Unexpected mutations after CRISPR–Cas9 editing in vivo

A Retraction to this article was published on 27 April 2018

This article has been updated

To the Editor:

CRISPR–Cas9 editing shows promise for correcting disease-causing mutations. For example, in a recent study we used CRISPR-Cas9 for sight restoration in blind rd1 mice by correcting a mutation in the Pde6b gene1. However, concerns persist regarding secondary mutations in regions not targeted by the single guide RNA (sgRNA)2. Algorithms generate likely off-target sites for a given gRNA, but these algorithms may miss mutations. Whole-genome sequencing (WGS) has been used to assess the presence of small insertions and deletions (indels)3 but not to probe for single-nucleotide variants (SNVs) in a whole organism. We performed WGS on a CRISPR–Cas9-edited mouse to identify all off-target mutations and found an unexpectedly high number of SNVs compared with the widely accepted assumption that CRISPR causes mostly indels at regions homologous to the sgRNA.

We tested four sgRNAs in cells then chose the sgRNA with the highest activity for in vivo targeting. DNA was isolated from two CRISPR-repaired mice (F03 and F05) and one uncorrected control1. CRISPR–Cas9-treated mice were sequenced at an average depth of 50×, and the control was sequenced at 30×. Variant calls were confirmed by at least 23× sequencing coverage (Supplementary Tables 1 and 2). Multiple variant-calling software pipelines identified indels and SNVs (Fig. 1 and Supplementary Methods).

Figure 1: CRISPR gene correction introduces an unexpectedly high number of mutations in a mouse model of gene therapy.
figure1

(a) Venn diagrams display SNVs detected in WGS data by the indicated bioinformatics tools. (b) Summary of variant types found in mouse F03, mouse F05, and shared between both mice.

In the CRISPR-treated mice, targeted alleles were repaired1. Off-target mutations were identified as those present in the CRISPR-treated animals but absent in the uncorrected control. All pipelines showed that F03 harbored 164 indels and 1,736 SNVs (63 and 885 of these, respectively, associated with known genes). F05 harbored 128 indels and 1,696 SNVs (51 and 865 of these, respectively, associated with known genes) (Fig. 1). The same 117 indels and 1,397 SNVs were detected in both of the CRISPR-treated mice, which indicated nonrandom targeting. SNVs appeared to slightly favor transitions over transversions (Supplementary Fig. 1). The mutation rate detected in CRISPR-treated mice was substantially higher than that generated by spontaneous germline mutations (3 to 4 indels and 90 to 100 SNVs, de novo, per generation)4,5.

As additional controls, each of the variants was compared with the FVB/NJ genome in the mouse dbSNP database (v138), and each of the SNVs was also compared with all 36 strains in the Mouse Genome Project (v3). None of the CRISPR-generated off-target mutations were found in any of these strains, which further confirmed that these WGS-identified SNVs were the result of CRISPR–Cas9 off targeting.

All pipelines identified 6 and 3 indels and 60 and 51 SNVs in F03 and F05 mice, respectively, in exonic regions only (Fig. 1); 5 indels and 24 SNVs caused nonsynonymous mutations in protein-coding sequences (Supplementary Tables 3 and 4). Of these, all five indels and one SNV (introducing a premature stop codon) were expected to be deleterious. Several mutated protein-coding genes were associated with a human and/or mouse phenotype (Supplementary Tables 3 and 4). Of the 29 coding-sequence variants, 7 variants were mutated identically in both mice. 24 CRISPR-associated variants were selected, and all were confirmed by Sanger sequencing (Supplementary Fig. 2 and Supplementary Methods). Among the top-fifty sequences predicted for off targeting, none were mutated. Additionally, there was poor sequence homology between the sgRNA and sequences near the actual off-target coding and noncoding variants (Supplementary Fig. 3). Our results suggest current in silico modeling cannot predict bona fide off-target sites.

Together, these results indicate that at least certain sgRNAs may target loci independently of their target in vivo. The unpredictable generation of these variants is of concern. The impact of the numerous mutations occurring in noncoding RNAs or other regulatory intragenic regions could be detrimental to key cellular processes (Supplementary Fig. 4 and Supplementary Table 5)6. Although our CRISPR-treated mice did not display obvious extraocular phenotypes, it is possible the mice may reveal phenotypes in time, when they are challenged or bred to homozygosity.

The present study demonstrates WGS analysis of both indels and SNVs as the most thorough method for identifying off-target mutations and shows a significantly higher number of potentially deleterious CRISPR–Cas9-induced mutations than have been previously reported3. It is not clear whether improved sgRNA design or use of high-fidelity Cas9 may reduce off-target mutations, or whether in vivo off targets are a general problem of any sgRNA. Our study places the onus on researchers to carefully assay their specific gRNA and Cas9 for off-target mutations. More work may be needed to increase the fidelity of CRISPR–Cas9 with regard to off-target mutation generation before the CRISPR platform can be used without risk, especially in the clinical setting. Future studies employing new CRISPR methods and reagents should consider using WGS to determine the presence of off-target mutations in vivo.

Data availability statement. Experimental design information is available at Bioproject (accession PRJNA382177). Sequencing data available at SRA: FVB mouse (accession SRR5450998), F03 mouse (accession SRR5450997), F05 mouse (accession SRR5450996).

AUTHOR CONTRIBUTIONS

K.A.S., W.-H.W., S.H.T., A.G.B., and V.B.M. designed experiments. S.H.T., A.G.B., and V.B.M. managed this study. W.-H.W. carried out mouse experiments. K.A.S., D.F.C., S.H.T., A.G.B., and V.B.M. analyzed sequencing data. K.A.S., W.H.W., S.H.T., D.F.C., A.G.B., and V.B.M. wrote the manuscript. All authors participated in discussion and revision of the manuscript.

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Change history

  • 14 June 2017

    Editorial Note: readers are alerted that the conclusions of this paper are subject to criticisms that are being considered by editors. A further editorial response will follow the resolution of these issues.

  • 25 July 2017

    Editorial Expression of Concern: The editors of Nature Methods are issuing an editorial expression of concern regarding this paper to alert our readers to concerns about interpretation of the data. Multiple groups have questioned the interpretation that single nucleotide changes seen in whole-genome sequences of two CRISPR–Cas9-treated mice are due to the CRISPR treatment. Since the background genetic variation between the control mouse and the CRISPR-treated animals is not known, an alternative proposed interpretation is that the observed changes are due to normal genetic variation. We are in contact with the critics and with the authors to examine this matter further. We will update our readers once these investigations are complete. All the authors do not agree with the journal's decision to issue an editorial expression of concern.

  • 30 March 2018

    This paper is being retracted because the genomic variants observed by the authors in two CRISPR-treated mice cannot be conclusively attributed to CRISPR–Cas9. The paper was a peer-reviewed Correspondence in the journal. The authors made their observation as part of their work on correction of a gene involved in blindness. The authors used mice of the inbred FVB/NJ strain from the JAX genetic quality control program that were purchased within months of each other and that were not bred in the authors' laboratory. The assumption was that this design was sufficient to control for genetic variation in an inbred strain. Since publication of the work, however, it has been brought to the journal's and the authors' attention that without parental controls or more analysis of genetic background, it is not certain that the variants reported are due to CRISPR treatment (https://doi.org/10.1038/nmeth.4559, https://doi.org/10.1038/nmeth.4552, https://doi.org/10.1038/nmeth.4553, https://doi.org/10.1038/nmeth.4541, https://doi.org/10.1038/nmeth.4554). The study is therefore being retracted to maintain the accuracy of the scientific record. S.H.T. and W.-H.W. agree with the retraction. K.A.S., D.F.C., A.G.B. and V.B.M. do not agree with the retraction. All authors note that there is very little whole-genome sequencing data on the effects of CRISPR treatment in vivo. The question of whether CRISPR has effects on the in vivo genome will require further study; the authors are carrying out follow-up studies using whole-genome sequencing.

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Acknowledgements

We acknowledge the efforts and expertise of the New York Genome Center. S. Wu assisted with data analysis. K.A.S. is supported by NIH grant F31EY026789. V.B.M. and A.G.B. are supported by NIH grants (R01EY026682, R01EY024665, R01EY025225, R01EY024698, R01NS098590 and R21AG050437) and Research to Prevent Blindness (RPB), New York, New York. The Bernard & Shirlee Brown Glaucoma Laboratory is supported by NIH grants (5P30EY019007, R01EY018213). The National Cancer Institute Core is supported by an NIH grant (5P30CA013696), the RPB Physician-Scientist Award, and unrestricted funds from RPB, New York, New York, USA. S.H.T. is a member of the RD-CURE Consortium and is supported by the Tistou and Charlotte Kerstan Foundation, the Schneeweiss Stem Cell Fund, New York State (grant C029572), the Crowley Family Fund, and the Gebroe Family Foundation.

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Correspondence to Alexander G Bassuk or Vinit B Mahajan.

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Integrated supplementary information

Supplementary Figure 1 CRISPR-dependent mutations favor transitions over transversions.

Heat maps represent the percentage of specific point mutation nucleotide changes detected in CRISPR-treated animals. For both animals, most mutations were G to A and C to T mutations.

Supplementary Figure 2 Sanger sequencing confirms CRISPR-induced mutations detected by WGS.

a. Example of a coding SNV confirmed to be heterozygous in F03. F05 is wildtype as is reported in Supplementary Tables 1 and 2. b. Example of an intronic SNV confirmed in both mice as reported in Supplementary Table 5. c. Example of an SNV in a snoRNA confirmed in both mice as reported in Supplementary Table 5.

Supplementary Figure 3 Sequence alignment of guide RNA to actual off-target regions does not show substantial homology.

a. The top-10 predicted, off-target regions aligned to the gRNA. Sequences are 80 to 95% homologous to the gRNA. b. Regions surrounding 10 selected, experimentally-observed SNVs in coding regions aligned to the gRNA. All regions were observed in both CRISPR-treated mice. Sequences are 15 to 45% homologous to the gRNA. c. Regions surrounding 10 selected, experimentallyobservedSNVs in non-coding regions aligned to the gRNA. All regions were observed in both CRISPR-treated mice. Sequences are 5-65% homologous to the gRNA. d. Regions surrounding 10 selected, experimentally-observed indels in both coding and non-coding regions aligned to the gRNA. All regions were observed in both CRISPR-treated mice. Sequences are 25 to 65% homologous to the gRNA.

Supplementary Figure 4 Off-target CRISPR mutations could cause unwanted phenotypes.

Pie charts show the SNVs and indels detected in WGS of CRISPR-treated animals based on assigned biotype. Biotypes were assigned by SNPEff software (Cingolani P, et al. Fly, 2012.). Intragenic regions were not assigned a biotype.

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Supplementary Figures 1–4, Supplementary Methods and Supplementary Tables 1–5 (PDF 3893 kb)

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Schaefer, K., Wu, WH., Colgan, D. et al. Unexpected mutations after CRISPR–Cas9 editing in vivo. Nat Methods 14, 547–548 (2017). https://doi.org/10.1038/nmeth.4293

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