UMMS Affiliation

RNA Therapeutics Institute

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Document Type



Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Cell Biology | Cells | Nucleic Acids, Nucleotides, and Nucleosides


RNA interference (RNAi) is a potent mechanism that silences mRNA and protein expression in all cells and tissue types. RNAi is known to exert many of its functional effects in the cytoplasm, and thus, the cellular localization of target mRNA may impact observed potency. Here, we demonstrate that cell identity has a profound impact on accessibility of apolipoprotein E (ApoE) mRNA to RNAi. We show that, whereas both neuronal and glial cell lines express detectable ApoE mRNA, in neuronal cells, ApoE mRNA is not targetable by RNAi. Screening of a panel of thirty-five chemically modified small interfering RNAs (siRNAs) did not produce a single hit in a neuronal cell line, whereas up to fifteen compounds showed strong efficacy in glial cells. Further investigation of the cellular localization of ApoE mRNA demonstrates that ApoE mRNA is partially spliced and preferentially localized to the nucleus ( approximately 80%) in neuronal cells, whereas more than 90% of ApoE mRNA is cytoplasmic in glial cells. Such an inconsistency in intracellular localization and splicing might provide an explanation for functional differences in RNAi compounds. Thus, cellular origin might have an impact on accessibility of mRNA to RNAi and should be taken into account during the screening process.


mRNA silencing, RNA interference, RNAi

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Copyright 2020 The Authors. This is an open access article under the CC BY license (

DOI of Published Version



Ferguson CM, Echeverria D, Hassler M, Ly S, Khvorova A. Cell Type Impacts Accessibility of mRNA to Silencing by RNA Interference. Mol Ther Nucleic Acids. 2020 Sep 4;21:384-393. doi: 10.1016/j.omtn.2020.06.006. Epub 2020 Jun 12. PMID: 32650236; PMCID: PMC7340969. Link to article on publisher's site

Journal/Book/Conference Title

Molecular therapy. Nucleic acids

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Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.