A U1i RNA that Enhances HIV-1 RNA Splicing with an Elongated Recognition Domain Is an Optimal Candidate for Combination HIV-1 Gene Therapy

Olivier Del Corpo; Ryan P Goguen; Camille M G Malard; Aïcha Daher; Susan Colby-Germinario; Robert J Scarborough; Anne Gatignol

doi:10.1016/j.omtn.2019.10.011

A U1i RNA that Enhances HIV-1 RNA Splicing with an Elongated Recognition Domain Is an Optimal Candidate for Combination HIV-1 Gene Therapy

Mol Ther Nucleic Acids. 2019 Dec 6:18:815-830. doi: 10.1016/j.omtn.2019.10.011. Epub 2019 Oct 18.

Authors

Olivier Del Corpo¹, Ryan P Goguen², Camille M G Malard², Aïcha Daher³, Susan Colby-Germinario³, Robert J Scarborough⁴, Anne Gatignol⁵

Affiliations

¹ Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada.
² Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
³ Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada.
⁴ Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada. Electronic address: robert.scarborough@mail.mcgill.ca.
⁵ Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada. Electronic address: anne.gatignol@mcgill.ca.

Abstract

U1 interference (U1i) RNAs can be designed to correct splicing defects and target pathogenic RNA, such as HIV-1 RNA. In this study, we show that U1i RNAs that enhance HIV-1 RNA splicing are more effective at inhibiting HIV-1 production compared to top U1i RNAs that inhibit polyadenylation of HIV-1 RNA. A U1i RNA was also identified targeting a site upstream of the first splice acceptor site in the Gag coding region that was effective at inhibiting HIV-1 production. U1-T6, which enhanced HIV-1 RNA splicing, was superior to an antiviral short hairpin RNA (shRNA) currently in clinical trials. To increase specificity, the recognition domain of U1-T6 was elongated by 3-6 nt. The elongated molecules inhibited HIV-1 production from different HIV-1 strains, including one with a mismatch in the target site. These results suggest that lengthening the recognition domain can enhance the specificity of U1i RNAs for their intended target sites while at the same time allowing them to tolerate single mismatch mutations. Overall, our results demonstrate that U1-T6 with an elongated recognition domain inhibits HIV-1 production and has both the efficacy and specificity to be a promising candidate for HIV-1 gene therapy.

Keywords: HIV; RNA therapy; U1 interference; U1 snRNA; gene therapy; polyadenylation; short hairpin RNA; small nuclear RNA; splicing.