Engineered nucleic acids and methods of use thereof

Abstract

Provided are compositions and methods for delivering biological moieties such as modified nucleic acids into cells to modulate protein expression. Such compositions and methods include the use of modified messenger RNAs, and are useful to treat or prevent diseases, disorders or conditions, or to improve a subject's heath or wellbeing.

1 .- 18 . (canceled) 
     
     
         19 . A method for inducing an alteration in cell fate in a mammalian cell, comprising the steps of:
 (a) providing a precursor cell; and   (b) contacting the precursor cell with an effective dose of a cell fate inductive polypeptide encoded by a nucleic acid comprising at least one nucleoside modification, and a translatable region encoding the recombinant polypeptide,   wherein an alteration in cell fate is induced.   
     
     
         20 . A method for enhancing protein product yield in a cell culture process, comprising the steps of:
 (a) providing a cell culture comprising a plurality of host cells; and   (b) contacting the cell culture with a composition comprising a nucleic acid comprising a translatable region and at least one nucleoside modification,   wherein the nucleic acid exhibits increased protein production efficiency in a cell culture into which the nucleic acid is introduced, relative to a corresponding unmodified nucleic acid.   
     
     
         21 . A method for optimizing expression of an engineered protein in a target cell, comprising the steps of:
 (a) providing a plurality of target cell types;   (b) independently contacting with each of the plurality of target cell types an isolated nucleic acid comprising a translatable region encoding an engineered polypeptide and at least one nucleoside modification; and   (c) detecting the presence and/or level of the engineered polypeptide in the plurality of target cell types,   thereby optimizing expression of an engineered polypeptide in a target cell.   
     
     
         22 . A method for inducing in vivo translation of a recombinant polypeptide in a mammalian subject in need thereof, comprising the step of administering to the subject an effective amount of a composition comprising a nucleic acid comprising:
 (i) a translatable region encoding the recombinant polypeptide; and   (ii) at least one nucleoside modification,   under conditions such that the nucleic acid is localized into a cell of the subject and the recombinant polypeptide is capable of being translated in the cell from the nucleic acid.   
     
     
         23 . A method for inducing translation of a recombinant polypeptide in a cell population, comprising the step of contacting the cell population with an effective amount of a composition comprising a nucleic acid comprising:
 (i) a translatable region encoding the recombinant polypeptide; and   (ii) at least one nucleoside modification,   under conditions such that the nucleic acid is localized into one or more cells of the cell population and the recombinant polypeptide is translated in the cell from the nucleic acid.   
     
     
         24 . A method of reducing the innate immune response of a cell to an exogenous nucleic acid, comprising the steps of:
 (a) contacting the cell with a first composition comprising a first amount of a first exogenous nucleic acid comprising a translatable region and at least one nucleoside modification;   (b) determining the level of the innate immune response of the cell to the first exogenous nucleic acid;   (c) contacting the cell with a second composition comprising either:   (i) a second amount of the first exogenous nucleic acid, wherein the second amount contains a lesser amount of the first exogenous nucleic acid as compared to the first amount; or   (ii) a first amount of a second exogenous nucleic acid,   
       thereby reducing the innate immune response of the cell. 
     
     
         25 . A method for silencing gene expression in a cell, comprising the step of contacting the cell with a nucleic acid comprising:
 (i) a translatable region encoding a polypeptide capable of directing sequence-specific histone H3 methylation, under conditions such that the polypeptide is translated and reduces gene transcription of a target gene; and   (ii) at least one nucleoside modification.   
     
     
         26 . A method of reducing cellular differentiation in a target cell population comprising a precursor cell, comprising the step of
 (a) contacting the target cell population with a composition comprising an effective amount of a nucleic acid comprising   (i) a translatable region encoding a polypeptide, and   (ii) at least one modified nucleoside,   under conditions such that the polypeptide is translated and reduces the differentiation of the precursor cell.   
     
     
         27 . A method of antagonizing a biological pathway in a cell, comprising the step of contacting the cell with an effective amount of a composition comprising a nucleic acid comprising:
 (i) a translatable region encoding a recombinant polypeptide; and   (ii) at least one nucleoside modification,   under conditions such that that the nucleic acid is localized into the cell and the recombinant polypeptide is capable of being translated in the cell from the nucleic acid, wherein the recombinant polypeptide inhibits the activity of a polypeptide functional in the biological pathway.   
     
     
         28 . A method of agonizing a biological pathway in a cell, comprising the step of contacting the cell with an effective amount of a composition comprising a nucleic acid comprising:
 (i) a translatable region encoding a recombinant polypeptide; and   (ii) at least one nucleoside modification,   under conditions such that the nucleic acid is localized into the cell and the recombinant polypeptide is capable of being translated in the cell from the nucleic acid, wherein the recombinant polypeptide induces the activity of a polypeptide functional in the biological pathway.   
     
     
         29 . A method for enhancing nucleic acid delivery into a cell population, comprising the steps of:
 (a) providing a cell culture comprising a plurality of host cells; and   (b) contacting the cell population with a composition comprising an enhanced nucleic acid comprising a translatable region and at least one nucleoside modification,   wherein the enhanced nucleic acid exhibits enhanced retention in the cell population, relative to a corresponding unmodified nucleic acid.   
     
     
         30 . A method for co-delivering nucleic acids into a cell population, comprising the steps of:
 (a) providing a cell culture comprising a plurality of host cells; and   (b) contacting the cell population with a composition comprising:   (i) a first enhanced nucleic acid comprising a translatable region and at least one nucleoside modification; and   (ii) a first unmodified nucleic acid,   wherein the composition does not substantially induce an innate immune response of the cell population.   
     
     
         31 . A method for delivering nucleic acids into a cell population, comprising the steps of:
 (a) providing a cell culture comprising a plurality of host cells;   (b) contacting the cell population with a first composition comprising:   (i) a first enhanced nucleic acid comprising a translatable region and at least one nucleoside modification; and   (ii) a first unmodified nucleic acid, wherein the composition does not substantially induce an innate immune response of the cell population; and   (c) contacting the cell population with a second composition comprising the first unmodified nucleic acid.