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Precision RNAi using synthetic shRNAmir target sites

View ORCID ProfileThomas Hoffmann, Alexandra Hörmann, Maja Corcokovic, Jakub Zmajkovic, View ORCID ProfileMatthias Hinterndorfer, Jasko Salkanovic, Fiona Spreitzer, View ORCID ProfileAnna Köferle, Katrin Gitschtaler, Alexandra Popa, Sarah Oberndorfer, Florian Andersch, Markus Schäfer, Michaela Fellner, Nicole Budano, Jan G. Ruppert, Paolo Chetta, Melanie Wurm, View ORCID ProfileJohannes Zuber, View ORCID ProfileRalph A. Neumüller
doi: https://doi.org/10.1101/2022.11.24.517802
Thomas Hoffmann
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
2Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
5Advantage Therapeutics GmbH, Karl-Farkas-Gasse 22, 1030 Vienna, Austria
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  • ORCID record for Thomas Hoffmann
Alexandra Hörmann
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Maja Corcokovic
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Jakub Zmajkovic
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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Matthias Hinterndorfer
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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  • ORCID record for Matthias Hinterndorfer
Jasko Salkanovic
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Fiona Spreitzer
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Anna Köferle
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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  • ORCID record for Anna Köferle
Katrin Gitschtaler
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Alexandra Popa
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Sarah Oberndorfer
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Florian Andersch
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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Markus Schäfer
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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Michaela Fellner
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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Nicole Budano
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Jan G. Ruppert
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Paolo Chetta
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Melanie Wurm
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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Johannes Zuber
1Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
4Medical University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
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  • For correspondence: [email protected] [email protected]
Ralph A. Neumüller
3Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
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  • For correspondence: [email protected] [email protected]
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Abstract

Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.

Competing Interest Statement

Alexandra Hormann, Maja Corcokovic, Jasko Salkanovic, Fiona Spreitzer, Anna Koferle, Katrin Gitschtaler, Alexandra Popa, Sarah Oberndorfer, Nicole Budano, Jan G. Ruppert, Paolo Chetta, Melanie Wurm and Ralph Neumuller: Full time employees Boehringer Ingelheim RCV. Johannes Zuber: Quantro Therapeutics GmbH (Co-founder, Scientific Advisor, Shareholder); Mirimus Inc. (Scientific Advisor, Shareholder); AstraZeneca-CRUK Functional Genomics Consortium (Scientific Advisor); Boehringer Ingelheim (Research Support).

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  • This version of the manuscript has been revised

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 07, 2023.
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Precision RNAi using synthetic shRNAmir target sites
Thomas Hoffmann, Alexandra Hörmann, Maja Corcokovic, Jakub Zmajkovic, Matthias Hinterndorfer, Jasko Salkanovic, Fiona Spreitzer, Anna Köferle, Katrin Gitschtaler, Alexandra Popa, Sarah Oberndorfer, Florian Andersch, Markus Schäfer, Michaela Fellner, Nicole Budano, Jan G. Ruppert, Paolo Chetta, Melanie Wurm, Johannes Zuber, Ralph A. Neumüller
bioRxiv 2022.11.24.517802; doi: https://doi.org/10.1101/2022.11.24.517802
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Precision RNAi using synthetic shRNAmir target sites
Thomas Hoffmann, Alexandra Hörmann, Maja Corcokovic, Jakub Zmajkovic, Matthias Hinterndorfer, Jasko Salkanovic, Fiona Spreitzer, Anna Köferle, Katrin Gitschtaler, Alexandra Popa, Sarah Oberndorfer, Florian Andersch, Markus Schäfer, Michaela Fellner, Nicole Budano, Jan G. Ruppert, Paolo Chetta, Melanie Wurm, Johannes Zuber, Ralph A. Neumüller
bioRxiv 2022.11.24.517802; doi: https://doi.org/10.1101/2022.11.24.517802

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