Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability

Abstract

In vitro-transcribed mRNAs encoding physiologically important proteins have considerable potential for therapeutic applications. However, in its present form, mRNA is unfeasible for clinical use because of its labile and immunogenic nature. Here, we investigated whether incorporation of naturally modified nucleotides into transcripts would confer enhanced biological properties to mRNA. We found that mRNAs containing pseudouridines have a higher translational capacity than unmodified mRNAs when tested in mammalian cells and lysates or administered intravenously into mice at 0.015-0.15 mg/kg doses. The delivered mRNA and the encoded protein could be detected in the spleen at 1, 4, and 24 hours after the injection, where both products were at significantly higher levels when pseudouridine-containing mRNA was administered. Even at higher doses, only the unmodified mRNA was immunogenic, inducing high serum levels of interferon-alpha (IFN-alpha). These findings indicate that nucleoside modification is an effective approach to enhance stability and translational capacity of mRNA while diminishing its immunogenicity in vivo. Improved properties conferred by pseudouridine make such mRNA a promising tool for both gene replacement and vaccination.

Figure 1. In vitro transcription and translation of nucleoside-modified mRNAs

(a) Aliquots of in vitro-transcribed TEVlucA₅₀ containing no or m5C-, m5U-, Ψ-, m6A-, or s2U-modified nucleosides were separated in a denaturing 1.4% agarose gel followed by ethidium bromide staining and ultraviolet illumination. (b) Rabbit reticulocyte lysate, wheat germ extract, and Escherichia coli S30 lysate were incubated in the presence of 50 ng/μl mRNA encoding firefly luciferase (TEVlucA₅₀) or Renilla luciferase (capRen). The mRNAs contained the indicated nucleoside modifications. Fold increase in translation was calculated by normalizing the measured relative light units to those obtained with nonmodified mRNA. Error bars indicate SEM (n = 4), and the dotted line represents the relative value obtained with unmodified mRNA in each of the lysates. (c) capRen mRNAs containing the indicated modification were translated in rabbit reticulocyte lysates supplemented with ³⁵S-labeled methionine. Aliquots of the lysates were separated by 15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the fluorogram of the gel is shown. (d) Formation of hydrogen bonds (red dots) between uridine [U] and adenosine [A], or pseudouridine [Ψ] and adenosine [A]. Structural differences between uridine and pseudouridine are highlighted with blue- and yellow-filled circles.

Figure 2. Translation of nucleoside-modified mRNAs in cells

(a–d) Cells seeded in 96-well plates were transfected with lipofectin-complexed mRNA (0.25 μg/well), and levels of the encoded proteins were measured by enzymatic assays. (a) 293 cells (5 × 10⁴ cells/well) and (b) bone marrow-derived murine dendritic cells (muDCs, 3 × 10⁴ cells/well) were transfected with capped Renilla luciferase-encoding mRNA (capRen) containing the indicated nucleoside modification and then assayed at 4 and 8 hours, respectively. Values were either (a) normalized to the measured relative light units (RLU) obtained with nonmodified mRNA and expressed as fold increase, or (b) presented directly as RLU measured in one-tenth of the total 25 μl lysate. (c) 293 cells (5 × 10⁴ cells/well) were transfected with firefly luciferase-encoding mRNAs that had 5′-cap (capLuc), 50-nt long 3′-poly(A) tail (TEVlucA₅₀), both, or none of these elements (capTEVlucA₅₀ and Luc, respectively) and contained either Ψ or no nucleoside modifications. Cells were lysed 4 hours later and luciferase activities were measured in aliquots (1/20th) of the total 50 μl lysates. (d) 293 cells (5 × 10⁴ cells/well) transfected with capTEVluc-A_n containing unmodified or Ψ-modified nucleosides were lysed at the indicated time points following transfection. Aliquots (1/20th) of the 50 μl lysates were assayed. Error bars in d are too small to visualize. (a–d) All values are expressed as the mean ± SEM (n = 3–10/point). (a) Values are from three independently performed experiments or (b–d) one representative of at least three experiments. (e) 293 cells (5 × 10⁴ cells/well) were transfected with lipofectin-complexed mRNAs (0.25 μg/well) encoding bacterial β-galactosidase (lacZ). The transcripts had cap and 3′-poly(A) tail that were either 30-nt long (caplacZ) or ~200-nt long (caplacZ-A_n). Constructs containing unmodified uridine (U) or pseudouridine (Ψ) nucleosides were tested. Cells were fixed and stained with X-gal, 24 hours post-transfection. Images were taken by inverted microscopy (original magnification ×4) from representative wells obtained in independently performed experiments (n = 3). (f) 293 cells were transfected with lipofectin-complexed capGFP-A_n mRNAs (0.25–3.0 μg/well, as indicated). The transcripts had cap and ~200-nt long poly(A) tail. Constructs containing unmodified uridine (U) or pseudouridine (Ψ) nucleosides were used. Cells were photographed at 24 hours post-transfection. Shown images are from representative wells obtained in one of the four independently performed experiments. (g) Expression of green fluorescent protein (GFP) in Chinese hamster ovary (CHO) cells and rat cortical neurons. CHO and rat neuronal cells, seeded at 5 × 10⁴ cells/well density in 96- and 48-well plates, respectively, were transfected with lipofectin-complexed capGFP-A_n containing pseudouridine (Ψ). Pictures taken at 24 hours post-transfection are representatives of 10 independently performed experiments.

Figure 3. Superior translation of Ψ-modified mrnA is independent of retinoic acid-inducible protein I (RIG-I)

Wild-type (wt) and RIGI(−/−) mouse embryonic fibroblasts cultured in 96-well plate (5 × 10⁴ cells/well) were transfected with lipofectin-complexed RNA (0.25 μg/well). (a) The RNA (ppplucA₅₀) contained unmodified uridine (U) or pseudouridine (Ψ), and had triphosphate at its 5′-end. (b) The RNA (capTEVluc-A_n) contained cap and long poly(A) tail. Upper panel, cells were lysed 4 hours later and luciferase activities were measured in the whole lysate. Values are measured in relative light units (RLU). Lower panel, cells were incubated for 24 hours and analyzed for interferon-β(IFN-β) by enzyme-linked immunosorbent assay. Values are expressed as the mean ± SEM (n = 4).

Figure 4. Ψ-modified mRNAs are nonimmunogenic and have a higher translational capacity than unmodified mRNA in mice

In vitro-transcribed capTEVlucA₅₀ (1,866 nt) with or without Ψ modifications were extended with long 3′-end poly(A) tail (+A_n) using poly(A) polymerase. Aliquots (1 μg) of mRNAs before and after poly(A) tailing were analyzed on denaturing agarose gel followed by ethidium bromide staining and ultraviolet (UV) illumination. The estimated lengths of poly(A) tails are ~200 nt. mRNAs used for the animal studies are indicated by asterisks. (b) Sixty-microliter aliquots of lipofectin-complexed mRNA (0.3 μg capTEVluc-A_n/mouse) containing Ψ modifications were administered by caudal vein injection. Animals were killed at 2 and 4 hours postinjection and luciferase activities were measured in aliquots (1/10th) of organs homogenized in lysis buffer. Values represent luciferase activities in the whole organs. Results with capRen were quantitatively identical except that liver and kidney had high endogenous Renilla luciferase-like activities (data not shown). (c,d) Lipofectin-complexed capTEVluc-A_n (0.3 μg/60 μl/animal) with or without Ψ modifications were intravenously (IV) delivered to mice. Animals were killed at 1, 4, and 24 hours postinjection and one-half of their spleens were processed for (c) luciferase measurements (d) while the other half for RNA analyses. Luciferase activities were measured in aliquots (1/5th) of the homogenate made from half of the spleens. Plotted values represent luciferase activities in the whole spleen and are expressed as the mean ± SEM. (n = 3 or 4/point). A similar pattern of expression was obtained in time-course experiments using capRen (data not shown). Dotted line represents background activity measured in spleen samples from animals injected only with lipofectin. (d) Aliquots of RNA (2 μg) isolated from the other half of spleens were analyzed by northern blot for luciferase, tumor necrosis factor-α (TNF-α) and β-actin. Autoradiograms and the corresponding ethidium bromide-stained, UV-visualized 28S and 18S rRNAs are presented. For luciferase, radiograms obtained after short and long exposure times (3 hours and 2 days) are shown. Animals, uninjected (control) and IV injected with uncomplexed lipofectin (lipofectin), were also processed. RNAs containing uridines (U) or pseudouridines (Ψ) are indicated. (e) The indicated amounts of lipofectin-complexed nucleic acids, capTEVluc-A_n mRNA with or without Ψ constituents and pCMVluc plasmid DNA in a volume of 60 μl/animal were delivered by IV injection into mice. Animals injected with mRNA or plasmid DNA were killed at 6 or 24 hours postinjection, respectively, and luciferase activities were measured in aliquots (1/10th) of their spleens homogenized in lysis buffer. Presented values were adjusted to signify luciferase activities in the whole organs (n = 3–5/point). The value from each animal is shown and the short horizontal lines indicate the mean; ND, not detectable. (f) Serum samples, collected during killing (6 hours postinjection) from the same animals that were processed for luciferase assessment shown in e, were analyzed by enzyme-linked immunosorbent assay which revealed that 3 μg of unmodified mRNA induced a higher level of interferon-α (IFN-α) than 3 μg of Ψ-modified mRNA did (P < 0.001). The levels of IFN-α induced by 3 μg of Ψ-modified mRNA were similar to those obtained when animals were injected with uncomplexed lipofectin (P = 0.19). Values are expressed as the mean ± SEM (n = 3 or 5 animals/group).