title: Impact of Oligonucleotide Structure, Chemistry, and Delivery Method on In Vitro Cytotoxicity.
abstract: Single-stranded (ss) 2'-fluoro (2'-F)-modified oligonucleotides (ONs) with a full phosphorothioate (PS) backbone have been reported to be cytotoxic and cause DNA double-strand breaks (DSBs) when transfected into HeLa cells. However, the molecular determinants of these effects have not been fully explored. In this study, we investigated the impact of ON structure, chemistry, delivery method, and cell type on in vitro cytotoxicity and DSBs. We found that ss PS-ONs were more cytotoxic than double-stranded (ds) PS-ONs, irrespective of the 2'-ribose chemistry, inclusive of the 2'-F modification. Cytotoxicity of ss ONs was most affected by the total PS content, with an additional contribution of 2'-F substitutions in HeLa, but not HepG2, cells. The relatively mild cytotoxicity of ds ONs was most impacted by long contiguous PS stretches combined with 2'-F substitutions. None of the tested ds 2'-F-modified PS-ONs caused DSBs, while the previously reported DSBs caused by ss 2'-F-modified PS-ONs were PS dependent. HeLa cells were more sensitive to ON-mediated toxicity when transfected with Lipofectamine 2000 versus Lipofectamine RNAiMax. Importantly, asialoglycoprotein receptor-mediated uptake of N-acetylgalactosamine-conjugated ss or ds PS-ONs, even those with long PS stretches and high 2'-F content, was neither cytotoxic nor caused DSBs at transfection-equivalent exposures. These results suggest that in vitro cytotoxicity and DSBs associated with ONs are delivery method dependent and primarily determined by single-stranded nature and PS content of ONs.
authors.affiliation: Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts.
authors.forename: Maja M
authors.initials: MM
authors.lastname: Janas
authors.affiliation: Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts.
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts.
authors.forename: Mark K
authors.initials: MK
authors.lastname: Schlegel
authors.affiliation: Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts.
authors.forename: Scott
authors.initials: S
authors.lastname: Waldron
authors.affiliation: Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts.
authors.forename: Satya
authors.initials: S
authors.lastname: Kuchimanchi
authors.affiliation: Alnylam Pharmaceuticals, Inc. , Cambridge, Massachusetts.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Barros
mesh_terms: D037263:Asialoglycoprotein Receptor / Q000737:chemistry / Q000378:metabolism; D002467:Cell Nucleus / Q000737:chemistry / Q000378:metabolism; D002470:Cell Survival; D053903:DNA Breaks, Double-Stranded; D016503:Drug Delivery Systems; D006367:HeLa Cells; D056945:Hep G2 Cells; D006801:Humans; D008055:Lipids / Q000737:chemistry; D058726:Nanoconjugates / Q000008:administration & dosage; D009687:Nuclear Proteins / Q000378:metabolism; D020320:Oligoribonucleotides, Antisense / Q000737:chemistry / Q000633:toxicity*; D054735:Phosphorothioate Oligonucleotides / Q000008:administration & dosage / Q000737:chemistry / Q000633:toxicity*; D034741:RNA, Small Interfering / Q000008:administration & dosage / Q000737:chemistry / Q000633:toxicity*; D016601:RNA-Binding Proteins / Q000378:metabolism; D014162:Transfection
chemical_list: D037263:Asialoglycoprotein Receptor; D008055:Lipids; C086724:Lipofectamine; D058726:Nanoconjugates; D009687:Nuclear Proteins; D020320:Oligoribonucleotides, Antisense; D054735:Phosphorothioate Oligonucleotides; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins
keywords: 2′-fluoro; antisense; cytotoxicity; oligonucleotide; phosphorothioate; siRNA