}, Alexander J Brandt^{4

5}, Alice Y Chan^{3

6}, Jessica T Cortez^{1

2

3

4}, Zhongmei Li^{2

3

4}, Jonathan M Woo^{2

3

4}, Youjin Lee^{2

3

4}, Claudia M B Carvalho⁷, Alyssa C Indart¹, Theodore L Roth^{1

2

3

4

5}, James Zou^{8

9}, Andrew P May⁹, James R Lupski⁷, Mark S Anderson³, F William Buaas¹⁰, Daniel S Rokhsar^{4

11

12}, Alexander Marson^{13

14

15

16

17

18}

Affiliations

¹ Biomedical Sciences Graduate Program, University of California, San Francisco, CA, 94143, USA.
² Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA.
³ Diabetes Center, University of California, San Francisco, CA, 94143, USA.
⁴ Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
⁵ Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
⁶ Department of Pediatrics, University of California, San Francisco, CA, 94143, USA.
⁷ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
⁸ Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
⁹ Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
¹⁰ Genetic Engineering Technologies, The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
¹¹ Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
¹² Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.
¹³ Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA. alexander.marson@ucsf.edu.
¹⁴ Diabetes Center, University of California, San Francisco, CA, 94143, USA. alexander.marson@ucsf.edu.
¹⁵ Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA. alexander.marson@ucsf.edu.
¹⁶ Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA. alexander.marson@ucsf.edu.
¹⁷ Department of Medicine, University of California, San Francisco, CA, 94143, USA. alexander.marson@ucsf.edu.
¹⁸ UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA. alexander.marson@ucsf.edu.

Abstract

A persistent concern with CRISPR-Cas9 gene editing has been the potential to generate mutations at off-target genomic sites. While CRISPR-engineering mice to delete a ~360 bp intronic enhancer, here we discovered a founder line that had marked immune dysregulation caused by a 24 kb tandem duplication of the sequence adjacent to the on-target deletion. Our results suggest unintended repair of on-target genomic cuts can cause pathogenic "bystander" mutations that escape detection by routine targeted genotyping assays.

Publication types

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

MeSH terms

Animals
Base Sequence
CRISPR-Cas Systems*
Cells, Cultured
DNA Damage
DNA Repair
Gene Duplication
Gene Editing / methods*
Gene Expression Regulation / immunology
Interleukin-2 Receptor alpha Subunit / genetics*
Interleukin-2 Receptor alpha Subunit / immunology
Mice, Inbred NOD
Mutation*
T-Lymphocytes / immunology*
T-Lymphocytes / metabolism
T-Lymphocytes, Regulatory / immunology*
T-Lymphocytes, Regulatory / metabolism

Substances

Il2ra protein, mouse
Interleukin-2 Receptor alpha Subunit

Abstract

Publication types

MeSH terms

Substances

Grants and funding