Three Recent Independent Studies Show Unwanted Chromosomal Changes in Human Embryos with CRISPR Gene Editing

CRISPR/Cas9 as the revolutionizing gene editing technology has been widely applied in many fields, from basic research, drug discovery, gene and cell therapy, disease diagnostics, to engineering various species for bioproduction. Due to the powerfulness of CRISPR and its potential in editing germline cells to fix genetic mutations, the debate over if human germline gene editing for preventing genetic disease is the “right” research direction has been ongoing for years. The debate is over both biological safety concerns and ethical issues.

Recently, three independent teams published on preprint server bioRxiv their findings on using CRISPR–Cas9 gene editing to remove genetic defects in human embryos. In all three studies, despite correct fixation of target gene, large DNA fragment deletion and reshuffling resulted from CRISPR editing is also revealed. These three studies published on bioRxiv are still awaiting peer-reviewed, yet their findings are already fusing the debate over safety concerns on human germline editing.

• The first team led by Kathy Niakan et al. from the Francis Crick Institute at UK used CRISPR/Cas9 to mutate the POU5F1 gene, and developed a comprehensive computational approach to assess on-target mutations. Among 18 edited embryos, edits beyond on-target locus and chromosome segmental loss and gain were observed in 22% of the embryos¹.
• The second team led by Dieter Egli et al. from Columbia University tried to use CRISPR/Cas9 to correct a mutation in EYS gene, which can lead to blindness. Out of 17 embryos, 15 (88%) embryos were modified via CRISPR induced end joining cell repair process. However, only 2 of them were mosaic, whereas the majority were nonmosaic zygotes that only had single modification. Further analysis found that unrepaired double stranded DNA breaks created by CRISPR/Cas9 could persist through mitosis stage and contributing to frequent chromosome loss².
• The third team led by Shoukhrat Mitalipov et al. from Oregon Health & Science University studied the efficacy of using CRISPR/Cas9 and a repair template for repairing a mutant gene in heart disease. Despite showing 40% repair of the target locus, extensive loss of heterozygosity is also observed³.
• These three studies underscored the necessity of further studying how CRISPR/Cas9 induced DNA breaks are repaired by various DNA repair mechanisms during different development stage in preimplantation human embryos.
• Will the moratorium on clinical uses of CRISPR for heritable genome editing ever be lifted? The question remains. We hope to see more studies exploring any safety concerns on using CRISPR for heritable genome editing in a research setting, as well as any potential ethical issues in the near future to shed light on this topic.

• Gregorio Alanis-Lobato et al. Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos, (2020). DOI: 10.1101/2020.06.05.135913
• Michael V. Zuccaro et al. Reading frame restoration at the EYS locus, and allele-specific chromosome removal after Cas9 cleavage in human embryos, (2020). DOI: 10.1101/2020.06.17.149237
• Dan Liang et al. FREQUENT GENE CONVERSION IN HUMAN EMBRYOS INDUCED BY DOUBLE STRAND BREAKS, (2020). DOI: 10.1101/2020.06.19.162214
• Heidi Ledford. CRISPR gene editing in human embryos wreaks chromosomal mayhem, Nature (2020). DOI: 10.1038/d41586-020-01906-4