Safe and stable generation of induced pluripotent stem cells using doggybone DNA vectors

Thornton, Christopher D, Fielding, Stuart, Karbowniczek, Kinga, Roig-Merino, Alicia, Burrows, Alyshea E, Fitzpatrick, Lorna M, Sharaireh, Aseel, Tite, John P, Mole, Sara E, Harbottle, Richard P, Caproni, Lisa J and McKay, Tristan R (2021) Safe and stable generation of induced pluripotent stem cells using doggybone DNA vectors. Molecular Therapy: Methods and Clinical Development, 23. pp. 348-358. ISSN 2329-0501

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Abstract

The application of induced pluripotent stem cells (iPSCs) in advanced therapies is increasing at pace, but concerns remain over their clinical safety profile. We report the first-ever application of doggybone DNA (dbDNA) vectors to generate human iPSCs. dbDNA vectors are closed-capped linear double-stranded DNA gene expression cassettes that contain no bacterial DNA and are amplified by a chemically defined, current good manufacturing practice (cGMP)-compliant methodology. We achieved comparable iPSC reprogramming efficiencies using transiently expressing dbDNA vectors with the same iPSC reprogramming coding sequences as the state-of-the-art OriP/EBNA1 episomal vectors but, crucially, in the absence of p53 shRNA repression. Moreover, persistent expression of EBNA1 from bacterially derived episomes resulted in stimulation of the interferon response, elevated DNA damage, and increased spontaneous differentiation. These cellular activities were diminished or absent in dbDNA-iPSCs, resulting in lines with a greater stability and safety potential for cell therapy.