Visualization Of In Vivo Gene Editing Heterogeneity At The Transcript Level With The BaseScope™ Duplex RNA In Situ Hybridization Assay

By Courtney Anderson, Xingyong Wu, Chao-Yi Yang, Bingqing Zhang, Christopher Bunker, James Wang, Ruby Hsu, Xiao-Jun Ma

Genome editing, revolutionized by the CRISPR/Cas9 system, is a powerful research tool and promising therapeutic strategy for human genetic diseases. The BaseScope™ RNA in situ hybridization (ISH) Assay is the only method available to quantify cell-specific CRISPR-edited transcripts, including single nucleotide changes, in the context of intact fixed tissue. In this report we illustrate one use of the BaseScope™ Duplex Assay to assess the heterogeneity of in vivo CRISPR/Cas9 gene editing in the mouse liver. The BaseScope™ assay can be utilized in gene editing applications to:

• Visualize tissue and cellular biodistribution of the gene edited transcripts
• Measure cell-specific Cas9 mRNA expression and guide-RNA in target tissues
• Identify gene edits in specific cell populations by duplexing RNA ISH cell marker probes and editspecific probes
• Discern if the CRISPR/Cas9-mediated mutation is mono- or bi-allelic with duplex of WT and edited probes