Multi-omic Analyses Reveal Minimal Impact of the CRISPR-Cas9 Nuclease on Cultured Human Cells

The
CRISPR-Cas9 system is a genomic editing tool widely used in
basic research and under investigation for potential applications
in gene therapies for human diseases. To accomplish genomic editing,
the system requires the expression of a prokaryotic DNA endonuclease
enzyme, Cas9, in host cells. Previous studies have mainly focused
on the specificity of Cas9 on the host genome, and thus it is unclear
whether this bacterium-derived enzyme affects the protein homeostasis
of host cells. Here we applied multi-omic analyses, including transcriptome,
proteome, phosphoproteome, Cas9-associated protein interactome, protein
synthesis, and histone epigenetic modification, to investigate the
cellular response of human cells upon the expression of Cas9. We demonstrate
that Cas9 has minimal impact on host cells. Our assessment of intracellular
effects of Cas9 paves a path for its broad applications in biological
studies and potential clinical translations.