title: Sequence-non-specific effects generated by various types of RNA interference triggers.
abstract: RNA interference triggers such as short interfering RNA (siRNA) or genetically encoded short hairpin RNA (shRNA) and artificial miRNA (sh-miR) are widely used to silence the expression of specific genes. In addition to silencing selected targets, RNAi reagents may induce various side effects, including immune responses. To determine the molecular markers of immune response activation when using RNAi reagents, we analyzed the results of experiments gathered in the RNAimmuno (v 2.0) and GEO Profiles databases. To better characterize and compare cellular responses to various RNAi reagents in one experimental system, we designed a reagent series in corresponding siRNA, D-siRNA, shRNA and sh-miR forms. To exclude sequence-specific effects the reagents targeted 3 different transcripts (Luc, ATXN3 and HTT). We demonstrate that RNAi reagents induce a broad variety of sequence-non-specific effects, including the deregulation of cellular miRNA levels. Typical siRNAs are weak stimulators of interferon response but may saturate the miRNA biogenesis pathway, leading to the downregulation of highly expressed miRNAs, whereas plasmid-based reagents induce known markers of immune response and may alter miRNA levels and their isomiR composition.
authors.affiliation: Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. Electronic address: Marta.olejniczak@ibch.poznan.pl.
authors.forename: Marta
authors.initials: M
authors.lastname: Olejniczak
authors.affiliation: Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. Electronic address: Martyna.urbanek@ibch.poznan.pl.
authors.forename: Martyna O
authors.initials: MO
authors.lastname: Urbanek
authors.affiliation: Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. Electronic address: edyjaw@ibch.poznan.pl.
authors.forename: Edyta
authors.initials: E
authors.lastname: Jaworska
authors.affiliation: Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. Electronic address: lukwitucki@gmail.com.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Witucki
authors.affiliation: Department of Bioinformatics, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. Electronic address: miszcz@amu.edu.pl.
authors.forename: Michal W
authors.initials: MW
authors.lastname: Szczesniak
authors.affiliation: Department of Bioinformatics, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland. Electronic address: izabel@amu.edu.pl.
authors.forename: Izabela
authors.initials: I
authors.lastname: Makalowska
authors.affiliation: Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. Electronic address: wlodkrzy@ibch.poznan.pl.
authors.forename: Wlodzimierz J
authors.initials: WJ
authors.lastname: Krzyzosiak
mesh_terms: D020868:Gene Silencing; D007111:Immunity, Cellular / Q000235:genetics*; D007372:Interferons / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000276:immunology; D034622:RNA Interference / Q000276:immunology*; D034741:RNA, Small Interfering / Q000235:genetics* / Q000276:immunology
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D007372:Interferons
keywords: Immune response; Off-target; RNA interference; RNAimmuno; isomiRs; miRNA; siRNA