Use of decoding trnas to boost protein expression or function

Abstract

The present disclosure relates to decoding tRNAs and their uses such as boosting protein expression or function or treating disorders.

Description

[0001] Use of Decoding tRNAs to Boost Protein Expression or Function

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This application claims the benefit under 35 U.S.C. §119(e) of the earlier filing date of U.S. Provisional Patent No. 63 / 676,713, filed on July 29, 2025, which is hereby incorporated by reference in its entirety.

[0004] GOVERNMENT INTERESTS

[0005] This invention was made with government support under HL153988 awarded by the National Institutes of Health. The government has certain rights in the invention.

[0006] REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

[0007] The contents of the electronic sequence listing (161118.06201SeqList.xml; Size: 414,648 bytes; and Date of Creation: July 25, 2025) is herein incorporated by reference in its entirety.

[0008] FIELD OF THE INVENTION

[0009] This disclosure relates to decoding tRNAs and their uses such as boosting protein expression or function or treating disorders.

[0010] BACKGROUND

[0011] The genetic code uses four nucleotides that form triplet “codons” which are the blueprint for protein translation. There are 64 codons in total, 61 of which are used to encode amino acids and three (UAG, UGA and UAA) encode the translation termination signal. Nonsense mutations change an amino acid codon to premature termination codon (PTC) generally through a single-nucleotide substitution, resulting in a defective truncated protein and severe forms of disease. Nonsense mutations account for greater than ten percent of all genetic diseases, accounting for nearly 1000 genetic human disorders, including cancer (Keeling, K. M., et cd., Therapeutics based on stop codon readthrough. Annual review of genomics and human genetics 15, 371-394, 2014). Cystic fibrosis (CF) follows suit with greater than ten percent of all CF patients having “class 1” PTC mutations (p.G542X; 2.5%, p.R553X; 0.9%, p.R1162X; 0.4% and p.W1282X; 1.2%), resulting in nearly complete loss of CFTR function and severe clinical manifestations (Rowe, S. M., et al., Cystic fibrosis. The New England journal of medicine 352,1992-2001, 2005). Because of the exceedingly high prevalence of nonsense mutations resulting in disease and a unifying mechanism, there has been concerted effort to identify PTC therapeutics. Indeed, much of the effort has been focused on development of small molecules that interact with the ribosomal decoding center to promote PTC readthrough. See Shalev, M. & Baasov, T. When Proteins Start to Make Sense: Fine- tuning Aminoglycosides for PTC Suppression Therapy. Medchemcomm 5, 1092-1105, (2014) and Baradaran-Heravi, A. et al. Novel small molecules potentiate premature termination codon readthrough by aminoglycosides. Nucleic Acids Res 44, 6583-6598, 2016).

[0012] However, all identified molecules to date suffer from low in vivo readthrough efficiency (Sabbavarapu, N. M. et al. Design of Novel Aminoglycoside Derivatives with Enhanced Suppression of Diseases-Causing Nonsense Mutations. ACS Med Chem Lett 7, 418-423, 2016) and / or toxicity because of ototoxicity and nephrotoxicity (Schacht, J. Antioxidant therapy attenuates aminoglycoside-induced hearing loss. Ann N Y Acad Sci 884, 125-130, 1999). Further, aminoglycoside like molecules that interact with the ribosomal decoding center have recently been identified to significantly impact translational fidelity resulting in amino acid mis-incorporation in all coding codons of the translatome, not just PTCs (Wangen, J. R. & Green, R. Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. eLife 9, e52611, 2020). Thus, there is a need for boosting protein function or treating disorders associated with PTC or low level protein expression.

[0013] SUMMARY

[0014] This disclosure addresses the need mentioned above in several aspects.

[0015] In one aspect, the disclosure provides an isolated, engineered, or non-naturally occurring transfer RNA (tRNA) comprising an RNA sequence encoded by a nucleic acid or DNA sequence selected from the group consisting of SEQ ID NOs: 409, 1-408, and 410-442 or those listed in Tables 1 and 2A-2D.

[0016] In some embodiments, the nucleic acid or DNA sequence is selected from (i) the group consisting of SEQ ID NOs: 1-216, or (ii) the group consisting of SEQ ID NOs: 1-30, or (iii) the group consisting of SEQ ID NOs: 409, 254-408, and 410-442.

[0017] In some embodiments, the nucleic acid or DNA sequence is selected from those that are listed in Tables 1 and 2A-2D and have a mean value above 1.0 or 2.0. tRNA containing these sequences have activation activities and can be used to increase the expression of a protein of interest.

[0018] In some embodiments, the nucleic acid or DNA sequence is one selected from those that are listed in Tables 1 and 2A-2D and have a mean value below 1.0. tRNA containing these sequences have inhibition activities and can be used to decrease the expression of a protein of interest. Examples include SEQ ID NOs: 217-253, and in particular SEQ ID NOs: 247 and 250-253. In some embodiments, the nucleic acid or DNA sequence is one selected from those that are listed in Tables 1 and 2A-2D and have a -loglO(q value) above 1.30.

[0019] In some embodiments, the nucleic acid or DNA sequence is selected from (A) the group consisting of SEQ ID NOs: 1-5, 7-9, 11, 13-14, 16-26, 28-31, 33-36, 39-40, 43-47, 50-53, 55, 58-65, 67, 69, 71-73, 76-78, 80, 83, 87, 90-92, 97-98, 100, 107, 110-111, 113, 116, 118, 125, 127, 130, 133, 140, 159, and 179, or (B) the group consisting of SEQ ID NOs: 1-5, 7-9, 11, 13- 14, 16-26, 28-30, or (C) the group consisting of SEQ ID NOs: 409, 282, 292, 293, 295, 372, 410, 412, 413, and 420, or (D) the group consisting of SEQ ID NOs: 409, 277, 286, 323, 336, 346, 355, 360, 361, 364, 372, 380, 382, 384, 389, 390, 398, 403, 411, 415, 420, 424, 425, 434, 435, and 437.

[0020] In some embodiments, the nucleic acid or DNA sequence is selected from the group

[0021] (C).

[0022] In some embodiments, the nucleic acid or DNA sequence is selected from the group

[0023] (D).

[0024] In some embodiments, the isolated tRNA described above comprises a T-arm, a D-arm, an anticodon-arm, and an acceptor arm comprising CCA at the 3’ end.

[0025] In some embodiments, the isolated tRNA described above further comprises a heterologous sequence or a modification.

[0026] In some embodiments, the isolated tRNA is 70 to 100 nucleotides in length.

[0027] In a second aspect, the disclosure provides a nucleic acid molecule comprising a nucleic acid sequence encoding or comprising the isolated tRNA described herein. In some examples, the nucleic acid molecule is DNA. Also provided is an expression cassette comprising a promoter and a nucleic acid sequence encoding the isolated tRNA described herein, wherein the promoter is operably linked to the nucleic acid sequence. Further provided is a vector comprising the nucleic acid molecule or the expression cassette. In some examples, the vector is a viral vector, a plasmid vector, a closed end DNA thread (CEDT) vector, or a minicircle (MC) vector. In some examples, the vector may further comprise one or more elements selected from the group consisting of a DNA nuclear targeting sequence (DTS), a transcription enhancing 5’ leader sequence (TELS), and a Barcoding Sequence (ABS).

[0028] In a third aspect, the disclosure features a composition comprising (i) the isolated tRNA, or the nucleic acid molecule, or the expression cassette, or the vector, and (ii) a pharmaceutically acceptable carrier. In some embodiments, the carrier comprises a liposome, or a nanoparticle or an exosome. In a fourth aspect, the disclosure provides a cell or a progeny thereof. The cell comprises the isolated tRNA, the nucleic acid molecule, or the expression cassette, or the vector.

[0029] In a fifth aspect, the disclosure provides a method of modulating the production of a protein in a cell. The method comprises introducing into the cell the isolated tRNA, or the nucleic acid molecule, or the expression cassette, or the vector.

[0030] In some embodiments, the modulating is increasing and in that case the nucleic acid or DNA sequence can be one selected from the group consisting of those having activation activity, such as (B) SEQ ID NOs: 1-5, 7-9, 11, 13-14, 16-26, and 28-30, or (C) SEQ ID NOs: 409, 282, 292, 293, 295, 372, 410, 412, 413, and 420, or (D) SEQ ID NOs: 409, 277, 286, 323, 336, 346, 355, 360, 361, 364, 372, 380, 382, 384, 389, 390, 398, 403, 411, 415, 420, 424, 425, 434, 435, and 437.

[0031] In some embodiments, the modulating is decreasing and in that case the nucleic acid or DNA sequence may be one selected from the group consisting of those having inhibition activity, such as SEQ ID NOs: 217-253, and in particular SEQ ID NOs: 247 and 250-253.

[0032] In some embodiments, the protein is a cystic fibrosis transmembrane conductance regulator (CFTR) protein. In that case, the nucleic acid or DNA sequence can be selected from the group (D).

[0033] The above-described tRNA, nucleic acid, expression cassette, vector, and cell can be used as a therapeutic agent for teating a disease or condition associated with an abnormal expression level of a protein in a subject in need thereof. Accordingly, this disclosure further provides a method of treating such a disease or condition. The method comprises administering to the subject (a) the isolated tRNA, or (b) a nucleic acid molecule encoding or comprising the isolated tRNA, or (c) an expression cassette comprising the nucleic acid molecule, or (d) a vector comprising the nucleic acid molecule or the expression cassette, or (e) a composition comprising the isolated tRNA, or the nucleic acid molecule, or the expression cassette, or the vector, or (f) a cell comprising the isolated tRNA, or the nucleic acid molecule, or the expression cassette, or the vector.

[0034] In some embodiments, the abnormal expression level is a decreased expression level of the protein. The tRNA containing the sequences have activation activities described above can be used to increase the expression of such a protein. Examples include a CFTR protein. In some embodiments, the disease or condition is a haploinsufficiency disorder. Examples of proteins involved include one encoded by a gene selected from the group consisting of AGGF1, ARHGAP31, BMPR2, CHD7, COL2A1, COL3A1, CTLA4, CTNNB1, DLL4, EHMT1, ELN, ENG, FAS, FBN1, F0XG1, GATA3, GLI3, GRN, IRF6, JAG1, KCNQ4, LMX1B, MBD5, MED13L, MITF, MNX1, MYCN, NFIA, NFIX, NOTCH1, NSD1, PAX3, PHIP, PRKAR1A, RAH, RBPJ, RPS14, RUNX2, SALL4, SCN1A, SETBP1, SHANK3, SHH, SHOX, SLC2A1 / GLUT1, SOXIO, SYNGAP1, TBX1, TBX3, TBX5, TCF4, TCOF1, TGIF1, TNXB, TRPS1, WT1, and ZIC2. Examples of the haploinsufficiency disorder include 5q-syndrome, Adams-Oliver syndrome 1, Adams-Oliver syndrome 3, Adams-Oliver syndrome 5, Adams- Oliver syndrome 6, Alagille syndrome 1, Autoimmune lymphoproliferative syndrome type IA, Autoimmune lymphoproliferative syndrome type V, Autosomal dominant deafness-2A, Brain malformations with or without urinary tract defects (BRMUTD), Carney complex type 1, CHARGE syndrome, Cleidocranial dysplasia, Currarino syndrome, Denys-Drash syndrome / Frasier syndrome, Developmental delay, intellectual disability, obesity, and dysmorphic features (DIDOD), DiGeorge syndrome (TBX1 -associated), Dravet syndrome, Duane-radial ray syndrome, Ehlers-Danlos syndrome (classic-like), Ehlers-Danlos syndrome (vascular type), Feingold syndrome 1, Frontotemporal lobar degeneration with TDP43 inclusions (FTLD-TDP), GRN-related, GLUT1 deficiency syndrome, Greig cephalopoly syndactyly syndrome, Hereditary hemorrhagic telangiectasia type 1, Holoprosencephaly 3, Holoprosencephaly 4, Holoprosencephaly 5, Holt-Oram syndrome, Hypoparathyroidism, sensorineural deafness, and renal disease (HDR), Kleefstra syndrome 1, Klippel-Trenaunay syndrome (AAGF -related), Leri-Weill dyschondrosteosis, Marfan syndrome, Mental retardation and distinctive facial features with or without cardiac defects (MRFACD), Mental retardation, autosomal dominant 1, Mental retardation, autosomal dominant 19, Mental retardation, autosomal dominant 29, Nail-patella syndrome (NPS), Phelan-McDermid syndrome, Pitt-Hopkins syndrome, Primary pulmonary hypertension 1, Rett syndrome (congenital variant), Smith-Magenis syndrome (RAI 1 -associated), Sotos syndrome 1, Sotos syndrome 2, Stickler syndrome type I, Supravalvular aortic stenosis, SYNGAP1- related intellectual disability, Treacher Collins syndrome, Trichorhinophalangeal syndrome type I, Ulnar-mammary syndrome, van der Woude syndrome 1, Waardenburg syndrome type 1, Waardenburg syndrome type 2A, and Waardenburg syndrome type 4C.

[0035] In some embodiments, the abnormal expression level is an increased expression level of the protein. The tRNA containing the sequences have inhibition activities described above can be used to decrease the expression of such a protein.

[0036] The cell mentioned above can be a mammalian cell, a vertebrate cell, an inveterate cell, a plant cell, a yeast cell, a fungus cell, or a bacterial cell. In a preferred embodiment, the cell is a human cell. In a more preferred embodiment, the cell is a bronchial epithelial cell. In some embodiments of the method, the administering may be carried out using a viral delivery, nanoparticle, polyethylenimine (PEI), receptor-targeted polyplex, liposome, exosome, electroporation or hydrodynamic injection.

[0037] The details of one or more embodiments of the disclosure are set forth in the description below. Other features, objectives, and advantages of the disclosure will be apparent from the description and from the claims.

[0038] BRIEF DESCRIPTION OF THE DRAWINGS

[0039] FIG. l is a diagram showing a map of CFTR-Nanolucificerase (Nluc) natural decoding- tRNA (“nd-tRNA”) reporter plasmid.

[0040] FIG. 2A is a diagram showing effects of certain nd-tRNAs on CFTR expression in 16HBE14o- cells, where those causing more than 1-fold increase on CFTR expression and having -logio(q-value) above 1.30 are in the open box, and those inhibiting the expression and having -logio(q-value) above 1.30 are in the shaded box.

[0041] FIG. 2B is a table showing the nd-tRNAs, the results of which are shown in FIG. 2A.

[0042] FIG. 2C is a diagram showing the same results as in FIG. 2A except that the open box contains those causing more than 2-fold increase.

[0043] FIG. 2D is a table showing the same results as in FIG. 2B, except the table includes those cause more than 2-fold increase.

[0044] FIG. 3 is a diagram showing tRNA utilization in CFTR in 16HBE14o- cells.

[0045] FIG. 4A is a map of a reporter plasmid for wobble-decoding-tRNA (“wd-tRNA”) screen (“WoBell RePorter”). “Wobbled [protein]” : for every instance (in the endogenous protein sequence) where a codon can be replaced with one that requires wobble interactions, it has been.

[0046] FIG. 4B is a map of a CFTR-encoding reporter plasmid for wd-tRNA screens (“ CFTR WoBell RePorter”). “De-wobbled [protein]”: inverse of “wobbled, ” that is, for every instance of a codon that requires wobble decoding, it has been replaced with one that can participate in canonical Watson-Crick decoding.

[0047] FIG. 5A is a diagram showing results of a screen using HEK293T cells.

[0048] FIG. 5B is a set of diagrams showing results of the screen using HEK293T cells.

[0049] FIG. 5C is a table showing the top performing tRNAs from the screen using HEK293T cells.

[0050] FIG. 6A is a diagram showing results of a wd-tRNA screen using 16HBE14o- cells (“WoBell CFTR-HBE”). FIG. 6B is a set of diagrams showing results of the wd-tRNA screen / WoBell CFTR- HBE screen.

[0051] FIG. 6C is a table showing the top performing tRNAs from the wd-tRNA screen / WoBell CFTR-HBE screen.

[0052] FIG. 7 is a diagram showing tRNA-seq quantification of tRNA abundance in I6HBE0- cells. For display purposes, isodecoders are grouped, but are readily discernable with tRNA- seq read depth. tRNA abundance does not correlate with tRNA gene copy number.

[0053] FIG 8A is a diagram showing nd-tRNA expression increases CFTR-NLuc expression in 16HBE14o- cells.

[0054] FIG 8B is a diagram showing that nd-tRNA expression does not correlate with CFTR codon abundance or endogenous codon abundance.

[0055] FIG. 9 shows that stable tRNA supplementation manipulates CFTR mRNA transcript stability. One-Way ANOVA and Tukey’s post-hoc test: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

[0056] FIGs. 10A and 10B show that tRNA supplementation manipulates CFTR protein expression. One-Way ANOVA and Tukey’s post-hoc test were used where *p < 0.05.

[0057] FIG. 11 shows that tRNA supplementation manipulates CFTR channel function: Ussing Chamber, where representative current traces are shown for each stable tRNA expressing HBE cell line.

[0058] FIG. 12 shows that tRNA supplementation manipulates CFTR channel function.

[0059] FIGs. 13 A and 13B show that tRNA supplementation manipulates CFTR channel function.

[0060] DETAILED DESCRIPTION OF THE INVENTION

[0061] This disclosure relates to use of decoding tRNAs to boost protein expression and / or function. Certain aspects of this disclosure are based, at least in part, on an unexpected discovery of ability of endogenous natural (nd-) tRNAs and wobble decoding (wd-) tRNAs to increase endogenous transcript and protein expression and / or function.

[0062] Protein expression is governed by a multitude of mechanisms, from genome arrangement to protein feedback regulation. One way to increase transgene expression is through codon optimization, a strategy that is routinely used in discovery research and for increased therapeutic total gene replacement approaches without changing the protein sequence. Public and proprietary prediction algorithms can be used to account for the coding region’s GC and CpG content, secondary mRNA structure, translation, translation pause sites, and cryptic splice sites. See, e.g., Bauer, A. P. et aL, The impact of intragenic CpG content on gene expression. Nucleic acids research 38, 3891-3908, 2010; Elhaik, E. & Tatarinova, T. GC3 biology in eukaryotes and prokaryotes. DNA Methyl ation-From Rijeka, Croatia: Genomics to Technology. InTech, 55-68 (2012); Kudla, G. et al.. High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS biology 4, el 80, 2006; Gebert, D., Jehn, J. & Rosenkranz, D. Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life. Open Biology 9, 190020, 2019; Oliver, K. E. et al. Slowing ribosome velocity restores folding and function of mutant CFTR. J Clin Invest 129, 5236-5253, 2019, and Kapustin, Y. et al. Cryptic splice sites and split genes. Nucleic Acids Research 39, 5837-5844, 2011). Additionally, the codon optimization algorithms take advantage of the degenerate nature of the genetic code and improve the codon adaptive index (CAI) (Sharp, P. M. & Li, W.-H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic acids research 15, 1281-1295 (1987)), which increases the codon content of the introduced transgene to match that of the highest expressed proteins in a given organism. Further, it is thought that the tRNA abundance of an organism (and likely a given tissue) is important for efficient translation of a transcript (Dittmar, K. A., Goodenbour, J. M. & Pan, T. Tissue-specific differences in human transfer RNA expression. PLoS Genet 2, e221, 2006).

[0063] The codon optimization approach is used to enhance expression of a given protein by making synonymous codon substitutions and is used in almost all total-gene-replacement therapy approaches to obtain therapeutic meaningful levels of transgene expression from very few delivered transcripts. One key components of codon optimization is the relative abundance of endogenous tRNAs in the target cell of the delivered cDNA or mRNA.

[0064] At this intersection are “wobble codons,” where no tRNAs directly decode the codons, but rather rely on tRNAs from the same family (isotype) to suppress with mismatches in the third nucleotide position of a codon. As wobble decoding is thought to be less efficient, most codon optimization algorithms remove wobble codons from the reading frames. Certain codons within the normal transcriptome require “wobble” decoding for proper translation of the correct amino acid. This requirement is due to the lack of endogenous tRNA species that make canonical Watson-Crick base pair interactions within the translational machinery. Many tRNAs participate in wobble decoding, however 13 do not exist within the human genome. Also, slower decoding rates occur at codons that participate in wobble decoding. This codon usage is likely facilitated evolutionarily by (1) the propensity for wobble decoding outright, and (2) the necessity for cells to carry out co-translational protein folding for certain proteins that require specific conformations, thereby regulating proper protein function through codon usage.

[0065] Thus, while one aspect of this disclosure is focused on determining the impact of supplementing natural decoding (nd-) tRNAs, another aspect is focused on novel wd-tRNAs and their uses to improve native protein expression, such as CFTR expression. This disclosure describes non-naturally occurring tRNAs, edited at their anticodon, that can form canonical Watson-Crick interactions with their corresponding mRNA codon within the ribosome, thereby improving translational speed and protein expression. As disclosed herein, to identify such tRNAs, a dual-reporter, all-in-one plasmid system was designed to inform which specific tRNA isodecoder within a tRNA family that, when edited, can improve protein expression in both a general reporter context and within a protein of interest, such as CFTR.

[0066] It was unexpected to find that certain wd-tRNAs as well as nd-tRNAs can increase endogenous transcript and protein expression and / or function. Thus, delivery or expression of such nd-tRNAs or wd-tRNAs in targets cells can themselves be therapeutic approaches for “boosting” CFTR protein expression from genes, e.g., that harbor class III- VI CF mutations (reduced function and expression) and in combination with existing or future small molecule therapeutics (e.g., Trikafta) and ACE-tRNAs to boost rescued CFTR express! on / functi on. Accordingly, in some embodiment, this disclosure also provides guidance on tRNA biology in airway epithelial cells and its interplay with CFTR translation form these approaches that include a guide for CFTR codon optimization for viral total gene replacement and super exon therapeutic approaches.

[0067] An ACE-tRNA is an engineered tRNA molecule whose sequence is engineered so that a PTC is effectively and therapeutically reverted back into the originally lost amino acid or a different amino acid. Such engineered tRNAs allow for "re-editing" of a disease-causing nonsense codon to a specific amino acid. Examples of ACE-tRNAs and related sequences include those described in International Application PCT / US2024 / 016802, WO2023150753, WO2021252354, W02019090154, W02019090169, and Lueck, J. D. et al. Nature communications 10, 822, 2019. The contents of each of these documents, including the ACE- tRNA sequences provided therein, are incorporated by reference.

[0068] Nucleic Acid Molecules

[0069] In one aspect, the disclosure provides an isolated or engineered or non-naturally occurring transfer RNA (tRNA) comprising of a RNA sequence encoded by a nucleic acid or DNA sequence selected from the group consisting of SEQ ID NOs: 409, 1-408, and 410-442 or those listed in Tables 1 and 2A-2D.

[0070] In some embodiments, the nucleic acid or DNA sequence is selected from (i) the group consisting of SEQ ID NOs: 1-216, or (ii) the group consisting of SEQ ID NOs: 1-30, or (iii) the group consisting of SEQ ID NOs: 409, 254-408, and 410-442.

[0071] In some embodiments, the nucleic acid or DNA sequence is selected from those that are listed in Tables 1 and 2A-2D and have a mean value above 1.0 or 2.0. tRNA containing these sequences have activation activities and can be used to increase the expression of a protein of interest.

[0072] In some embodiments, the nucleic acid or DNA sequence is one selected from those that are listed in Tables 1 and 2A-2D and have a mean value below 1.0. tRNA containing these sequences have inhibition activities and can be used to decrease the expression of a protein of interest. Examples include SEQ ID NOs: 217-253, and in particular SEQ ID NOs: 247 and 250-253.

[0073] In some embodiments, the nucleic acid or DNA sequence is one selected from those that are listed in Tables 1 and 2A-2D and have a -loglO(q value) above 1.30.

[0074] In some embodiments, the nucleic acid or DNA sequence is selected from (A) the group consisting of SEQ ID NOs: 1-5, 7-9, 11, 13-14, 16-26, 28-31, 33-36, 39-40, 43-47, 50-53, 55, 58-65, 67, 69, 71-73, 76-78, 80, 83, 87, 90-92, 97-98, 100, 107, 110-111, 113, 116, 118, 125, 127, 130, 133, 140, 159, and 179, or (B) the group consisting of SEQ ID NOs: 1-5, 7-9, 11, 13- 14, 16-26, 28-30, or (C) the group consisting of SEQ ID NOs: 409, 282, 292, 293, 295, 372, 410, 412, 413, and 420, or (D) the group consisting of SEQ ID NOs: 409, 277, 286, 323, 336, 346, 355, 360, 361, 364, 372, 380, 382, 384, 389, 390, 398, 403, 411, 415, 420, 424, 425, 434, 435, and 437.

[0075] In some embodiments, the nucleic acid or DNA sequence is selected from the group

[0076] (C).

[0077] In some embodiments, the nucleic acid or DNA sequence is selected from the group

[0078] (D).

[0079] In some embodiments, the isolated tRNA described above comprises a T-arm, a D-arm, an anticodon-arm, and an acceptor arm comprising CCA at the 3’ end.

[0080] In some embodiments, the isolated tRNA described above further comprises a heterologous sequence or a modification.

[0081] In some embodiments, the isolated tRNA is 70 to 100 nucleotides in length. Expression Cassette and Expression Vectors

[0082] In some embodiments, this disclosure provides an expression cassette, comprising or consisting of a nucleic acid as described above. Where such nucleic acid may not already comprise a promoter, the expression cassette may additionally comprise a promoter. Thus, an expression cassette according to the present invention comprises, in 5' to 3' direction, a promoter, an upstream control element, a 5’ leader segment, a coding segment encoding a tRNA, a 3’ trailer segment, and optionally a terminator or other elements. In some embodiments, the coding segment comprises one of these listed in Tables 1 and 2A-2B.

[0083] The expression cassette can allow for an easy transfer of a target gene into an organism, preferably a cell and preferably a disease cell. The expression cassette of the present disclosure is preferably comprised in a vector. Thus, the vector of the present disclosure allows to transform a cell with a target gene or a combination of multiple genes while achieving a high expression or activity of the target gene. Correspondingly the disclosure provides a host cell comprising an expression cassette according to the present disclosure or a nucleic acid according to the present disclosure. The nucleic acid may also comprise a promoter or enhancer such as to allow for the expression of the target gene.

[0084] Introduction of Nucleic Acid Encoding tRNAs to Cells

[0085] Exogenous genetic material (e.g., a nucleic acid, an expression cassette, or an expression vector encoding one or more therapeutic tRNAs) can be introduced into a target cell or cells of interest in vivo by genetic transfer methods, such as transfection or transduction, to provide a genetically modified cell or cells or progeny thereof. Various expression vectors (z.e., vehicles for facilitating delivery of exogenous genetic material into a target cell) are known to one of ordinary skill in the art. As used herein, "exogenous genetic material" refers to a nucleic acid or an oligonucleotide, either natural or synthetic, that is not naturally found in the cells; or if it is naturally found in the cells, it is not transcribed or expressed at biologically significant levels by the cells. Thus, "exogenous genetic material" includes, for example, a non-naturally occurring nucleic acid that can be transcribed into a tRNA.

[0086] As used herein, "transfection of cells" refers to the acquisition by a cell of new genetic material by incorporation of added nucleic acid (DNA, RNA, or a hybrid thereof). Thus, transfection refers to the introducing of nucleic acid into a cell using physical or chemical methods. Several transfection techniques are known to those of ordinary skill in the art including calcium phosphate nucleic acid co-precipitation, strontium phosphate nucleic acid co-precipitation, DEAE-dextran, electroporation, cationic liposome-mediated transfection, and tungsten particle-facilitated microparticle bombardment. In contrast, "transduction of cells" refers to the process of transferring nucleic acid into a cell using a DNA or RNA virus. An RNA virus (z.e., a retrovirus) for transferring a nucleic acid into a cell is referred to herein as a transducing chimeric retrovirus. Exogenous genetic material contained within the retrovirus is incorporated into the genome of the transduced cell. A cell that has been transduced with a chimeric DNA virus (e.g., an adenovirus carrying a cDNA encoding a therapeutic agent), does not have the exogenous genetic material incorporated into its genome but is capable of expressing the exogenous genetic material that is retained extrachromosomally within the cell.

[0087] Typically, the exogenous genetic material may include a heterologous gene (coding for a therapeutic RNA or protein) together with a promoter to control transcription of the new gene. The promoter characteristically has a specific nucleotide sequence necessary to initiate transcription. Optionally, the exogenous genetic material further includes additional sequences (z.e., enhancers) required to obtain the desired gene transcription activity. For the purpose of this discussion, an "enhancer" is simply any non-translated DNA sequence that works contiguous with the coding sequence (in cis) to change the basal transcription level dictated by the promoter. The exogenous genetic material may be introduced into the cell genome immediately downstream from the promoter so that the promoter and coding sequence are operatively linked so as to permit transcription of the coding sequence. A retroviral expression vector may include an exogenous promoter element to control transcription of the inserted exogenous gene. Such exogenous promoters include both constitutive and inducible promoters.

[0088] Naturally occurring and synthetic constitutive promoters control the expression of essential cell functions. As a result, a gene under the control of a constitutive promoter is expressed under all conditions of cell growth. Exemplary constitutive promoters include the promoters for the following genes that encode certain constitutive or "housekeeping" functions: hypoxanthine phosphoribosyl transferase (HPRT), dihydrofolate reductase (DHFR), adenosine deaminase, phosphoglycerol kinase (PGK), pyruvate kinase, phosphoglycerol mutase, the actin promoter, ubiquitin, elongation factor- 1 and other constitutive promoters known to those of skill in the art. In addition, many viral promoters function constitutively in eucaryotic cells. These include the early and late promoters of SV40; the long terminal repeats (LTRs) of Moloney Leukemia Virus and other retroviruses; and the thymidine kinase promoter of Herpes Simplex Virus, among many others. Accordingly, any of the above-referenced constitutive promoters can be used to control transcription of a heterologous gene insert. Genes that are under the control of inducible promoters are expressed only or to a greater degree, in the presence of an inducing agent, (e.g., transcription under control of the metallothionein promoter is greatly increased in presence of certain metal ions). Inducible promoters include responsive elements (REs) which stimulate transcription when their inducing factors are bound. For example, there are REs for serum factors, steroid hormones, retinoic acid and cyclic AMP. Promoters containing a particular RE can be chosen in order to obtain an inducible response and in some cases, the RE itself may be attached to a different promoter, thereby conferring inducibility to the recombinant gene. Thus, by selecting the appropriate promoter (constitutive versus inducible; strong versus weak), it is possible to control both the existence and level of expression of a therapeutic agent in the genetically modified cell. If the gene encoding the therapeutic agent is under the control of an inducible promoter, delivery of the therapeutic agent in situ is triggered by exposing the genetically modified cell in situ to conditions for permitting transcription of the therapeutic agent, e.g., by injection of specific inducers of the inducible promoters which control transcription of the agent. For example, in situ expression by genetically modified cells of a therapeutic agent encoded by a gene under the control of the metallothionein promoter, is enhanced by contacting the genetically modified cells with a solution containing the appropriate (z.e., inducing) metal ions in situ.

[0089] Accordingly, the amount of therapeutic agent that is delivered in situ is regulated by controlling such factors as: (1) the nature of the promoter used to direct transcription of the inserted gene, (z.e., whether the promoter is constitutive or inducible, strong or weak); (2) the number of copies of the exogenous gene that are inserted into the cell; (3) the number of transduced / transfected cells that are administered (e.g., implanted) to the patient; (4) the size of the implant (e.g., graft or encapsulated expression system); (5) the number of implants; (6) the length of time the transduced / transfected cells or implants are left in place; and (7) the production rate of the therapeutic agent by the genetically modified cell. Selection and optimization of these factors for delivery of a therapeutically effective dose of a particular therapeutic agent is deemed to be within the scope of one of ordinary skill in the art without undue experimentation, taking into account the above-disclosed factors and the clinical profile of the patient.

[0090] In addition to at least one promoter and at least one heterologous nucleic acid encoding the therapeutic agent, the expression vector may include a selection gene, for example, a neomycin resistance gene, for facilitating selection of cells that have been transfected or transduced with the expression vector. Alternatively, the cells are transfected with two or more expression vectors, at least one vector containing the gene(s) encoding the therapeutic agent(s), the other vector containing a selection gene. The selection of a suitable promoter, enhancer, selection gene, and / or signal sequence is deemed to be within the scope of one of ordinary skill in the art without undue experimentation.

[0091] A tRNA construct or coding sequence of the present disclosure can be inserted into any type of target or host cell. In the context of an expression vector, the vector can be readily introduced into a host cell, eukaryotic or prokaryotic, e.g., mammalian, bacterial, yeast, or insect cell by any method in the art. For example, the expression vector can be transferred into a host cell by physical, chemical, or biological means.

[0092] Physical methods for introducing a polynucleotide into a host cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and / or exogenous nucleic acids are well-known in the art. See, for example, Sambrook et al. (2012, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York).

[0093] Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian, e.g., human cells. Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like. See, for example, U.S. Pat. Nos. 5,350,674 and 5,585,362.

[0094] Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. An exemplary colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (e.g., an artificial membrane vesicle).

[0095] Addition of DNA binding proteins such as Transcription Factor A Mitochondria (TFAM) can be used to condense DNA and shield charge. Due to the small size and compact shape, the DNA:Protein (DNP) complexes can then be delivered to cells by cell penetrating peptides, PEG derivative, liposomes or electroporation. In some instances, DNA binding proteins can encode nuclear localization signals to actively transport of DNPs from the cytoplasm to the nucleus where the DNA vectors are transcribed.

[0096] In the case where a non-viral delivery system is utilized, an exemplary delivery vehicle is a liposome. The use of lipid formulations is contemplated for the introduction of the nucleic acids into a host cell (in vitro, ex vivo or in vivo). In another aspect, the nucleic acid may be associated with a lipid. The nucleic acid associated with a lipid may be encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a micelle, or otherwise associated with a lipid. Lipid, lipid / DNA or lipid / expression vector associated compositions are not limited to any particular structure in solution. For example, they may be present in a bilayer structure, as micelles, or with a "collapsed" structure. They may also simply be interspersed in a solution, possibly forming aggregates that are not uniform in size or shape. Lipids are fatty substances which may be naturally occurring or synthetic lipids. For example, lipids include the fatty droplets that naturally occur in the cytoplasm as well as the class of compounds which contain long- chain aliphatic hydrocarbons and their derivatives, such as fatty acids, alcohols, amines, amino alcohols, and aldehydes.

[0097] Lipids suitable for use can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine ("DMPC") can be obtained from Sigma, St. Louis, MO; dicetyl phosphate ("DCP") can be obtained from K & K Laboratories (Plainview, NY); cholesterol ("Choi") can be obtained from Calbiochem-Behring; dimyristyl phosphatidylglycerol ("DMPG") and other lipids may be obtained from Avanti Polar Lipids, Inc. (Birmingham, AL). Stock solutions of lipids in chloroform or chloroform / methanol can be stored at about -20°C. Chloroform is used as the only solvent since it is more readily evaporated than methanol.

[0098] "Liposome" is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Liposomes can be characterized as having vesicular structures with a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh etal., 1991 Glycobiology 5: 505-10). However, compositions that have different structures in solution than the normal vesicular structure are also encompassed. For example, the lipids may assume a micellar structure or merely exist as nonuniform aggregates of lipid molecules. Also contemplated are lipofectamine-nucleic acid complexes.

[0099] The nucleic acid molecule described herein can be administered via electroporation, such as by a method described in U.S. Patent No. 7,664,545, the contents of which are incorporated herein by reference. The electroporation can be by a method and / or apparatus described in U.S. Patent Nos. 6,302,874; 5,676,646; 6,241,701; 6,233,482; 6,216,034; 6,208,893; 6,192,270; 6,181,964; 6,150,148; 6,120,493; 6,096,020; 6,068,650; and 5,702,359, the contents of which are incorporated herein by reference in their entirety. The electroporation may be carried out via a minimally invasive device.

[0100] The minimally invasive electroporation device ("MID") may be an apparatus for injecting the composition described above and associated fluid into body tissue. The device may comprise a hollow needle, DNA cassette, and fluid delivery means, wherein the device is adapted to actuate the fluid delivery means in use so as to concurrently (for example, automatically) inject DNA into body tissue during insertion of the needle into the said body tissue. This has the advantage that the ability to inject the DNA and associated fluid gradually while the needle is being inserted leads to a more even distribution of the fluid through the body tissue. The pain experienced during injection may be reduced due to the distribution of the DNA being injected over a larger area.

[0101] The MID may inject the composition into tissue without the use of a needle. The MID may inject the composition as a small stream or jet with such force that the composition pierces the surface of the tissue and enters the underlying tissue and / or muscle. The force behind the small stream or jet may be provided by expansion of a compressed gas, such as carbon dioxide through a micro-orifice within a fraction of a second. Examples of minimally invasive electroporation devices, and methods of using them, are described in published U.S. Patent Application No. 20080234655; U.S. Patent No. 6,520,950; U.S. Patent No. 7,171,264; U.S. Patent No. 6,208,893; U.S. Patent NO. 6,009,347; U.S. Patent No. 6,120,493; U.S. Patent No. 7,245,963; U.S. Patent No. 7,328,064; and U.S. Patent No. 6,763,264, the contents of each of which are herein incorporated by reference. The MID may comprise an injector that creates a high-speed jet of liquid that painlessly pierces the tissue. Such needle-free injectors are commercially available. Examples of needle-free injectors that can be utilized herein include those described in U.S. Patent Nos. 3,805,783; 4,447,223; 5,505,697; and 4,342,310, the contents of each of which are herein incorporated by reference.

[0102] A desired composition in a form suitable for direct or indirect electrotransport may be introduced (e.g., injected) using a needle-free injector into the tissue to be treated, usually by contacting the tissue surface with the injector so as to actuate delivery of a jet of the agent, with sufficient force to cause penetration of the composition into the tissue. For example, if the tissue to be treated is mucosa, skin or muscle, the agent is projected towards the mucosal or skin surface with sufficient force to cause the agent to penetrate through the stratum corneum and into dermal layers, or into underlying tissue and muscle, respectively.

[0103] Needle-free injectors are well suited to deliver compositions to all types of tissues, particularly to skin and mucosa. In some embodiments, a needle-free injector may be used to propel a liquid that contains the composition to the surface and into the subject's skin or mucosa. Representative examples of the various types of tissues that can be treated using the methods disclosed herein include pancreas, larynx, nasopharynx, hypopharynx, oropharynx, lip, throat, lung, heart, kidney, muscle, breast, colon, prostate, thymus, testis, skin, mucosal tissue, ovary, blood vessels, or any combination thereof.

[0104] The MID may have needle electrodes that electroporate the tissue. By pulsing between multiple pairs of electrodes in a multiple electrode array, for example set up in rectangular or square patterns, provides improved results over that of pulsing between a pair of electrodes. Disclosed, for example, in U.S. Patent No. 5,702,359 entitled "Needle Electrodes for Mediated Delivery of Drugs and Genes" is an array of needles wherein a plurality of pairs of needles may be pulsed during the therapeutic treatment. In that application, which is incorporated herein by reference as though fully set forth, needles were disposed in a circular array, but have connectors and switching apparatus enabling a pulsing between opposing pairs of needle electrodes. A pair of needle electrodes for delivering recombinant expression vectors to cells may be used. Such a device and system is described in U.S. Patent No. 6,763,264, the contents of which are herein incorporated by reference. Alternatively, a single needle device may be used that allows injection of the DNA and electroporation with a single needle resembling a normal injection needle and applies pulses of lower voltage than those delivered by presently used devices, thus reducing the electrical sensation experienced by the patient.

[0105] The MID may comprise one or more electrode arrays. The arrays may comprise two or more needles of the same diameter or different diameters. The needles may be evenly or unevenly spaced apart. The needles may be between 0.005 inches and 0.03 inches, between 0.01 inches and 0.025 inches; or between 0.015 inches and 0.020 inches. The needle may be 0.0175 inches in diameter. The needles may be 0.5 mm, 1.0 mm, 1.5 mm, 2.0 mm, 2.5 mm, 3.0 mm, 3.5 mm, 4.0 mm, or more spaced apart.

[0106] The MID may consist of a pulse generator and a two or more-needle composition injectors that deliver the composition and electroporation pulses in a single step. The pulse generator may allow for flexible programming of pulse and injection parameters via a flash card operated personal computer, as well as comprehensive recording and storage of electroporation and patient data. The pulse generator may deliver a variety of volt pulses during short periods of time. For example, the pulse generator may deliver three 15 volt pulses of 100 ms in duration. An example of such a MID is the ELGEN 1000 system, described in U.S. Patent No. 7,328,064, the contents of which are herein incorporated by reference.

[0107] The MID may be a CELLECTRA (INOVIO Pharmaceuticals) device and system, which is a modular electrode system, that facilitates the introduction of a macromolecule, such as a DNA, into cells of a selected tissue in a body or plant. The modular electrode system may comprise a plurality of needle electrodes; a hypodermic needle; an electrical connector that provides a conductive link from a programmable constant-current pulse controller to the plurality of needle electrodes; and a power source. An operator can grasp the plurality of needle electrodes that are mounted on a support structure and firmly insert them into the selected tissue in a body or plant. The macromolecules are then delivered via the hypodermic needle into the selected tissue. The programmable constant-current pulse controller is activated, and constantcurrent electrical pulse is applied to the plurality of needle electrodes. The applied constantcurrent electrical pulse facilitates the introduction of the macromolecule into the cell between the plurality of electrodes. Cell death due to overheating of cells is minimized by limiting the power dissipation in the tissue by virtue of constant-current pulses. The Cellectra device and system is described in U.S. Patent No. 7,245,963, the contents of which are herein incorporated by reference. The MID may be an ELGEN 1000 system (INOVIO Pharmaceuticals). The ELGEN 1000 system may comprise device that provides a hollow needle; and fluid delivery means, wherein the apparatus is adapted to actuate the fluid delivery means in use to concurrently (for example automatically) inject fluid, the described composition herein, into body tissue during insertion of the needle into the said body tissue. The advantage is the ability to inject the fluid gradually while the needle is being inserted leads to a more even distribution of the fluid through the body tissue. It is also believed that the pain experienced during injection is reduced due to the distribution of the volume of fluid being injected over a larger area.

[0108] In addition, the automatic injection of fluid facilitates automatic monitoring and registration of an actual dose of fluid injected. This data can be stored by a control unit for documentation purposes if desired.

[0109] It will be appreciated that the rate of injection could be either linear or non-linear and that the injection may be carried out after the needles have been inserted through the skin of the subject to be treated and while they are inserted further into the body tissue, such as tumor tissue, skin, tissue, liver tissue, and muscle tissue. The apparatus further comprises needle insertion means for guiding insertion of the needle into the body tissue. The rate of fluid injection is controlled by the rate of needle insertion. This has the advantage that both the needle insertion and injection of fluid can be controlled such that the rate of insertion can be matched to the rate of injection as desired. It also makes the apparatus easier for a user to operate. If desired means for automatically inserting the needle into body tissue could be provided.

[0110] A user could choose when to commence injection of fluid. Ideally however, injection is commenced when the tip of the needle has reached muscle tissue, and the apparatus may include means for sensing when the needle has been inserted to a sufficient depth for injection of the fluid to commence. This means that injection of fluid can be prompted to commence automatically when the needle has reached a desired depth (which can normally be the depth at which muscle tissue begins). The depth at which muscle tissue begins could for example be taken to be a preset needle insertion depth such as a value of 4 mm which would be deemed sufficient for the needle to get through the skin layer.

[0111] The sensing means may comprise an ultrasound probe. The sensing means may comprise a means for sensing a change in impedance or resistance. In this case, the means may not as such record the depth of the needle in the body tissue but can rather be adapted to sense a change in impedance or resistance as the needle moves from a different type of body tissue into muscle. Either of these alternatives provides a relatively accurate and simple to operate means of sensing that injection may commence. The depth of insertion of the needle can further be recorded if desired and could be used to control injection of fluid such that the volume of fluid to be injected is determined as the depth of needle insertion is being recorded.

[0112] The apparatus may further comprise: a base for supporting the needle; and a housing for receiving the base therein, wherein the base is moveable relative to the housing such that the needle is retracted within the housing when the base is in a first rearward position relative to the housing and the needle extends out of the housing when the base is in a second forward position within the housing. This is advantageous for a user as the housing can be lined up on the skin of a patient, and the needles can then be inserted into the patient's skin by moving the housing relative to the base.

[0113] As stated above, it is desirable to achieve a controlled rate of fluid injection such that the fluid is evenly distributed over the length of the needle as it is inserted into the skin. The fluid delivery means may comprise piston driving means adapted to inject fluid at a controlled rate. The piston driving means could for example be activated by a servo motor. However, the piston driving means may be actuated by the base being moved in the axial direction relative to the housing. It will be appreciated that alternative means for fluid delivery could be provided. Thus, for example, a closed container which can be squeezed for fluid delivery at a controlled or non-controlled rate could be provided in the place of a syringe and piston system.

[0114] The apparatus described above could be used for any type of injection. It is however envisaged to be particularly useful in the field of electroporation and so it may further comprise means for applying a voltage to the needle. This allows the needle to be used not only for injection but also as an electrode during, electroporation. This is particularly advantageous as it means that the electric field is applied to the same area as the injected fluid. There has traditionally been a problem with electroporation in that it is very difficult to accurately align an electrode with previously injected fluid and so users have tended to inject a larger volume of fluid than is required over a larger area and to apply an electric field over a higher area to attempt to guarantee an overlap between the injected substance and the electric field. As described herein, both the volume of fluid injected, and the size of electric field applied may be reduced while achieving a good fit between the electric field and the fluid.

[0115] Regardless of the method used to introduce exogenous nucleic acids into a host cell, in order to confirm the presence of the recombinant nucleic acid sequence in the host cell, a variety of assays may be performed. Such assays include, for example, "molecular biological" assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR; "biochemical" assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELISAs and Western blots) or other assays known to those of skill in the art.

[0116] Disease Conditions and Methods of Treatment

[0117] Certain embodiments of the present disclosure provide a method of treating a disease or disorder, such as associated with insufficient protein expression or PTCs, in a mammal (such as a human) comprising administering a vector encoding a therapeutic agent (e.g., a tRNA disclosed herein alone or in combination with an ACE-tRNA,) as described herein to the mammal. Certain embodiments of the present disclosure provide a use of a therapeutic agent or vector encoding a therapeutic agent as described herein to prepare a medicament useful for treating the disease in a mammal.

[0118] One example of the disease or condition associated with insufficient protein expression is a haploinsufficiency disorder. Examples of proteins involved in such a disorder include one encoded by a gene selected from the group consisting of AGGF1, ARHGAP31, BMPR2, CHD7, C0L2A1, C0L3A1, CTLA4, CTNNB1, DLL4, EHMT1, ELN, ENG, FAS, FBN1, F0XG1, GATA3, GLI3, GRN, IRF6, JAG1, KCNQ4, LMX1B, MBD5, MED13L, MITF, MNX1, MYCN, NFIA, NFIX, NOTCH1, NSD1, PAX3, PHIP, PRKAR1A, RAI1, RBPJ, RPS14, RUNX2, SALL4, SCN1A, SETBP1, SHANK3, SHH, SHOX, SLC2A1 / GLUT1, SOXIO, SYNGAP1, TBX1, TBX3, TBX5, TCF4, TCOF1, TGIF1, TNXB, TRPS1, WT1, and ZIC2. Examples of the haploinsufficiency disorder include 5q-syndrome, Adams-Oliver syndrome 1, Adams-Oliver syndrome 3, Adams-Oliver syndrome 5, Adams-Oliver syndrome 6, Alagille syndrome 1, Autoimmune lymphoproliferative syndrome type IA, Autoimmune lymphoproliferative syndrome type V, Autosomal dominant deafness-2A, Brain malformations with or without urinary tract defects (BRMUTD), Carney complex type 1, CHARGE syndrome, Cleidocranial dysplasia, Currarino syndrome, Denys-Drash syndrome / Frasier syndrome, Developmental delay, intellectual disability, obesity, and dysmorphic features (DIDOD), DiGeorge syndrome (TBX1 -associated), Dravet syndrome, Duane-radial ray syndrome, Ehlers-Danlos syndrome (classic-like), Ehlers-Danlos syndrome (vascular type), Feingold syndrome 1, Frontotemporal lobar degeneration with TDP43 inclusions (FTLD- TDP), GRN-related, GLUT1 deficiency syndrome, Greig cephalopoly syndactyly syndrome, Hereditary hemorrhagic telangiectasia type 1, Holoprosencephaly 3, Holoprosencephaly 4, Holoprosencephaly 5, Holt-Oram syndrome, Hypoparathyroidism, sensorineural deafness, and renal disease (HDR), Kleefstra syndrome 1, Klippel-Trenaunay syndrome (AAGF -related), Leri-Weill dyschondrosteosis, Marfan syndrome, Mental retardation and distinctive facial features with or without cardiac defects (MRFACD), Mental retardation, autosomal dominant 1, Mental retardation, autosomal dominant 19, Mental retardation, autosomal dominant 29, Nail-patella syndrome (NPS), Phelan-McDermid syndrome, Pitt-Hopkins syndrome, Primary pulmonary hypertension 1, Rett syndrome (congenital variant), Smith-Magenis syndrome (RAI 1 -associated), Sotos syndrome 1, Sotos syndrome 2, Stickler syndrome type I, Supravalvular aortic stenosis, SYNGAP1 -related intellectual disability, Treacher Collins syndrome, Trichorhinophalangeal syndrome type I, Ulnar-mammary syndrome, van der Woude syndrome 1, Waardenburg syndrome type 1, Waardenburg syndrome type 2 A, and Waardenburg syndrome type 4C.

[0119] Diseases or disorders associated with PTCs include, but are not limited to, variants of Duchenne muscular dystrophies and Becker muscular dystrophies due to a PTC in dystrophin, retinoblastoma due to a PTC in RBI, neurofibromatosis due to a PTC in NF1 or NF2, ataxiatelangiectasia due to a PTC in ATM, Tay-Sachs disease due to a PTC in HEXA, cystic fibrosis due to a PTC in CFTR, Wilm's tumor due to a PTC in WT1, hemophilia A due to a PTC in factor VIII, hemophilia B due to a PTC in factor IX, p53-associated cancers due to a PTC in p53, Menkes disease, Ullrich's disease, P-Thalassemia due to a PTC in betaglobin, type 2A and type 3 von Willebrand disease due to a PTC in Willebrand factor, Robinow syndrome, brachydactyly type B (shortening of digits and metacarpal s), inherited susceptibility to mycobacterial infection due to a PTC in IFNGR1, inherited retinal disease due to a PTC in CRX, inherited bleeding tendency due to a PTC in Coagulation factor X, inherited blindness due to a PTC in Rhodopsin, congenital neurosensory deafness and colonic agangliosis due to a PTC in SOXIO and inherited neural devel op-mental defect including neurosensory deafness, colonic agangliosis, peripheral neuropathy and central dysmyelinating leukodystrophy due to a PTC in SOX 10, Liddle's syndrome, xeroderma pigmentosum, Fanconi's anemia, anemia, hypothyroidism, p53-associated cancers (e.g., p53 squamal cell carcinoma, p53 hepatocellular carcinoma, p53 ovarian carcinoma), esophageal carcinoma, osteocarcinoma, ovarian carcinoma, hepatocellular carcinoma, breast cancer, hepatocellular carcinoma, fibrous histiocytoma, ovarian carcinoma, SRY sex reversal, triosephosphate isomerase-anemia, diabetes and ricketsand many others. The present disclosure in one embodiment includes compositions and methods for treating cystic fibrosis by reversing the effects of mutations present that are associated with nonsense mutations through introduction of the tRNAs of the disclosure. Additional disorders include Hurler Syndrome, Dravet Syndrome, Spinal Muscular Dystrophy, Usher Syndrome, Aniridia, Choroideremia, Ocular Coloboma, Retinitis pigmentosa, dystrophic epidermolysis bullosa, Pseudoxanthoma elasticum, Alagille Snydrome, Waardenburg-Shah, infantile neuronal ceroid lipofuscinosis, Cystinosis, X-linked nephrogenic diabetes insipidus, and Polycystic kidney disease.

[0120] Diseases or disorders associated with PTCs that can be treated by the molecules and methods described herein also include a number of eye diseases. Examples of the diseases and genes with the specific mutations include:

[0121] Cone dystrophies (Stargardt's disease (STGD1), cone-rod dystrophy, retinitis pigmentosa (RP), and increased susceptibility to age-related macular degeneration): KCNV2 Glul43X; KCNV2 Glu306X; KCNV2 Gln76X; KCNV2 Glul48X; CACNA2D4, Tyr802X; CACNA2D4, Arg628X; RP2, Argl20X; Rho, Ser334X; Rpe65, Arg44X; PDE6A, and Lys455X;

[0122] Congenital stationary night blindness 2 (CSNB2): CACNA1F, Arg958X; CACNA1F, and Arg830X;

[0123] Congenital stationary night blindness 1 (CSNB1): TRPM1, Glnl lX; TRPM1, Lys294X; TRPM1, Arg977X; TRPM1, Ser882X; NYX, and W350X;

[0124] Best Disease or BVMD, BEST1, Tyr29X; BEST1, Arg200X; BEST1, and Ser517X; Leber congenital amaurosis (LCA): KCNJ13, Trp53X; KCNJ13, Argl66X; CEP290, Argl51X; CEP290, Glyl890X; CEP290, Lysl575X; CEP290, Argl271X; CEP290, Argl782X; CRB1, Cysl332X; GUCY2D, Ser448X; GUCY2D, Arg41091X; LCA5, Gln279X; RDH12, Tyrl94X; RDH12, Glu275X; SPATA7, ArglO8X; TULP1, and Gln301X;

[0125] Usher syndrome 1 : USH1C, Arg31X; PCDH15, Arg3X; PCDH15, Arg245X; PCDH15, Arg643X; PCDH15, Arg929X; IQCB1, Arg461X; IQCB1, Arg489X; PDE6A, Gln69X; ALMS1, Ser999X; ALMS1, and Arg3804X;

[0126] Aniridia: Pax6 and Glyl94X;

[0127] Ocular coloboma: Pax2 and Argl39X;

[0128] Lambl, Arg524X;

[0129] Choroideremia: REP1 and Gln32X.

[0130] According to one aspect, a cell expression system for expressing a therapeutic agent in a mammalian recipient is provided. The expression system (also referred to herein as a "genetically modified cell") comprises a cell and an expression vector for expressing the therapeutic agent. Expression vectors include, but are not limited to, viruses, plasmids, and other vehicles for delivering heterologous genetic material to cells. Accordingly, the term "expression vector" as used herein refers to a vehicle for delivering heterologous genetic material to a cell. In particular, the expression vector can be a CEDT or MC minivector as described in WO2021252354. Other examples of the expression vector include a recombinant adenoviral, adeno-associated virus, or lentivirus or retrovirus vector.

[0131] The expression vector further includes a promoter for controlling transcription of the heterologous gene. The promoter may be an inducible promoter. The expression system is suitable for administration to the mammalian recipient. The expression system may comprise a plurality of non-immortalized genetically modified cells, each cell containing at least one gene encoding at least one therapeutic agent.

[0132] The cell expression system can be formed in vivo. According to yet another aspect, a method for treating a mammalian recipient in vivo is provided. The method includes introducing an expression vector for expressing a heterologous gene product into a cell of the patient in situ, such as via intravenous administration. To form the expression system in vivo, an expression vector for expressing the therapeutic agent is introduced in vivo into the mammalian recipient i.v.

[0133] According to yet another aspect, a method for treating a mammalian recipient in vivo is provided. The method includes introducing the target therapeutic agent into the patient in vivo. The expression vector for expressing the heterologous gene may include an inducible promoter for controlling transcription of the heterologous gene product. Accordingly, delivery of the therapeutic agent in situ is controlled by exposing the cell in situ to conditions, which induce transcription of the heterologous gene.

[0134] The present disclosure provides methods of treating a disease in a subject (e.g., a mammal) by administering an expression vector encoding a tRNA disclosed herein alone or in combination with an ACE-tRNA, to a cell or patient. For the gene therapy methods, a person having ordinary skill in the art of molecular biology and gene therapy would be able to determine, without undue experimentation, the appropriate dosages and routes of administration of the expression vector used in the novel methods of the present disclosure.

[0135] In certain embodiments, the agents and methods described herein can be used for the treatment / management of diseases, such as those caused by PTCs. Examples include, but are not limited to, Duchenne and Becker muscular dystrophies, retinoblastoma, neurofibromatosis, ataxia- telangiectasia, Tay-Sachs disease, cystic fibrosis, Wilm's tumor, hemophilia A, hemophilia B, Menkes disease, Ullrich's disease, P-Thalassemia, type 2A and type 3 von Willebrand disease, Robinow syndrome, brachydactyly type B (shortening of digits and metacarpals), inherited susceptibility to mycobacterial infection, inherited retinal disease, inherited bleeding tendency, inherited blindness, congenital neurosensory deafness and colonic agangliosis and inherited neural develop-mental defect including neurosensory deafness, colonic agangliosis, peripheral neuropathy and central dysmyelinating leukodystrophy, Liddle's syndrome, xeroderma pigmentosum, Fanconi's anemia, anemia, hypothyroidism, p53- associated cancers (e.g., p53 squamal cell carcinoma, p53 hepatocellular carcinoma, p53 ovarian carcinoma), esophageal carcinoma, osteocarcinoma, ovarian carcinoma, hepatocellular carcinoma, breast cancer, hepatocellular carcinoma, fibrous histiocytoma, ovarian carcinoma, SRY sex reversal, triosephosphate isomerase-anemia, diabetes and rickets. This therapy is advantageous in that it provides improved stop codon suppression specificity. The therapeutic tRNAs of the present disclosure can target a specific stop-codon, TGA for instance, thus reducing off-target effects at stop-codons unrelated to disease, in some embodiments. The present therapy is also advantageous in that it provides amino-acid specificity. The expressed tRNA can be engineered to specifically replace the amino acid that was lost via insertion of a disease stop codon, thus negating any spurious effects on protein stability, folding and trafficking, in some embodiments. Formulations

[0136] Once the cassette, vector, or another form of a therapeutic produced in accordance with this disclosure has been generated and purified in a sufficient quantity, a process of the disclosure may further comprise its formulation, for example as a therapeutic nucleic acid or DNA composition. A therapeutic nucleic acid or DNA composition comprises a therapeutic nucleic acid or DNA molecule encoding a tRNA as provided herein. Such a composition can comprise a therapeutically effective amount of the nucleic acid or DNA in a form suitable for administration by a desired route e.g., an aerosol, an injectable composition or a formulation suitable for oral, mucosal or topical administration. Formulation of nucleic acid or DNA as a conventional pharmaceutical preparation may be done using standard pharmaceutical formulation chemistries and methodologies, which are available to those skilled in the art.

[0137] Any pharmaceutically acceptable carrier or excipient may be used. Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle. These excipients, vehicles and auxiliary substances are generally pharmaceutical agents which may be administered without undue toxicity and which, in the case of vaccine compositions will not induce an immune response in the individual receiving the composition. A suitable carrier may be a liposome.

[0138] Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol and ethanol. Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. It is also preferred, although not required, that the preparation can contain a pharmaceutically acceptable excipient that serves as a stabilizer, particularly for peptide, protein or other like molecules if they are to be included in the composition. Examples of suitable carriers that also act as stabilizers for peptides include, without limitation, pharmaceutical grades of dextrose, sucrose, lactose, trehalose, mannitol, sorbitol, inositol, dextran, and the like. Other suitable carriers include, again without limitation, starch, cellulose, sodium or calcium phosphates, citric acid, tartaric acid, glycine, high molecular weight polyethylene glycols (PEGs), and combination thereof. A thorough discussion of pharmaceutically acceptable excipients, vehicles and auxiliary substances is available in REMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991), incorporated herein by reference. The agents e.g., a nucleic acid, an expression cassette, or an expression vector) of the disclosure can be administered so as to result in a reduction in at least one symptom associated with a disease (such as a genetic disease, e.g., cystic fibrosis). The amount administered varies depending on various factors including, but not limited to, the composition chosen, the particular disease, the weight, the physical condition, and the age of the subject, and whether prevention or treatment is to be achieved. Such factors can be readily determined by the clinician employing animal models or other test systems that are well known to the art.

[0139] The present disclosure envisions treating a disease or disorder by the administration of an agent, e.g., tRNA or an expression vector disclosed in this disclosure. Administration of the therapeutic agents in accordance with the present disclosure may be continuous or intermittent, depending, for example, upon the recipient's physiological condition, whether the purpose of the administration is therapeutic or prophylactic, and other factors known to skilled practitioners. The administration of the agents of the disclosure may be essentially continuous over a preselected period of time or may be in a series of spaced doses. Both local and systemic administration is contemplated.

[0140] One or more suitable unit dosage forms having the therapeutic agent(s) of the disclosure, which, as discussed below, may optionally be formulated for sustained release (for example using microencapsulation), can be administered by a variety of routes including parenteral, including by intravenous and intramuscular routes, as well as by direct injection into the diseased tissue. The formulations may, where appropriate, be conveniently presented in discrete unit dosage forms and may be prepared by any of the methods well known to pharmacy. Such methods may include the step of bringing into association the therapeutic agent with liquid carriers, solid matrices, semi-solid carriers, finely divided solid carriers or combinations thereof, and then, if necessary, introducing or shaping the product into the desired delivery system.

[0141] When the therapeutic agents of the disclosure are prepared for administration, they may be combined with a pharmaceutically acceptable carrier, diluent or excipient to form a pharmaceutical formulation, or unit dosage form. The total active ingredients in such formulations include from 0.1 to 99.9% by weight of the formulation. A pharmaceutically acceptable carrier can be a carrier, diluent, excipient, and / or salt that is compatible with the other ingredients of the formulation, and not deleterious to the recipient thereof. The active ingredient for administration may be present as a powder or as granules; as a solution, a suspension or an emulsion. Pharmaceutical formulations containing the therapeutic agents of the disclosure can be prepared by procedures known in the art using well-known and readily available ingredients. The therapeutic agents of the disclosure can also be formulated as solutions appropriate for parenteral administration, for instance by intramuscular, subcutaneous or intravenous routes. The pharmaceutical formulations of the therapeutic agents of the disclosure can also take the form of an aqueous or anhydrous solution or dispersion, or alternatively the form of an emulsion or suspension.

[0142] Thus, the therapeutic agent may be formulated for parenteral administration (e.g., by injection, for example, bolus injection or continuous infusion) and may be presented in unit dose form in ampules, pre-filled syringes, small volume infusion containers or in multi-dose containers with an added preservative. The active ingredients may take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, and may contain formulary agents such as suspending, stabilizing and / or dispersing agents. Alternatively, the active ingredients may be in powder form, obtained by aseptic isolation of sterile solid or by lyophilization from solution, for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water, before use.

[0143] It will be appreciated that the unit content of active ingredient or ingredients contained in an individual aerosol dose of each dosage form need not in itself constitute an effective amount for treating the particular indication or disease since the necessary effective amount can be reached by administration of a plurality of dosage units. Moreover, the effective amount may be achieved using less than the dose in the dosage form, either individually, or in a series of administrations.

[0144] The pharmaceutical formulations of the present disclosure may include, as optional ingredients, pharmaceutically acceptable carriers, diluents, solubilizing or emulsifying agents, and salts of the type that are well-known in the art. Specific non-limiting examples of the carriers and / or diluents that are useful in the pharmaceutical formulations of the present disclosure include water and physiologically acceptable buffered saline solutions such as phosphate buffered saline solutions pH 7.0-8.0 and water.

[0145] Nanoparticle Compositions

[0146] In some embodiments, the pharmaceutical compositions disclosed herein are formulated as lipid nanoparticles (LNP), such as those described in WO2020263883, WO2013123523, W02012170930, WO2011127255 and W02008103276; and

[0147] US20130171646, each of which is herein incorporated by reference in its entirety. Accordingly, the present disclosure provides nanoparticle compositions comprising (i) a lipid composition comprising a delivery agent, and (ii) at least one nucleic acid, such as a tRNA or a DNA encoding the tRNA, e.g., a cassette or a vector. In such a nanoparticle composition, the lipid composition disclosed herein can encapsulate the nucleic acid.

[0148] Nanoparticle compositions are typically sized on the order of micrometers or smaller and can include a lipid bilayer. Nanoparticle compositions encompass lipid nanoparticles (LNPs), liposomes (e.g., lipid vesicles), and lipoplexes. For example, a nanoparticle composition can be a liposome having a lipid bilayer with a diameter of 500 nm or less.

[0149] Nanoparticle compositions include, for example, lipid nanoparticles, liposomes, and lipoplexes. In some embodiments, nanoparticle compositions are vesicles including one or more lipid bilayers. In certain embodiments, a nanoparticle composition includes two or more concentric bilayers separated by aqueous compartments. Lipid bilayers can be functionalized and / or crosslinked to one another. Lipid bilayers can include one or more ligands, proteins, or channels.

[0150] In one embodiment, a lipid nanoparticle comprises an ionizable lipid, a structural lipid, a phospholipid, and nucleic acid of interest. In some embodiments, the LNP comprises an ionizable lipid, a PEG- modified lipid, a sterol and a structural lipid. In some embodiments, the LNP has a molar ratio of about 20-60% ionizable lipid: about 5-25% structural lipid: about 25-55% sterol; and about 0.5-15% PEG- modified lipid.

[0151] In some embodiments, the LNP has a poly dispersity value of less than 0.4. In some embodiments, the LNP has a net neutral charge at a neutral pH. In some embodiments, the LNP has a mean diameter of 50-150 nm. In some embodiments, the LNP has a mean diameter of 80-100 nm.

[0152] As generally defined herein, the term “lipid” refers to a small molecule that has hydrophobic or amphiphilic properties. Lipids may be naturally occurring or synthetic. Examples of classes of lipids include, but are not limited to, fats, waxes, sterol-containing metabolites, vitamins, fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides, and prenol lipids. In some instances, the amphiphilic properties of some lipids lead them to form liposomes, vesicles, or membranes in aqueous media.

[0153] In some embodiments, a lipid nanoparticle may comprise an ionizable lipid. As used herein, the term “ionizable lipid” has its ordinary meaning in the art and may refer to a lipid comprising one or more charged moieties. In some embodiments, an ionizable lipid may be positively charged or negatively charged. An ionizable lipid may be positively charged, in which case it can be referred to as “cationic lipid.” In certain embodiments, an ionizable lipid molecule may comprise an amine group, and can be referred to as an ionizable amino lipid. As used herein, a “charged moiety” is a chemical moiety that carries a formal electronic charge, e.g., monovalent (+1, or -1), divalent (+2, or -2), trivalent (+3, or -3), etc. The charged moiety may be anionic (i.e., negatively charged) or cationic (i.e., positively charged). Examples of positively charged moieties include amine groups (e.g., primary, secondary, and / or tertiary amines), ammonium groups, pyridinium group, guanidine groups, and imidizolium groups. In a particular embodiment, the charged moieties can comprise amine groups. Examples of negatively- charged groups or precursors thereof, include carboxylate groups, sulfonate groups, sulfate groups, phosphonate groups, phosphate groups, hydroxyl groups, and the like. The charge of the charged moiety may vary, in some cases, with the environmental conditions, for example, changes in pH may alter the charge of the moiety, and / or cause the moiety to become charged or uncharged. In general, the charge density of the molecule may be selected as desired.

[0154] IN some embodiments, the ionizable lipid is an ionizable amino lipid, sometimes referred to in the art as an “ionizable cationic lipid,” In one embodiment, the ionizable amino lipid may have a positively charged hydrophilic head and a hydrophobic tail that are connected via a linker structure. In addition to these, an ionizable lipid may also be a lipid including a cyclic amine group. In one embodiment, the ionizable lipid may be selected from, but not limited to, an ionizable lipid described in WO2013086354 and WO2013116126; the contents of each of which are herein incorporated by reference in their entirety. In yet another embodiment, the ionizable lipid may be selected from, but not limited to, formula CLI- CLXXXXII of US Patent No. 7,404,969; each of which is herein incorporated by reference in their entirety.

[0155] In one embodiment, the lipid may be a cleavable lipid such as those described in WO2012170889, which is incorporated by reference in its entirety. In one embodiment, the lipid may be synthesized by methods known in the art and / or as described in WO2013086354, the contents of each of which are herein incorporated by reference in their entirety.

[0156] Nanoparticle compositions can be characterized by a variety of methods. For example, microscopy (e.g., transmission electron microscopy or scanning electron microscopy) can be used to examine the morphology and size distribution of a nanoparticle composition. Dynamic light scattering or potentiometry (e.g., potentiometric titrations) can be used to measure zeta potentials. Dynamic light scattering can also be utilized to determine particle sizes. Instruments such as the Zetasizer Nano ZS (Malvern Instruments Ltd, Malvern, Worcestershire, UK) can also be used to measure multiple characteristics of a nanoparticle composition, such as particle size, poly dispersity index, and zeta potential. The size of the nanoparticles can help counter biological reactions such as, but not limited to, inflammation, or can increase the biological effect of the polynucleotide. As used herein, “size” or “mean size” in the context of nanoparticle compositions refers to the mean diameter of a nanoparticle.

[0157] In one embodiment, the nucleic acid described herein can formulated in lipid nanoparticles having a diameter from about 10 to about 100 nm. In one embodiment, the nanoparticles have a diameter from about 10 to 500 nm. In one embodiment, the nanoparticle has a diameter greater than 100 nm. In some embodiments, the largest dimension of a nanoparticle composition is 1 pm or shorter (e.g., 1 pm, 900 nm, 800 nm, 700 nm, 600 nm, 500 nm, 400 nm, 300 nm, 200 nm, 175 nm, 150 nm, 125 nm, 100 nm, 75 nm, 50 nm, or shorter).

[0158] A nanoparticle composition can be relatively homogenous. A poly dispersity index can be used to indicate the homogeneity of a nanoparticle composition, e.g., the particle size distribution of the nanoparticle composition. A small (e.g., less than 0.3) poly dispersity index generally indicates a narrow particle size distribution. A nanoparticle composition can have a poly dispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, or 0.25. In some embodiments, the poly dispersity index of a nanoparticle composition disclosed herein can be from about 0.10 to about 0.20.

[0159] The zeta potential of a nanoparticle composition can be used to indicate the electrokinetic potential of the composition. For example, the zeta potential can describe the surface charge of a nanoparticle composition. Nanoparticle compositions with relatively low charges, positive or negative, are generally desirable, as more highly charged species can interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the zeta potential of a nanoparticle composition disclosed herein can be from about -10 mV to about +20 mV, from about -10 mV to about +15 mV, from about 10 mV to about +10 mV, from about -10 mV to about +5 mV, from about -10 mV to about 0 mV, from about -10 mV to about -5 mV, from about -5 mV to about +20 mV, from about -5 mV to about +15 mV, from about -5 mV to about +10 mV, from about -5 mV to about +5 mV, from about -5 mV to about 0 mV, from about 0 mV to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV to about +15 mV, or from about +5 mV to about +10 mV.

[0160] The term “encapsulation efficiency” of a nucleic acid / polynucleotide describes the amount of the nucleic acid / polynucleotide that is encapsulated by or otherwise associated with a nanoparticle composition after preparation, relative to the initial amount provided. As used herein, “encapsulation” can refer to complete, substantial, or partial enclosure, confinement, surrounding, or encasement. Encapsulation efficiency is desirably high (e.g., close to 100%). The encapsulation efficiency can be measured, for example, by comparing the amount of the nucleic acid / polynucleotide in a solution containing the nanoparticle composition before and after breaking up the nanoparticle composition with one or more organic solvents or detergents.

[0161] Fluorescence can be used to measure the amount of free polynucleotide in a solution. For the nanoparticle compositions described herein, the encapsulation efficiency of a nucleic acid / polynucleotide can be at least 50%, for example 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency can be at least 80%. In certain embodiments, the encapsulation efficiency can be at least 90%.

[0162] The amount of a nucleic acid / polynucleotide present in a pharmaceutical composition disclosed herein can depend on multiple factors such as the size of the nucleic acid / polynucleotide, desired target and / or application, or other properties of the nanoparticle composition as well as on the properties of the nucleic acid / polynucleotide. For example, the amount of a nucleic acid / polynucleotide useful in a nanoparticle composition can depend on the size (expressed as length, or molecular mass), sequence, and other characteristics of the nucleic acid / polynucleotide. The relative amounts of a nucleic acid / polynucleotide in a nanoparticle composition can also vary. The relative amounts of the lipid composition and the nucleic acid / polynucleotide present in a lipid nanoparticle composition of the present disclosure can be optimized according to considerations of efficacy and tolerability.

[0163] In addition to providing nanoparticle compositions, the present disclosure also provides methods of producing lipid nanoparticles comprising encapsulating a polynucleotide. Such method comprises using any of the pharmaceutical compositions disclosed herein and producing lipid nanoparticles in accordance with methods of production of lipid nanoparticles known in the art. See, e.g., Wang et al. (2015)“Delivery of oligonucleotides with lipid nanoparticles” Adv. Drug Deliv. Rev. 87:68-80; Silva et al. (2015)“Delivery Systems for Biopharmaceuticals. Part I: Nanoparticles and Microparticles” Curr. Pharm. Technol.16: 940- 954; Naseri et al. (2015)“ Solid Lipid Nanoparticles and Nanostructured Lipid Carriers: Structure, Preparation and Application” Adv. Pharm. Bull. 5:305-13; Silva etal. (2015) “Lipid nanoparticles for the delivery of biopharmaceuticals” Curr. Pharm. Biotechnol.16:291-302, and references cited therein.

[0164] Lipid nanoparticle formulations typically comprise one or more lipids. In some embodiments, the lipid is an ionizable lipid (e.g., an ionizable amino lipid), sometimes referred to in the art as an “ionizable cationic lipid”. In some embodiments, lipid nanoparticle formulations further comprise other components, including a phospholipid, a structural lipid, and a molecule capable of reducing particle aggregation, for example a PEG or PEG-modified lipid.

[0165] Exemplary ionizable lipids include, but not limited to, any one of Compounds 1-342 disclosed herein, DLin-MG-DMA (MG), DLin-DMA, DLenDMA, DLin-D-DMA, DLin-K- DMA, DLin-M- C2-DMA, DLin-K-DMA, DLin-KC2-DMA, DLin-KG-DMA, DLin-KC4- DMA, DLin-C2K-DMA, DLin-MP-DMA, DODMA, 98N12-5, G2-200, DLin-C-DAP, DLin- DAC, DLinDAP, DLinAP, DLin- EG-DMA, DLin-2-DMAP, KL10, KL22, KL25, Octyl- CLinDMA, Octyl-CLinDMA (2R), Octyl- CLinDMA (2S), and any combination thereof. Other exemplary ionizable lipids include, (13Z,16Z)- N, N-dimethyl-3 -nonyldocosa- 13, 16- dien-1 -amine (L608), (20Z,23Z)-N,N-dimethylnonacosa-20,23- dien-10-amine, (17Z,20Z)- N,N-dimemylhexacosa- 17,20-dien-9-amine, (16Z, 19Z)-N5N- dimethylpentacosa- 16,19-dien- 8-amine, (13Z, 16Z)-N,N-dimethyldocosa- 13,16-dien-5-amine, ( 12Z, 15Z)-N,N- dimethylhenicosa-12,15-dien-4-amine, (14Z,17Z)-N,N-dimethyltricosa-14,17-dien-6- amine, (15Z, 18Z)-N,N-dimethyltetracosa-l 5, 18-dien-7-amine, (18Z,21Z)-N,N-dimethylheptacosa- 18,21 -dien- 10-amine, ( 15Z, 18Z)-N,N-dimethyltetracosa- 15,18-dien-5-amine, (14Z, 17Z)- N,N- dimethyltricosa-14,17-dien-4-amine, (19Z,22Z)-N,N-dimeihyloctacosa-19,22-dien-9- amine, (18Z,2 lZ)-N,N-dimethylheptacosa- 18,21 -dien-8-amine, ( 17Z,20Z)-N,N- dimethylhexacosa- 17,20- dien-7-amine, (16Z, 19Z)-N,N-dimethylpentacosa- 16,19-dien-6- amine, (22Z,25Z)-N,N- dimethylhentriaconta-22,25-dien-10-amine, (21Z,24Z)-N,N- dimethyltriaconta-21 ,24-dien-9-amine, (18Z)-N,N-dimetylheptacos- 18-en- 10-amine, ( 17Z)- N,N-dimethylhexacos- 17-en-9-amine, ( 19Z,22Z)- N,N-dimethyloctacosa- 19,22-dien-7- amine, N,N-dimethylheptacosan-l 0-amine, (20Z,23Z)-N-ethyl- N-methylnonacosa-20,23- dien-10-amine, 1-[(1 lZ,14Z)-l-nonylicosa-l l,14-dien-l-yl]pyrrolidine, (20Z)-N,N- dimethylheptacos-20-en-l 0-amine, (15Z)-N,N-dimethyl eptacos-15 -en-10-amine, (14Z)- N,N- dimethylnonacos- 14-en- 10-amine, ( 17Z)-N,N-dimethylnonacos- 17-en- 10-amine, (24Z)-N,N- dimethyltritriacont-24-en-l 0-amine, (20Z)-N,N-dimethylnonacos-20-en-l 0-amine, (22Z)- N,N- dimethylhentriacont-22-en-l 0-amine, (16Z)-N,N-dimethylpentacos-16-en-8-amine, (12Z,15Z)-N,N- dimethyl-2-nonylhenicosa-12,15-dien-l-amine, N,N-dimethyl-l-[(lS,2R)-2- octylcyclopropyl] eptadecan-8-amine, 1-[(1 S,2R)-2-hexylcyclopropyl]-N,N- dimethylnonadecan-10-amine, N,N- dimethyl-l-[(l S,2R)-2-octylcyclopropyl]nonadecan-10- amine, N,N-dimethyl-21-[(lS,2R)-2- octylcyclopropyl]henicosan-l 0-amine, N,N-dimethyl-l- [(lS,2S)-2-{[(lR,2R)-2- pentylcyclopropyl]methyl}cyclopropyl]nonadecan-l 0-amine, N,N- dimethyl-1- [( 1 S,2R)-2- octylcyclopropyl]hexadecan-8-amine, N,N-dimethyl-[(lR,2S)-2- undecyIcyclopropyl]tetradecan-5- amine, N,N-dimethyl-3-{7-[(lS,2R)-2- octylcyclopropyl]heptyl}dodecan-l -amine, l-[(lR,2S)-2- heptylcyclopropyl]-N,N- dimethyloctadecan-9-amine, 1-[(1 S,2R)-2-decylcyclopropyl]-N,N- dimethylpentadecan-6- amine, N,N-dimethyl-l-[(lS,2R)-2-octylcyclopropyl]pentadecan-8-amine, R- N,N-dimethyl-l- [(9Z,12Z)-octadeca-9,12-dien-l-yloxy]-3-(octyloxy)propan-2-amine, S-N,N- dimethyl-1- [(9Z,12Z)-octadeca-9,12-dien-l-yloxy]-3-(octyloxy)propan-2-amine, l-{2-[(9Z,12Z)- octadeca-9,12-dien-l-yloxy]-l-[(octyloxy)methyl]ethyl}pyrrolidine, (2S)-N,N-dimethyl-l- [(9Z,12Z)-octadeca-9,12-dien-l-yloxy]-3-[(5Z)-oct-5-en-l-yloxy]propan-2-amine, l-{2- [(9Z, 12Z)- octadeca-9, 12-dien- 1 -yloxy]- 1 -[(octyloxy)methyl]ethyl } azetidine, (2 S)- 1 -

[0166] (hexyloxy)-N,N-dimethyl- 3-[(9Z,12Z)-octadeca-9,12-dien-l-yloxy]propan-2-amine, (2S)-1- (heptyloxy)-N,N-dimethyl-3- [(9Z, 12Z)-octadeca-9, 12-dien- l-yloxy]propan-2-amine, N,N- dimethyl-l-(nonyloxy)-3-[(9Z,12Z)- octadeca-9, 12-dien- l-yloxy]propan-2-amine, N,N- dimethyl-l-[(9Z)-octadec-9-en-l-yloxy]-3- (octyloxy)propan-2-amine; (2S)-N,N-dimethyl-l- [(6Z,9Z,12Z)-octadeca-6,9,12-trien-l-yloxy]-3- (octyloxy)propan-2-amine, (2S)-1- [(1 lZ,14Z)-icosa-l l,14-dien-l-yloxy]-N,N-dimethyl-3- (pentyloxy)propan-2-amine, (2S)-1- (hexyloxy)-3-[(l lZ,14Z)-icosa-l l,14-dien-l-yloxy]-N,N- dimethylpropan-2-amine, 1-

[0167] [(1 lZ,14Z)-icosa-l l,14-dien-l-yloxy]-N,N-dimethyl-3-(octyloxy)propan- 2-amine, 1-

[0168] [(13Z, 16Z)-docosa- 13,16-dien-l-yloxy]-N,N-dimethyl-3 -(octyloxy)propan-2-amine, (2S)- 1 - [(13Z, 16Z)-docosa- 13,16-dien- 1 -yloxy]-3 -(hexyloxy)-N,N-dimethylpropan-2-amine, (2S)- 1 - [(13Z)-docos- 13 -en- 1 -yloxy]-3 -(hexyloxy)-N,N-dimethylpropan-2-amine, 1 -[(13Z)-docos-

[0169] 13-en-l- yloxy]-N,N-dimethyl-3-(octyloxy)propan-2-amine, l-[(9Z)-hexadec-9-en-l-yloxy]- N,N-dimethyl-3- (octyloxy )propan-2-amine, (2R)-N,N-dimethyl-H(l-metoyloctyl)oxy]-3- [(9Z,12Z)-octadeca-9,12- dien-l-yloxy]propan-2-amine, (2R)-l-[(3,7-dimethyloctyl)oxy]- N,N-dimethyl-3-[(9Z,12Z)-octadeca- 9,12-dien-l-yloxy]propan-2-amine, N,N-dimethyl-l- (octyloxy)-3-({8-[(lS,2S)-2-{[(lR,2R)-2- pentylcyclopropyl]methyl}cyclopropyl]octyl}oxy)propan-2-amine, N,N-dimethyl-l-{[8-(2- oclylcyclopropyl)octyl]oxy}-3-(octyloxy)propan-2-amine, and (11E,2OZ,23Z)-N,N- dimethylnonacosa-1 l,20,2-trien-10-amine, and any combination thereof.

[0170] Phospholipids include, but are not limited to, glycerophospholipids such as phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, phosphatidylinositols, phosphatidy glycerols, and phosphatidic acids. Phospholipids also include phosphosphingolipid, such as sphingomyelin. In some embodiments, the phospholipids are DLPC, DMPC, DOPC, DPPC, DSPC, DUPC, 18:0 Diether PC, DLnPC, DAPC, DHAPC, DOPE, 4ME 16:0 PE, DSPE, DLPE, DLnPE, DAPE, DHAPE, DOPG, and any combination thereof. In some embodiments, the phospholipids are MPPC, MSPC, PMPC, PSPC, SMPC, SPPC, DHAPE, DOPG, and any combination thereof. In some embodiments, the amount of phospholipids (e.g., DSPC) in the lipid composition ranges from about 1 mol% to about 20 mol%.

[0171] The structural lipids include sterols and lipids containing sterol moieties. In some embodiments, the structural lipids include cholesterol, fecosterol, sitosterol, ergosterol, campesterol, stigmasterol, brassicasterol, tomatidine, tomatine, ursolic acid, alpha-tocopherol, and mixtures thereof. In some embodiments, the structural lipid is cholesterol. In some embodiments, the amount of the structural lipids (e.g., cholesterol) in the lipid composition ranges from about 20 mol% to about 60 mol%.

[0172] The PEG-modified lipids include PEG-modified phosphatidylethanolamine and phosphatidic acid, PEG-ceramide conjugates (e.g., PEG-CerC4 or PEG-CerC20), PEG- modified dialkylamines and PEG-modified l,2-diacyloxypropan-3 -amines. Such lipids are also referred to as PEGylated lipids. For example, a PEG lipid can be PEG-c-DOMG, PEG-DMG, PEG-DLPE, PEG DMPE, PEG-DPPC, or a PEG-DSPE lipid. In some embodiments, the PEG- lipid are 1,2-dimyristoyl-sn-glycerol methoxypolyethylene glycol (PEG-DMG), 1,2- distearoyl-sn-glycero-3-phosphoethanolamine-N- [amino(polyethylene glycol)] (PEG-DSPE), PEG-disteryl glycerol (PEG-DSG), PEG-dipalmetoleyl, PEG-dioleyl, PEG-distearyl, PEG- diacylglycamide (PEG-DAG), PEG-dipalmitoyl phosphatidylethanolamine (PEG-DPPE), or PEG-1, 2-dimyristyloxlpropyl-3-amine (PEG-c-DMA). In some embodiments, the PEG moiety has a size of about 1000, 2000, 5000, 10,000, 15,000 or 20,000 Daltons. In some embodiments, the amount of PEG-lipid in the lipid composition ranges from about 0 mol% to about 5 mol%.

[0173] In some embodiments, the LNP formulations described herein can additionally comprise a permeability enhancer molecule. Non-limiting permeability enhancer molecules are described in US20050222064, herein incorporated by reference in its entirety.

[0174] The LNP formulations can further contain a phosphate conjugate. The phosphate conjugate can increase in vivo circulation times and / or increase the targeted delivery of the nanoparticle. Phosphate conjugates can be made by the methods described in, e.g., WO2013033438 or US20130196948. The LNP formulation can also contain a polymer conjugate (e.g., a water-soluble conjugate) as described in, e.g., US20130059360, US20130196948, and US20130072709. Each of the references is herein incorporated by reference in its entirety. The LNP formulations can comprise a conjugate to enhance the delivery of nanoparticles in a subject. Further, the conjugate can inhibit phagocytic clearance of the nanoparticles in a subject. In some embodiments, the conjugate can be a "self peptide designed from the human membrane protein CD47 (e.g., the "self1particles described by Rodriguez et al, Science 2013339, 971-975, herein incorporated by reference in its entirety). As shown by Rodriguez et al. the self-peptides delayed macrophage-mediated clearance of nanoparticles which enhanced delivery of the nanoparticles.

[0175] The LNP formulations can comprise a carbohydrate carrier. As a non-limiting example, the carbohydrate carrier can include, but is not limited to, an anhydride-modified phytoglycogen or glycogen-type material, phytoglycogen octenyl succinate, phytoglycogen beta-dextrin, anhydride- modified phytoglycogen beta-dextrin (e.g., W02012109121, which is incorporated by reference in its entirety).

[0176] The LNP formulations can be coated with a surfactant or polymer to improve the delivery of the particle. In some embodiments, the LNP can be coated with a hydrophilic coating such as, but not limited to, PEG coatings and / or coatings that have a neutral surface charge as described in US20130183244, which is incorporated by reference in its entirety.

[0177] The LNP formulations can be engineered to alter the surface properties of particles so that the lipid nanoparticles can penetrate the mucosal barrier as described in U.S. Pat. No. 8,241,670 or WO2013110028, each of which is herein incorporated by reference in its entirety. The LNP engineered to penetrate mucus can comprise a polymeric material (i.e., a polymeric core) and / or a polymer-vitamin conjugate and / or a tri-block co-polymer. The polymeric material can include, but is not limited to, polyamines, polyethers, polyamides, polyesters, polycarbamates, polyureas, polycarbonates, poly(styrenes), polyimides, polysulfones, polyurethanes, polyacetylenes, polyethylenes, polyethyeneimines, polyisocyanates, polyacrylates, polymethacrylates, polyacrylonitriles, and polyarylates.

[0178] LNP engineered to penetrate mucus can also include surface altering agents such as, but not limited to, anionic proteins (e.g., bovine serum albumin), surfactants (e.g., cationic surfactants such as for example dimethyldioctadecyl-ammonium bromide), sugars or sugar derivatives (e.g., cyclodextrin), nucleic acids, polymers (e.g., heparin, polyethylene glycol and pol oxamer), mucolytic agents (e.g., N-acetylcysteine, mugwort, bromelain, papain, clerodendrum, acetylcysteine, bromhexine, carbocisteine, eprazinone, mesna, ambroxol, sobrerol, domiodol, letosteine, stepronin, tiopronin, gelsolin, thymosin b4 dornase alfa, neltenexine, erdosteine) and various DNases including rhDNase. In some embodiments, the mucus penetrating LNP can be a hypotonic formulation comprising a mucosal penetration enhancing coating. The formulation can be hypotonic for the epithelium to which it is being delivered. Non-limiting examples of hypotonic formulations can be found in, e.g., WO2013110028, which is incorporated by reference in its entirety.

[0179] In some embodiments, the nucleic acids described herein can be formulated for controlled release and / or targeted delivery. As used herein, "controlled release" refers to a pharmaceutical composition or compound release profile that conforms to a particular pattern of release to affect a therapeutic outcome. In one embodiment, the nucleic acids can be encapsulated into a delivery agent described herein and / or known in the art for controlled release and / or targeted delivery. As used herein, the term "encapsulate" means to enclose, surround or encase. As it relates to the formulation of the nucleic acids of the disclosure, encapsulation can be substantial, complete or partial. The term "substantially encapsulated" means that at least greater than 50, 60, 70, 80, 85, 90, 95, 96, 97, 98, 99, or greater than 99% of the pharmaceutical composition or compound of the disclosure can be enclosed, surrounded or encased within the delivery agent. "Partially encapsulation" means that less than 10, 10, 20, 30, 4050 or less of the pharmaceutical composition or compound of the disclosure can be enclosed, surrounded or encased within the delivery agent.

[0180] In some embodiments, the nucleic acid composition can be formulated for sustained release. As used herein, "sustained release" refers to a pharmaceutical composition or compound that conforms to a release rate over a specific period of time. The period of time can include, but is not limited to, hours, days, weeks, months and years. As a non-limiting example, the sustained release nanoparticle composition described herein can be formulated as disclosed in W02010075072, US20100216804, US20110217377, US20120201859 and US20130150295, each of which is herein incorporated by reference in their entirety. In some embodiments, the nanoparticle composition can be formulated to be target specific, such as those described in WO2008121949, W02010005726, W02010005725, WO2011084521 WO201 1084518, US20100069426, US20120004293 and US20100104655, each of which is herein incorporated by reference in its entirety.

[0181] Administration

[0182] Once the cassette, vector, or another form of a therapeutic produced in accordance with this disclosure has been generated and purified in a sufficient quantity, a process of the disclosure may further comprise its formulation, for example as a therapeutic nucleic acid or DNA composition. A therapeutic nucleic acid or DNA composition comprises a therapeutic nucleic acid or DNA molecule encoding a tRNA as provided herein. Such a composition can comprise a therapeutically effective amount of the nucleic acid or DNA in a form suitable for administration by a desired route e.g., an aerosol, an injectable composition or a formulation suitable for oral, mucosal or topical administration. Formulation of nucleic acid or DNA as a conventional pharmaceutical preparation may be done using standard pharmaceutical formulation chemistries and methodologies, which are available to those skilled in the art.

[0183] Any pharmaceutically acceptable carrier or excipient may be used. Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle. These excipients, vehicles and auxiliary substances are generally pharmaceutical agents which may be administered without undue toxicity and which, in the case of vaccine compositions will not induce an immune response in the individual receiving the composition. A suitable carrier may be a liposome.

[0184] Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol and ethanol. Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. It is also preferred, although not required, that the preparation can contain a pharmaceutically acceptable excipient that serves as a stabilizer, particularly for peptide, protein or other like molecules if they are to be included in the composition. Examples of suitable carriers that also act as stabilizers for peptides include, without limitation, pharmaceutical grades of dextrose, sucrose, lactose, trehalose, mannitol, sorbitol, inositol, dextran, and the like. Other suitable carriers include, again without limitation, starch, cellulose, sodium or calcium phosphates, citric acid, tartaric acid, glycine, high molecular weight polyethylene glycols (PEGs), and combination thereof. A thorough discussion of pharmaceutically acceptable excipients, vehicles and auxiliary substances is available in REMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991), incorporated herein by reference.

[0185] The agents e.g., a nucleic acid, an expression cassette, or an expression vector) of the disclosure can be administered so as to result in a reduction in at least one symptom associated with a disease (such as a genetic disease, e.g., cystic fibrosis). The amount administered varies depending on various factors including, but not limited to, the composition chosen, the particular disease, the weight, the physical condition, and the age of the subject, and whether prevention or treatment is to be achieved. Such factors can be readily determined by the clinician employing animal models or other test systems that are well known to the art. The present disclosure envisions treating a disease or disorder by the administration of an agent, e.g., tRNA or an expression vector disclosed in this disclosure. Administration of the therapeutic agents in accordance with the present disclosure may be continuous or intermittent, depending, for example, upon the recipient's physiological condition, whether the purpose of the administration is therapeutic or prophylactic, and other factors known to skilled practitioners. The administration of the agents of the disclosure may be essentially continuous over a preselected period of time or may be in a series of spaced doses. Both local and systemic administration is contemplated.

[0186] One or more suitable unit dosage forms having the therapeutic agent(s) of the disclosure, which, as discussed below, may optionally be formulated for sustained release (for example using microencapsulation), can be administered by a variety of routes including parenteral, including by intravenous and intramuscular routes, as well as by direct injection into the diseased tissue. The formulations may, where appropriate, be conveniently presented in discrete unit dosage forms and may be prepared by any of the methods well known to pharmacy. Such methods may include the step of bringing into association the therapeutic agent with liquid carriers, solid matrices, semi-solid carriers, finely divided solid carriers or combinations thereof, and then, if necessary, introducing or shaping the product into the desired delivery system.

[0187] When the therapeutic agents of the disclosure are prepared for administration, they may be combined with a pharmaceutically acceptable carrier, diluent or excipient to form a pharmaceutical formulation, or unit dosage form. The total active ingredients in such formulations include from 0.1 to 99.9% by weight of the formulation. A pharmaceutically acceptable carrier can be a carrier, diluent, excipient, and / or salt that is compatible with the other ingredients of the formulation, and not deleterious to the recipient thereof. The active ingredient for administration may be present as a powder or as granules; as a solution, a suspension or an emulsion.

[0188] Pharmaceutical formulations containing the therapeutic agents of the disclosure can be prepared by procedures known in the art using well-known and readily available ingredients. The therapeutic agents of the disclosure can also be formulated as solutions appropriate for parenteral administration, for instance by intramuscular, subcutaneous or intravenous routes. The pharmaceutical formulations of the therapeutic agents of the disclosure can also take the form of an aqueous or anhydrous solution or dispersion, or alternatively the form of an emulsion or suspension. Thus, the therapeutic agent may be formulated for parenteral administration e.g., by injection, for example, bolus injection or continuous infusion) and may be presented in unit dose form in ampules, pre-filled syringes, small volume infusion containers or in multi-dose containers with an added preservative. The active ingredients may take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and / or dispersing agents. Alternatively, the active ingredients may be in powder form, obtained by aseptic isolation of sterile solid or by lyophilization from solution, for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water, before use.

[0189] It will be appreciated that the unit content of active ingredient or ingredients contained in an individual aerosol dose of each dosage form need not in itself constitute an effective amount for treating the particular indication or disease since the necessary effective amount can be reached by administration of a plurality of dosage units. Moreover, the effective amount may be achieved using less than the dose in the dosage form, either individually, or in a series of administrations.

[0190] The pharmaceutical formulations of the present disclosure may include, as optional ingredients, pharmaceutically acceptable carriers, diluents, solubilizing or emulsifying agents, and salts of the type that are well-known in the art. Specific non-limiting examples of the carriers and / or diluents that are useful in the pharmaceutical formulations of the present disclosure include water and physiologically acceptable buffered saline solutions such as phosphate buffered saline solutions pH 7.0-8.0 and water.

[0191] Nanoparticle Compositions

[0192] In some embodiments, the pharmaceutical compositions disclosed herein are formulated as lipid nanoparticles (LNP), such as those described in WO2020263883, WO2013123523, W02012170930, WO2011127255 and W02008103276; and

[0193] US20130171646, each of which is herein incorporated by reference in its entirety. Accordingly, the present disclosure provides nanoparticle compositions comprising (i) a lipid composition comprising a delivery agent, and (ii) at least one nucleic acid, such as a tRNA or a DNA encoding the tRNA, e.g., a cassette or a vector. In such a nanoparticle composition, the lipid composition disclosed herein can encapsulate the nucleic acid.

[0194] Nanoparticle compositions are typically sized on the order of micrometers or smaller and can include a lipid bilayer. Nanoparticle compositions encompass lipid nanoparticles (LNPs), liposomes e.g., lipid vesicles), and lipoplexes. For example, a nanoparticle composition can be a liposome having a lipid bilayer with a diameter of 500 nm or less.

[0195] Nanoparticle compositions include, for example, lipid nanoparticles, liposomes, and lipoplexes. In some embodiments, nanoparticle compositions are vesicles including one or more lipid bilayers. In certain embodiments, a nanoparticle composition includes two or more concentric bilayers separated by aqueous compartments. Lipid bilayers can be functionalized and / or crosslinked to one another. Lipid bilayers can include one or more ligands, proteins, or channels.

[0196] In one embodiment, a lipid nanoparticle comprises an ionizable lipid, a structural lipid, a phospholipid, and nucleic acid of interest. In some embodiments, the LNP comprises an ionizable lipid, a PEG- modified lipid, a sterol and a structural lipid. In some embodiments, the LNP has a molar ratio of about 20-60% ionizable lipid: about 5-25% structural lipid: about 25-55% sterol; and about 0.5-15% PEG- modified lipid.

[0197] In some embodiments, the LNP has a poly dispersity value of less than 0.4. In some embodiments, the LNP has a net neutral charge at a neutral pH. In some embodiments, the LNP has a mean diameter of 50-150 nm. In some embodiments, the LNP has a mean diameter of 80-100 nm.

[0198] As generally defined herein, the term “lipid” refers to a small molecule that has hydrophobic or amphiphilic properties. Lipids may be naturally occurring or synthetic. Examples of classes of lipids include, but are not limited to, fats, waxes, sterol-containing metabolites, vitamins, fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides, and prenol lipids. In some instances, the amphiphilic properties of some lipids lead them to form liposomes, vesicles, or membranes in aqueous media.

[0199] In some embodiments, a lipid nanoparticle may comprise an ionizable lipid. As used herein, the term “ionizable lipid” has its ordinary meaning in the art and may refer to a lipid comprising one or more charged moieties. In some embodiments, an ionizable lipid may be positively charged or negatively charged. An ionizable lipid may be positively charged, in which case it can be referred to as “cationic lipid.” In certain embodiments, an ionizable lipid molecule may comprise an amine group, and can be referred to as an ionizable amino lipid. As used herein, a “charged moiety” is a chemical moiety that carries a formal electronic charge, e.g., monovalent (+1, or -1), divalent (+2, or -2), trivalent (+3, or -3), etc. The charged moiety may be anionic (i.e., negatively charged) or cationic (i.e., positively charged). Examples of positively charged moieties include amine groups (e.g., primary, secondary, and / or tertiary amines), ammonium groups, pyridinium group, guanidine groups, and imidizolium groups. In a particular embodiment, the charged moieties can comprise amine groups. Examples of negatively- charged groups or precursors thereof, include carboxylate groups, sulfonate groups, sulfate groups, phosphonate groups, phosphate groups, hydroxyl groups, and the like. The charge of the charged moiety may vary, in some cases, with the environmental conditions, for example, changes in pH may alter the charge of the moiety, and / or cause the moiety to become charged or uncharged. In general, the charge density of the molecule may be selected as desired.

[0200] IN some embodiments, the ionizable lipid is an ionizable amino lipid, sometimes referred to in the art as an “ionizable cationic lipid,” In one embodiment, the ionizable amino lipid may have a positively charged hydrophilic head and a hydrophobic tail that are connected via a linker structure. In addition to these, an ionizable lipid may also be a lipid including a cyclic amine group. In one embodiment, the ionizable lipid may be selected from, but not limited to, an ionizable lipid described in WO2013086354 and WO2013116126; the contents of each of which are herein incorporated by reference in their entirety. In yet another embodiment, the ionizable lipid may be selected from, but not limited to, formula CLI- CLXXXXII of US Patent No. 7,404,969; each of which is herein incorporated by reference in their entirety.

[0201] In one embodiment, the lipid may be a cleavable lipid such as those described in WO2012170889, which is incorporated by reference in its entirety. In one embodiment, the lipid may be synthesized by methods known in the art and / or as described in WO2013086354, the contents of each of which are herein incorporated by reference in their entirety.

[0202] Nanoparticle compositions can be characterized by a variety of methods. For example, microscopy (e.g., transmission electron microscopy or scanning electron microscopy) can be used to examine the morphology and size distribution of a nanoparticle composition. Dynamic light scattering or potentiometry (e.g., potentiometric titrations) can be used to measure zeta potentials. Dynamic light scattering can also be utilized to determine particle sizes. Instruments such as the Zetasizer Nano ZS (Malvern Instruments Ltd, Malvern, Worcestershire, UK) can also be used to measure multiple characteristics of a nanoparticle composition, such as particle size, poly dispersity index, and zeta potential. The size of the nanoparticles can help counter biological reactions such as, but not limited to, inflammation, or can increase the biological effect of the polynucleotide. As used herein, “size” or “mean size” in the context of nanoparticle compositions refers to the mean diameter of a nanoparticle.

[0203] In one embodiment, the nucleic acid described herein can formulated in lipid nanoparticles having a diameter from about 10 to about 100 nm. In one embodiment, the nanoparticles have a diameter from about 10 to 500 nm. In one embodiment, the nanoparticle has a diameter greater than 100 nm. In some embodiments, the largest dimension of a nanoparticle composition is 1 pm or shorter (e.g., 1 pm, 900 nm, 800 nm, 700 nm, 600 nm, 500 nm, 400 nm, 300 nm, 200 nm, 175 nm, 150 nm, 125 nm, 100 nm, 75 nm, 50 nm, or shorter).

[0204] A nanoparticle composition can be relatively homogenous. A poly dispersity index can be used to indicate the homogeneity of a nanoparticle composition, e.g., the particle size distribution of the nanoparticle composition. A small (e.g., less than 0.3) poly dispersity index generally indicates a narrow particle size distribution. A nanoparticle composition can have a poly dispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, or 0.25. In some embodiments, the poly dispersity index of a nanoparticle composition disclosed herein can be from about 0.10 to about 0.20.

[0205] The zeta potential of a nanoparticle composition can be used to indicate the electrokinetic potential of the composition. For example, the zeta potential can describe the surface charge of a nanoparticle composition. Nanoparticle compositions with relatively low charges, positive or negative, are generally desirable, as more highly charged species can interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the zeta potential of a nanoparticle composition disclosed herein can be from about -10 mV to about +20 mV, from about -10 mV to about +15 mV, from about 10 mV to about +10 mV, from about -10 mV to about +5 mV, from about -10 mV to about 0 mV, from about -10 mV to about -5 mV, from about -5 mV to about +20 mV, from about -5 mV to about +15 mV, from about -5 mV to about +10 mV, from about -5 mV to about +5 mV, from about -5 mV to about 0 mV, from about 0 mV to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV to about +15 mV, or from about +5 mV to about +10 mV.

[0206] The term “encapsulation efficiency” of a nucleic acid / polynucleotide describes the amount of the nucleic acid / polynucleotide that is encapsulated by or otherwise associated with a nanoparticle composition after preparation, relative to the initial amount provided. As used herein, “encapsulation” can refer to complete, substantial, or partial enclosure, confinement, surrounding, or encasement. Encapsulation efficiency is desirably high (e.g., close to 100%). The encapsulation efficiency can be measured, for example, by comparing the amount of the nucleic acid / polynucleotide in a solution containing the nanoparticle composition before and after breaking up the nanoparticle composition with one or more organic solvents or detergents. Fluorescence can be used to measure the amount of free polynucleotide in a solution. For the nanoparticle compositions described herein, the encapsulation efficiency of a nucleic acid / polynucleotide can be at least 50%, for example 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency can be at least 80%. In certain embodiments, the encapsulation efficiency can be at least 90%.

[0207] The amount of a nucleic acid / polynucleotide present in a pharmaceutical composition disclosed herein can depend on multiple factors such as the size of the nucleic acid / polynucleotide, desired target and / or application, or other properties of the nanoparticle composition as well as on the properties of the nucleic acid / polynucleotide. For example, the amount of a nucleic acid / polynucleotide useful in a nanoparticle composition can depend on the size (expressed as length, or molecular mass), sequence, and other characteristics of the nucleic acid / polynucleotide. The relative amounts of a nucleic acid / polynucleotide in a nanoparticle composition can also vary. The relative amounts of the lipid composition and the nucleic acid / polynucleotide present in a lipid nanoparticle composition of the present disclosure can be optimized according to considerations of efficacy and tolerability.

[0208] In addition to providing nanoparticle compositions, the present disclosure also provides methods of producing lipid nanoparticles comprising encapsulating a polynucleotide. Such method comprises using any of the pharmaceutical compositions disclosed herein and producing lipid nanoparticles in accordance with methods of production of lipid nanoparticles known in the art. See, e.g., Wang et al. (2015)“Delivery of oligonucleotides with lipid nanoparticles” Adv. Drug Deliv. Rev. 87:68-80; Silva et al. (2015)“Delivery Systems for Biopharmaceuticals. Part I: Nanoparticles and Microparticles” Curr. Pharm. Technol.16: 940- 954; Naseri et al. (2015)“ Solid Lipid Nanoparticles and Nanostructured Lipid Carriers: Structure, Preparation and Application” Adv. Pharm. Bull. 5:305-13; Silva etal. (2015) “Lipid nanoparticles for the delivery of biopharmaceuticals” Curr. Pharm. Biotechnol.16:291-302, and references cited therein.

[0209] Lipid nanoparticle formulations typically comprise one or more lipids. In some embodiments, the lipid is an ionizable lipid (e.g., an ionizable amino lipid), sometimes referred to in the art as an “ionizable cationic lipid”. In some embodiments, lipid nanoparticle formulations further comprise other components, including a phospholipid, a structural lipid, and a molecule capable of reducing particle aggregation, for example a PEG or PEG-modified lipid. Exemplary ionizable lipids include, but not limited to, any one of Compounds 1-342 disclosed herein, DLin-MG-DMA (MG), DLin-DMA, DLenDMA, DLin-D-DMA, DLin-K- DMA, DLin-M- C2-DMA, DLin-K-DMA, DLin-KC2-DMA, DLin-KG-DMA, DLin-KC4- DMA, DLin-C2K-DMA, DLin-MP-DMA, DODMA, 98N12-5, G2-200, DLin-C-DAP, DLin- DAC, DLinDAP, DLinAP, DLin- EG-DMA, DLin-2-DMAP, KL10, KL22, KL25, Octyl- CLinDMA, Octyl-CLinDMA (2R), Octyl- CLinDMA (2S), and any combination thereof. Other exemplary ionizable lipids include, (13Z,16Z)- N, N-dimethyl-3 -nonyldocosa- 13, 16- dien-1 -amine (L608), (20Z,23Z)-N,N-dimethylnonacosa-20,23- dien-10-amine, (17Z,20Z)- N,N-dimemylhexacosa- 17,20-dien-9-amine, (16Z, 19Z)-N5N- dimethylpentacosa- 16,19-dien- 8-amine, (13Z, 16Z)-N,N-dimethyldocosa- 13,16-dien-5-amine, ( 12Z, 15Z)-N,N- dimethylhenicosa-12,15-dien-4-amine, (14Z,17Z)-N,N-dimethyltricosa-14,17-dien-6- amine, (15Z, 18Z)-N,N-dimethyltetracosa-l 5, 18-dien-7-amine, (18Z,21Z)-N,N-dimethylheptacosa- 18,21 -dien- 10-amine, ( 15Z, 18Z)-N,N-dimethyltetracosa- 15,18-dien-5-amine, (14Z, 17Z)- N,N- dimethyltricosa-14,17-dien-4-amine, (19Z,22Z)-N,N-dimeihyloctacosa-19,22-dien-9- amine, (18Z,2 lZ)-N,N-dimethylheptacosa- 18,21 -dien-8-amine, ( 17Z,20Z)-N,N- dimethylhexacosa- 17,20- dien-7-amine, (16Z, 19Z)-N,N-dimethylpentacosa- 16,19-dien-6- amine, (22Z,25Z)-N,N- dimethylhentriaconta-22,25-dien-10-amine, (21Z,24Z)-N,N- dimethyltriaconta-21 ,24-dien-9-amine, (18Z)-N,N-dimetylheptacos- 18-en- 10-amine, ( 17Z)- N,N-dimethylhexacos- 17-en-9-amine, ( 19Z,22Z)- N,N-dimethyloctacosa- 19,22-dien-7- amine, N,N-dimethylheptacosan-l 0-amine, (20Z,23Z)-N-ethyl- N-methylnonacosa-20,23- dien-10-amine, 1-[(1 lZ,14Z)-l-nonylicosa-l l,14-dien-l-yl]pyrrolidine, (20Z)-N,N- dimethylheptacos-20-en-l 0-amine, (15Z)-N,N-dimethyl eptacos-15-en-l 0-amine, (14Z)- N,N- dimethylnonacos- 14-en- 10-amine, ( 17Z)-N,N-dimethylnonacos- 17-en- 10-amine, (24Z)-N,N- dimethyltritriacont-24-en-l 0-amine, (20Z)-N,N-dimethylnonacos-20-en-l 0-amine, (22Z)- N,N- dimethylhentriacont-22-en-l 0-amine, (16Z)-N,N-dimethylpentacos-16-en-8-amine, (12Z,15Z)-N,N- dimethyl-2-nonylhenicosa-12,15-dien-l-amine, N,N-dimethyl-l-[(lS,2R)-2- octylcyclopropyl] eptadecan-8-amine, 1-[(1 S,2R)-2-hexylcyclopropyl]-N,N- dimethylnonadecan-10-amine, N,N- dimethyl-l-[(l S,2R)-2-octylcyclopropyl]nonadecan-10- amine, N,N-dimethyl-21-[(lS,2R)-2- octylcyclopropyl]henicosan-l 0-amine, N,N-dimethyl-l- [(lS,2S)-2-{[(lR,2R)-2- pentylcyclopropyl]methyl}cyclopropyl]nonadecan-l 0-amine, N,N- dimethyl-l-[(l S,2R)-2- octylcyclopropyl]hexadecan-8-amine, N,N-dimethyl-[(lR,2S)-2- undecy!cyclopropyl]tetradecan-5- amine, N,N-dimethyl-3-{7-[(lS,2R)-2- octylcyclopropyl]heptyl}dodecan-l -amine, l-[(lR,2S)-2- heptylcyclopropyl]-N,N- dimethyloctadecan-9-amine, 1-[(1 S,2R)-2-decylcyclopropyl]-N,N- dimethylpentadecan-6- amine, N,N-dimethyl-l-[(lS,2R)-2-octylcyclopropyl]pentadecan-8-amine, R- N,N-dimethyl-l- [(9Z,12Z)-octadeca-9,12-dien-l-yloxy]-3-(octyloxy)propan-2-amine, S-N,N- dimethyl-1- [(9Z,12Z)-octadeca-9,12-dien-l-yloxy]-3-(octyloxy)propan-2-amine, l-{2-[(9Z,12Z)- octadeca-9,12-dien-l-yloxy]-l-[(octyloxy)methyl]ethyl}pyrrolidine, (2S)-N,N-dimethyl-l- [(9Z,12Z)-octadeca-9,12-dien-l-yloxy]-3-[(5Z)-oct-5-en-l-yloxy]propan-2-amine, l-{2- [(9Z, 12Z)- octadeca-9, 12-dien- 1 -yloxy]- 1 -[(octyloxy)methyl]ethyl } azetidine, (2 S)- 1 -

[0210] (hexyloxy)-N,N-dimethyl- 3-[(9Z,12Z)-octadeca-9,12-dien-l-yloxy]propan-2-amine, (2S)-1- (heptyloxy)-N,N-dimethyl-3- [(9Z, 12Z)-octadeca-9, 12-dien- l-yloxy]propan-2-amine, N,N- dimethyl-l-(nonyloxy)-3-[(9Z,12Z)- octadeca-9, 12-dien- l-yloxy]propan-2-amine, N,N- dimethyl-l-[(9Z)-octadec-9-en-l-yloxy]-3- (octyloxy)propan-2-amine; (2S)-N,N-dimethyl-l- [(6Z,9Z,12Z)-octadeca-6,9,12-trien-l-yloxy]-3- (octyloxy)propan-2-amine, (2S)-1- [(1 lZ,14Z)-icosa-l l,14-dien-l-yloxy]-N,N-dimethyl-3- (pentyloxy)propan-2-amine, (2S)-1- (hexyloxy)-3-[(l lZ,14Z)-icosa-l l,14-dien-l-yloxy]-N,N- dimethylpropan-2-amine, 1-

[0211] [(1 lZ,14Z)-icosa-l l,14-dien-l-yloxy]-N,N-dimethyl-3-(octyloxy)propan- 2-amine, 1-

[0212] [(13Z, 16Z)-docosa- 13,16-dien-l-yloxy]-N,N-dimethyl-3 -(octyloxy)propan-2-amine, (2S)- 1 - [(13Z, 16Z)-docosa- 13,16-dien- 1 -yloxy]-3 -(hexyloxy)-N,N-dimethylpropan-2-amine, (2S)- 1 - [(13Z)-docos- 13 -en- 1 -yloxy]-3 -(hexyloxy)-N,N-dimethylpropan-2-amine, 1 -[(13Z)-docos-

[0213] 13 -en- 1 - yloxy]-N,N-dimethyl-3 -(octyloxy )propan-2-amine, 1 -[(9Z)-hexadec-9-en- 1 -yloxy]- N,N-dimethyl-3- (octyloxy )propan-2-amine, (2R)-N,N-dimethyl-H(l-metoyloctyl)oxy]-3- [(9Z,12Z)-octadeca-9,12- dien-l-yloxy]propan-2-amine, (2R)-l-[(3,7-dimethyloctyl)oxy]- N,N-dimethyl-3-[(9Z,12Z)-octadeca- 9,12-dien-l-yloxy]propan-2-amine, N,N-dimethyl-l- (octyloxy)-3-({8-[(lS,2S)-2-{[(lR,2R)-2- pentylcyclopropyl]methyl}cyclopropyl]octyl}oxy)propan-2-amine, N,N-dimethyl-l-{[8-(2- oclylcyclopropyl)octyl]oxy}-3-(octyloxy)propan-2-amine, and (11E,2OZ,23Z)-N,N- dimethylnonacosa-1 l,20,2-trien-10-amine, and any combination thereof.

[0214] Phospholipids include, but are not limited to, glycerophospholipids such as phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, phosphatidylinositols, phosphatidy glycerols, and phosphatidic acids. Phospholipids also include phosphosphingolipid, such as sphingomyelin. In some embodiments, the phospholipids are DLPC, DMPC, DOPC, DPPC, DSPC, DUPC, 18:0 Diether PC, DLnPC, DAPC, DHAPC, DOPE, 4ME 16:0 PE, DSPE, DLPE, DLnPE, DAPE, DHAPE, DOPG, and any combination thereof. In some embodiments, the phospholipids are MPPC, MSPC, PMPC, PSPC, SMPC, SPPC, DHAPE, DOPG, and any combination thereof. In some embodiments, the amount of phospholipids (e.g., DSPC) in the lipid composition ranges from about 1 mol% to about 20 mol%.

[0215] The structural lipids include sterols and lipids containing sterol moieties. In some embodiments, the structural lipids include cholesterol, fecosterol, sitosterol, ergosterol, campesterol, stigmasterol, brassicasterol, tomatidine, tomatine, ursolic acid, alpha-tocopherol, and mixtures thereof. In some embodiments, the structural lipid is cholesterol. In some embodiments, the amount of the structural lipids (e.g., cholesterol) in the lipid composition ranges from about 20 mol% to about 60 mol%.

[0216] The PEG-modified lipids include PEG-modified phosphatidylethanolamine and phosphatidic acid, PEG-ceramide conjugates (e.g., PEG-CerC4 or PEG-CerC20), PEG- modified dialkylamines and PEG-modified l,2-diacyloxypropan-3 -amines. Such lipids are also referred to as PEGylated lipids. For example, a PEG lipid can be PEG-c-DOMG, PEG-DMG, PEG-DLPE, PEG DMPE, PEG-DPPC, or a PEG-DSPE lipid. In some embodiments, the PEG- lipid are 1,2-dimyristoyl-sn-glycerol methoxypolyethylene glycol (PEG-DMG), 1,2- distearoyl-sn-glycero-3-phosphoethanolamine-N- [amino(polyethylene glycol)] (PEG-DSPE), PEG-disteryl glycerol (PEG-DSG), PEG-dipalmetoleyl, PEG-dioleyl, PEG-distearyl, PEG- diacylglycamide (PEG-DAG), PEG-dipalmitoyl phosphatidylethanolamine (PEG-DPPE), or PEG-1, 2-dimyristyloxlpropyl-3-amine (PEG-c-DMA). In some embodiments, the PEG moiety has a size of about 1000, 2000, 5000, 10,000, 15,000 or 20,000 Daltons. In some embodiments, the amount of PEG-lipid in the lipid composition ranges from about 0 mol% to about 5 mol%.

[0217] In some embodiments, the LNP formulations described herein can additionally comprise a permeability enhancer molecule. Non-limiting permeability enhancer molecules are described in US20050222064, herein incorporated by reference in its entirety.

[0218] The LNP formulations can further contain a phosphate conjugate. The phosphate conjugate can increase in vivo circulation times and / or increase the targeted delivery of the nanoparticle. Phosphate conjugates can be made by the methods described in, e.g., WO2013033438 or US20130196948. The LNP formulation can also contain a polymer conjugate (e.g., a water-soluble conjugate) as described in, e.g., US20130059360, US20130196948, and US20130072709. Each of the references is herein incorporated by reference in its entirety.

[0219] The LNP formulations can comprise a conjugate to enhance the delivery of nanoparticles in a subject. Further, the conjugate can inhibit phagocytic clearance of the nanoparticles in a subject. In some embodiments, the conjugate can be a "self1peptide designed from the human membrane protein CD47 (e.g., the "self1particles described by Rodriguez et al, Science 2013339, 971-975, herein incorporated by reference in its entirety). As shown by Rodriguez et al. the self-peptides delayed macrophage-mediated clearance of nanoparticles which enhanced delivery of the nanoparticles.

[0220] The LNP formulations can comprise a carbohydrate carrier. As a non-limiting example, the carbohydrate carrier can include, but is not limited to, an anhydride-modified phytoglycogen or glycogen-type material, phytoglycogen octenyl succinate, phytoglycogen beta-dextrin, anhydride- modified phytoglycogen beta-dextrin (e.g., W02012109121, which is incorporated by reference in its entirety).

[0221] The LNP formulations can be coated with a surfactant or polymer to improve the delivery of the particle. In some embodiments, the LNP can be coated with a hydrophilic coating such as, but not limited to, PEG coatings and / or coatings that have a neutral surface charge as described in US20130183244, which is incorporated by reference in its entirety.

[0222] The LNP formulations can be engineered to alter the surface properties of particles so that the lipid nanoparticles can penetrate the mucosal barrier as described in U.S. Pat. No. 8,241,670 or WO2013110028, each of which is herein incorporated by reference in its entirety. The LNP engineered to penetrate mucus can comprise a polymeric material (i.e., a polymeric core) and / or a polymer-vitamin conjugate and / or a tri-block co-polymer. The polymeric material can include, but is not limited to, polyamines, polyethers, polyamides, polyesters, polycarbamates, polyureas, polycarbonates, poly(styrenes), polyimides, polysulfones, polyurethanes, polyacetylenes, polyethylenes, polyethyeneimines, polyisocyanates, polyacrylates, polymethacrylates, polyacrylonitriles, and polyarylates.

[0223] LNP engineered to penetrate mucus can also include surface altering agents such as, but not limited to, anionic proteins (e.g., bovine serum albumin), surfactants (e.g., cationic surfactants such as for example dimethyldioctadecyl-ammonium bromide), sugars or sugar derivatives (e.g., cyclodextrin), nucleic acids, polymers (e.g., heparin, polyethylene glycol and pol oxamer), mucolytic agents (e.g., N-acetylcysteine, mugwort, bromelain, papain, clerodendrum, acetylcysteine, bromhexine, carbocisteine, eprazinone, mesna, ambroxol, sobrerol, domiodol, letosteine, stepronin, tiopronin, gelsolin, thymosin b4 dornase alfa, neltenexine, erdosteine) and various DNases including rhDNase. In some embodiments, the mucus penetrating LNP can be a hypotonic formulation comprising a mucosal penetration enhancing coating. The formulation can be hypotonic for the epithelium to which it is being delivered. Non-limiting examples of hypotonic formulations can be found in, e.g., WO2013110028, which is incorporated by reference in its entirety. In some embodiments, the nucleic acids described herein can be formulated for controlled release and / or targeted delivery. As used herein, "controlled release" refers to a pharmaceutical composition or compound release profile that conforms to a particular pattern of release to effect a therapeutic outcome. In one embodiment, the nucleic acids can be encapsulated into a delivery agent described herein and / or known in the art for controlled release and / or targeted delivery. As used herein, the term "encapsulate" means to enclose, surround or encase. As it relates to the formulation of the nucleic acids of the disclosure, encapsulation can be substantial, complete or partial. The term "substantially encapsulated" means that at least greater than 50, 60, 70, 80, 85, 90, 95, 96, 97, 98, 99, or greater than 99% of the pharmaceutical composition or compound of the disclosure can be enclosed, surrounded or encased within the delivery agent. "Partially encapsulation" means that less than 10, 10, 20, 30, 4050 or less of the pharmaceutical composition or compound of the disclosure can be enclosed, surrounded or encased within the delivery agent.

[0224] In some embodiments, the nucleic acid composition can be formulated for sustained release. As used herein, "sustained release" refers to a pharmaceutical composition or compound that conforms to a release rate over a specific period of time. The period of time can include, but is not limited to, hours, days, weeks, months and years. As a non-limiting example, the sustained release nanoparticle composition described herein can be formulated as disclosed in W02010075072, US20100216804, US20110217377, US20120201859 and US20130150295, each of which is herein incorporated by reference in their entirety. In some embodiments, the nanoparticle composition can be formulated to be target specific, such as those described in WO2008121949, W02010005726, W02010005725, WO2011084521 WO201 1084518, US20100069426, US20120004293 and US20100104655, each of which is herein incorporated by reference in its entirety.

[0225] Administration

[0226] The above-described therapeutic agents and compositions can be used for treating, protecting against, and / or preventing a disease in a subject in need thereof by administering one or more composition described herein to the subject.

[0227] Such agents and compositions can be administered in dosages and by techniques well known to those skilled in the medical arts taking into consideration such factors as the age, sex, weight, and condition of the particular subject, and the route of administration. The composition dose can be between 1 pg to 10 mg active component / kg body weight / time, and can be 20 pg to 10 mg component / kg body weight / time. The agent or composition can be administered prophylactically or therapeutically. In therapeutic applications, the agents or compositions are administered to a subject in need thereof in an amount sufficient to elicit a therapeutic effect. An amount adequate to accomplish this is defined as "therapeutically effective dose." Amounts effective for this use will depend on, e.g., the particular composition of the composition regimen administered, the manner of administration, the stage and severity of the disease, the general state of health of the subject, and the judgment of the prescribing physician.

[0228] The agent or composition can be administered by methods well known in the art as described in Donnelly et al. (Ann. Rev. Immunol. 15:617-648 (1997)), U.S. Pat. No. 5,580,859, U.S. Pat. No. 5,703,055, and U.S. Pat. No. 5,679,647, the contents of all of which are incorporated herein by reference in their entirety. The nucleic acid, such as DNA, of the composition can be complexed to particles or beads that can be administered to an individual, for example, using a vaccine gun. One skilled in the art would know that the choice of a pharmaceutically acceptable carrier, including a physiologically acceptable compound, depends, for example, on the route of administration of the expression vector. The composition can be delivered via a variety of routes. Typical delivery routes include parenteral administration, e.g., intradermal, intramuscular or subcutaneous delivery. Other routes include oral administration, intranasal, and intravaginal routes. For the nucleic acid of the composition, such as DNA in particular, the composition can be delivered to the interstitial spaces of tissues of an individual (U.S. Pat. Nos. 5,580,859 and 5,703,055, the contents of all of which are incorporated herein by reference in their entirety). The composition can also be administered to muscle, or can be administered via intradermal or subcutaneous injections, or transdermally, such as by iontophoresis. Epidermal administration of the composition can also be employed. Epidermal administration can involve mechanically or chemically irritating the outermost layer of epidermis to stimulate an immune response to the irritant (U.S. Pat. No. 5,679,647).

[0229] In one embodiment, the composition can be formulated for administration via the nasal passages. Formulations suitable for nasal administration, wherein the carrier is a solid, can include a coarse powder having a particle size, for example, in the range of about 10 to about 500 microns which is administered in the manner in which snuff is taken, i.e., by rapid inhalation through the nasal passage from a container of the powder held close up to the nose. The formulation can be a nasal spray, nasal drops, or by aerosol administration by nebulizer. The formulation can include aqueous or oily solutions of the composition.

[0230] The composition can be a liquid preparation such as a suspension, syrup or elixir. The composition can also be a preparation for parenteral, subcutaneous, intradermal, intramuscular or intravenous administration (e.g., injectable administration), such as a sterile suspension or emulsion.

[0231] The composition can be incorporated into liposomes, microspheres or other polymer matrices (U.S. Pat. No. 5,703,055; Gregoriadis, Liposome Technology, Vols. Ito III (2nd ed. 1993), the contents of which are incorporated herein by reference in their entirety). Liposomes can consist of phospholipids or other lipids, and can be nontoxic, physiologically acceptable and metabolizable carriers that are relatively simple to make and administer.

[0232] The tRNA or nucleic acid molecule encoding the tRNA may be administered by different routes including orally, parenterally, sublingually, transdermally, rectally, transmucosally, topically, via inhalation, via buccal administration, intrapleurally, intravenous, intraarterial, intraperitoneal, subcutaneous, intramuscular, intranasal, intrathecal, and intraarticular or combinations thereof. For veterinary use, the composition may be administered as a suitably acceptable formulation in accordance with normal veterinary practice. The veterinarian can readily determine the dosing regimen and route of administration that is most appropriate for a particular animal. The composition may be administered by traditional syringes, needleless injection devices, "microprojectile bombardment gone guns", or other physical methods such as electroporation ("EP"), "hydrodynamic method", or ultrasound.

[0233] The tRNA or nucleic acid molecule encoding the tRNA may be delivered to a mammal by several well-known technologies including injection with and without in vivo electroporation, liposome mediated, nanoparticle facilitated, recombinant vectors such as recombinant adenovirus, recombinant adenovirus associated virus and recombinant vaccinia. The tRNA or nucleic acid molecule encoding the tRNA may be delivered via injection, such as DNA injection, and along with in vivo electroporation.

[0234] Electroporation

[0235] Administration of the composition via electroporation may be accomplished using electroporation devices that can be configured to deliver to a desired tissue of a mammal a pulse of energy effective to cause reversible pores to form in cell membranes, and preferable the pulse of energy is a constant current similar to a preset current input by a user. The electroporation device may comprise an electroporation component and an electrode assembly or handle assembly. The electroporation component may include and incorporate one or more of the various elements of the electroporation devices, including: controller, current waveform generator, impedance tester, waveform logger, input element, status reporting element, communication port, memory component, power source, and power switch. The electroporation may be accomplished using an in vivo electroporation device, for example CELLECTRA EP system or ELGEN electroporator to facilitate transfection of cells by the plasmid.

[0236] The electroporation component may function as one element of the electroporation devices, and the other elements are separate elements (or components) in communication with the electroporation component. The electroporation component may function as more than one element of the electroporation devices, which may be in communication with still other elements of the electroporation devices separate from the electroporation component. The elements of the electroporation devices existing as parts of one electromechanical or mechanical device may not be limited as the elements can function as one device or as separate elements in communication with one another. The electroporation component may be capable of delivering the pulse of energy that produces the constant current in the desired tissue, and includes a feedback mechanism. The electrode assembly may include an electrode array having a plurality of electrodes in a spatial arrangement, wherein the electrode assembly receives the pulse of energy from the electroporation component and delivers same to the desired tissue through the electrodes. At least one of the plurality of electrodes is neutral during delivery of the pulse of energy and measures impedance in the desired tissue and communicates the impedance to the electroporation component. The feedback mechanism may receive the measured impedance and can adjust the pulse of energy delivered by the electroporation component to maintain the constant current.

[0237] A plurality of electrodes may deliver the pulse of energy in a decentralized pattern. The plurality of electrodes may deliver the pulse of energy in the decentralized pattern through the control of the electrodes under a programmed sequence, and the programmed sequence is input by a user to the electroporation component. The programmed sequence may comprise a plurality of pulses delivered in sequence, wherein each pulse of the plurality of pulses is delivered by at least two active electrodes with one neutral electrode that measures impedance, and wherein a subsequent pulse of the plurality of pulses is delivered by a different one of at least two active electrodes with one neutral electrode that measures impedance.

[0238] The feedback mechanism may be performed by either hardware or software. The feedback mechanism may be performed by an analog closed-loop circuit. The feedback occurs every 50 pP, 20 pP, 10 or 1 pP, but is preferably real-time feedback or instantaneous (z.e., substantially instantaneous as determined by available techniques for determining response time). The neutral electrode may measure the impedance in the desired tissue and communicates the impedance to the feedback mechanism, and the feedback mechanism responds to the impedance and adjusts the pulse of energy to maintain the constant current at a value similar to the preset current. The feedback mechanism may maintain the constant current continuously and instantaneously during the delivery of the pulse of energy.

[0239] Examples of electroporation devices and electroporation methods that may facilitate delivery of the compositions described herein, include those described in US7245963 and US2005 / 0052630, the contents of which are hereby incorporated by reference in their entirety. Other electroporation devices and electroporation methods known in the art can also be used for facilitating delivery of the compositions. See, e.g., US9452285, US7245963, US5273525, US6110161, US6958060, US6939862, US6697669, US 7328064 and US 2005 / 0052630.

[0240] Definitions

[0241] A nucleic acid or polynucleotide refers to a DNA molecule (e.g., a cDNA or genomic DNA), an RNA molecule (e.g. , an mRNA), or a DNA or RNA analog. A DNA or RNA analog can be synthesized from nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.

[0242] A “non-natural” or “engineered ” or recombinant nucleic acid refers to a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid, but it may comprise a fragment of a naturally occurring genomic nucleic acid, in some embodiments. The term therefore covers, for example, (a) a nucleic acid which has the sequence of part of a naturally occurring nucleic acid molecule but is not flanked by both of the sequences that flank that part of the molecule as it naturally occurs; (b) a nucleic acid incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment that does not occur in nature; (d) a recombinant nucleotide sequence that does not occur in nature; or (e) an engineered nucleotide sequence that does not occur in nature. The nucleic acid described above can be used to express a tRNA of this disclosure. For this purpose, one can operatively linked the nucleic acid to suitable regulatory sequences to generate an expression vector.

[0243] A "recombinant nucleic acid” is a combination of nucleic acid sequences that are joined together using recombinant technology and procedures used to join together nucleic acid sequences. The terms “heterologous” DNA molecule and “heterologous” nucleic acid, as used herein, each refer to a molecule that originates from a source foreign to the particular host cell or, if from the same source, is modified from its original form. Thus, a heterologous gene in a host cell includes a gene that is endogenous to the particular host cell but has been modified through, for example, the use of shuffling or recombination. When used to describe two nucleic acid segments, the terms mean that the two nucleic acid segments are not from the same gene or, if form the same gene, one or both of them are modified from the original forms. The terms also include non-naturally occurring multiple copies of a naturally occurring DNA molecule. Thus, the terms refer to a nucleic acid segment that is foreign or heterologous to the cell, or homologous to the cell but in a position within the host cell nucleic acid in which the element is not ordinarily found. Exogenous DNA segments are expressed to yield exogenous RNAs or polypeptides. A "homologous DNA molecule" is a DNA molecule that is naturally associated with a host cell into which it is introduced.

[0244] The term "isolated” nucleic acid molecule refers to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end or an analog thereof, that has been separated from at least about 50 percent of polypeptides, peptides, lipids, carbohydrates, polynucleotides or other materials with which the nucleic acid is naturally found when total nucleic acid is isolated from the source cells. Preferably, an isolated nucleic acid molecule is substantially free from any other contaminating nucleic acid molecules or other molecules that are found in the natural environment of the nucleic acid that would interfere with its use in polypeptide production or its therapeutic, diagnostic, prophylactic or research use.

[0245] A vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. The vector may or may not be capable of autonomous replication or integrate into a host DNA. Examples of the vector include a plasmid, cosmid, or viral vector. The vector includes a nucleic acid in a form suitable for expression of a nucleic acid of interest in a host cell. Preferably the vector includes one or more regulatory sequences operatively linked to the nucleic acid sequence to be expressed.

[0246] A "regulatory sequence" includes promoters, enhancers, and other expression control elements (e.g., polyadenylation signals). Regulatory sequences include those that direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and / or inducible sequences. The design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein or RNA desired, and the like. The expression vector can be introduced into host cells to produce an RNA or a polypeptide of interest. A promoter is defined as a DNA sequence that directs RNA polymerase to bind to DNA and initiate RNA synthesis. A strong promoter is one which causes RNAs to be initiated at high frequency.

[0247] A "promoter" is a nucleotide sequence which initiates and regulates transcription of a polynucleotide. Promoters can include inducible promoters (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), repressible promoters (where expression of a polynucleotide sequence operably linked to the promoter is repressed by an analyte, cofactor, regulatory protein, etc.), and constitutive promoters. It is intended that the term "promoter" or "control element" includes full-length promoter regions and functional (e.g., controls transcription or translation) segments of these regions.

[0248] "Operably linked" refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function. Thus, a given promoter operably linked to a nucleic acid sequence is capable of effecting the expression of that sequence when the proper enzymes are present. The promoter need not be contiguous with the sequence, so long as it functions to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between the promoter sequence and the nucleic acid sequence, and the promoter sequence can still be considered "operably linked" to the coding sequence. Thus, the term "operably linked" is intended to encompass any spacing or orientation of the promoter element and the DNA sequence of interest which allows for initiation of transcription of the DNA sequence of interest upon recognition of the promoter element by a transcription complex.

[0249] "Expression cassette" as used herein means a nucleic acid sequence capable of directing expression of a particular nucleotide sequence in an appropriate host cell, which may include a promoter operably linked to the nucleotide sequence of interest that may be operably linked to termination signals. It also may include sequences required for proper translation of the nucleotide sequence. The coding region usually codes for an RNA or protein of interest. The expression cassette including the nucleotide sequence of interest may be chimeric. The expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. The expression of the nucleotide sequence in the expression cassette may be under the control of a constitutive promoter or of a regulatable promoter that initiates transcription only when the host cell is exposed to some particular stimulus. In the case of a multicellular organism, the promoter can also be specific to a particular tissue or organ or stage of development. In certain embodiments, the promoter is a PGK, CMV, RSV, HI or U6 promoter (Pol II and Pol III promoters).

[0250] A "nucleic acid fragment" is a portion of a given nucleic acid molecule. The term "substantial identity" of polynucleotide sequences means that a polynucleotide comprises a sequence that has at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, or at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, or at least 90%, 91%, 92%, 93%, or 94%), or even at least 95%, 96%, 97%, 98%, or 99% sequence identity, compared to a reference sequence using one of the alignment programs described using standard parameters.

[0251] As used herein, "reference sequence" or "original sequence" is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full length cDNA or gene sequence or isolated nucleic acid sequence.

[0252] As used herein "minivector" refers to a mini-sized and circular DNA vector system, e.g., a double stranded circular DNA (e.g, a mini circle) or a closed linear DNA molecule (e.g., CEDT), lacking a bacterial origin of replication and an antibiotic selection gene, and having a size of about 100 bp up to about 5 k bp. It can be obtained, for example, by site-specific recombination of a parent plasmid to eliminate plasmid sequences outside of the recombination sites. It contains, for example, a nucleic acid molecule with merely the transgene expression cassette, including promoter and a nucleic acid sequence of interest, wherein the nucleic acid sequence may be, for example, a tRNA for e.g., suppressing PTCs, and, importantly, no bacterial-originated sequences.

[0253] The term "subject" includes human and non-human animals. The preferred subject for treatment is a human. As used herein, the terms "subject" and "patient" are used interchangeably irrespective of whether the subject has or is currently undergoing any form of treatment. As used herein, the terms "subject" and "subjects" may refer to any vertebrate, including, but not limited to, a mammal (e.g, cow, pig, camel, llama, horse, goat, rabbit, sheep, hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate (for example, a monkey, such as a cynomolgous monkey, chimpanzee, etc) and a human). In one embodiment, the subject is a human. In another embodiment, the subject is an experimental, non-human animal or animal suitable as a disease model.

[0254] A disease or disorder associated with a PTC or nonsense mutation, PTC-associated disease, or PTC-associated disease refers to any conditions caused or characterized by one or more nonsense mutations change an amino acid codon to PTC through a single-nucleotide substitution, resulting in a defective truncated protein. As used herein, “treating” or “treatment” refers to administration of a compound or agent to a subject who has a disorder or is at risk of developing the disorder with the purpose to cure, alleviate, relieve, remedy, delay the onset of, prevent, or ameliorate the disorder, the symptom of the disorder, the disease state secondary to the disorder, or the predisposition toward the disorder. The terms "prevent," "preventing," "prevention," "prophylactic treatment" and the like refer to reducing the probability of developing a disorder or condition in a subject, who does not have, but is at risk of or susceptible to developing a disorder or condition. "Ameliorating" generally refers to the reduction in the number or severity of signs or symptoms of a disease or disorder.

[0255] The terms "prevent," "preventing" and "prevention" generally refer to a decrease in the occurrence of disease or disorder in a subject. The prevention may be complete, e.g., the total absence of the disease or disorder in the subject. The prevention may also be partial, such that the occurrence of the disease or disorder in the subject is less than that which would have occurred without embodiments of the present disclosure. "Preventing" a disease generally refers to inhibiting the full development of a disease.

[0256] The term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo or ex vivo. A “pharmaceutically acceptable carrier,” after administered to or upon a subject, does not cause undesirable physiological effects. The carrier in the pharmaceutical composition must be “acceptable” also in the sense that it is compatible with the active ingredient and can be capable of stabilizing it. One or more solubilizing agents can be utilized as pharmaceutical carriers for delivery of an active compound. Examples of a pharmaceutically acceptable carrier include, but are not limited to, biocompatible vehicles, adjuvants, additives, and diluents to achieve a composition usable as a dosage form. Examples of other carriers include colloidal silicon oxide, magnesium stearate, cellulose, and sodium lauryl sulfate.

[0257] The term “about” generally refers to plus or minus 10% of the indicated number. For example, “about 10%” may indicate a range of 9% to 11%, and “about 1” may mean from 0.9- 1.1. Other meanings of “about” may be apparent from the context, such as rounding off, so, for example “about 1” may also mean from 0.5 to 1.4.

[0258] Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. EXAMPLES

[0259] Example 1 Quantification of tRNA abundance in primary human bronchial epithelial (hBE) and 16HBE14ocells.

[0260] In this example, short-read RNA-seq quantification of endogenous tRNAs in ‘WT’ 16HBE14o- cells was performed to determine tRNA abundance for reference of nd-tRNA supplementation studies. The results are shown in FIGs. 3, 7 and 8. Relative endogenous tRNA abundance were determined by a robust LC-MS / MS approach. Results from the studies can be used to determine if there is correlation between the most potent ndtRNAs ability to boost hCFTR expression in 16HBE14o- and primary hBEs and their endogenous expression. Indeed, it is anticipated that supplementation of tRNAs of low abundance will have the greatest impact on hCFTR expression and subsequent function.

[0261] Interestingly and unexpectedly, the preliminary RNA-seq based tRNA quantification did not agree with a previously published comparative tRNA microarray study in a similar cell type (Polte, C. et al. Assessing cell-specific effects of genetic variations using tRNA microarrays. BMC Genomics 20, 549, 2019). Furthermore, the preliminary analysis indicates that the abundance of tRNAs does not correlate with the number of tRNA genes that encode them, as previously hypothesized in e.g., Mauro, V. P. & Chappell, S. A. A critical analysis of codon optimization in human therapeutics. Trends Mol Med 20, 604-613, 2014.

[0262] Example 2 Supplementation of nd-tRNAs to boost CFTR Expression.

[0263] In this example, assays were carried out to generate and screen all unique nd-tRNAs to determine their ability to increase CFTR channel expression.

[0264] Briefly, a High Throughput Cloning (HTC) and Screening (HTS) plasmid (FIG. 1) was generated to encode the hCFTR-NLuc fusion cDNA behind a short ubiquitin promoter with one of 260 unique nd-tRNA sequences (1 : 1; nd-tRNA:hCFTR-NLuc), as previously published in Lueck, J. D. et al. Engineered transfer RNAs for suppression of premature termination codons. Nature Communications 10, 822, 2019). The library was then transfected into 16HBE14o- cells and measured NLuc luminescence as a proxy for hCFTR expression (FIGs. 3 and 8). The results are shown Table 1. Table 1

[0265]

[0266]

[0267]

[0268]

[0269]

[0270]

[0271]

[0272]

[0273]

[0274]

[0275]

[0276]

[0277]

[0278]

[0279]

[0280]

[0281]

[0282] Interestingly, it was found that exogenous expression of several nd-tRNAs sequences (each dot represents a unique nd-tRNA sequence) can significantly boost hCFTR-NLuc expression >2-fold (scrambled tRNA was used as control), but differ significantly in their ability to boost hCFTR expression, even across isodecoders (colored dots represent isodecoders; FIG. 8 A). Of note the nd-tRNAs with the highest impact on hCFTR-NLuc expression do not suppress codons within the NLuc CDS. As found with ACE-tRNA screen, not all tRNAs have equal function. It was predicted that the nd-tRNAs with the highest impact on hCFTR-NLuc expression would be the most abundant codons in the hCFTR transcript and / or the lowest abundant isodecoder in the “tRNAome.” However, analysis shows this correlation does not hold true, indicating that the mechanism is more complicated than tRNA abundance (FIG. 8B). Similar screens were also carried out in HEK293T cells to determine if cellular context influences nd-tRNA’ s ability to boost in hCFTR-NLuc expression (n=3 technical replicates; n=5 biological replicates).

[0283] To ensure that the presence of a c-terminal NLuc and exogenous expression are not confounding these results the top-performing nd-tRNAs (>2-fold boost in CFTR expression) are encoded into lentivirus (2 copies / virus). They are then used to generate stable nd-tRNA 16HBE14o- cell lines (MOI 4-10). Assays are then carried out to measure their impact on CFTR transcript (qRT-PCR) and protein abundance (WB) and CFTR function (Ussing ISC measurements). The top 5-7 nd-tRNA performers in 16HBE14o- cells are delivered to basal primary hBE cells (MOI 4) and differentiated for 4 weeks on filters under air-liquid interface (ALI) conditions before the transepithelial Cl- current is measured in Ussing chambers (Marquez Loza, L. I. et al. Increased CFTR expression and function from an optimized lentiviral vector for cystic fibrosis gene therapy. Mol Ther Methods Clin Dev 21, 94-106, (2021)) (n=6). Total RNA is isolated and CFTR transcript abundance is quantified by qRT- PCR (n=3). Western Blot (WB) assays are also performed to determine the impact of nd- tRNAs on the proportion of C and B band populations of CFTR protein as described in Ko, W., et al., Efficient suppression of endogenous CFTR nonsense mutations using anticodon- engineered transfer RNAs. Mol Ther Nucleic Acids 28, 685-701, doi: 10.1016 / j.omtn.2022.04.033 (2022), or Marquez Loza, L. I. et al. Increased CFTR expression and function from an optimized lentiviral vector for cystic fibrosis gene therapy. Mol Ther Methods Clin Dev 21, 94-106, (2021). Example 3 Delivery of wd-tRNAs to boost CFTR expression.

[0284] As done with nd-tRNAs, wd-tRNAs library was generated. This library consists of 189 wd-tRNAs. Briefly, every unique isotype sequence with a complementing wobble suppressing anticodon, of which there are 13, were cloned into an HTC / HTS CFTR-NLuc plasmid. 16HBE14o- cells were transfected with the plasmids in 96-well format and assays were carried out to determine the top performing wd-tRNAs by NLuc luminescence using a plate reader (n=3 technical replicates; n=5 biological replicates). The results are shown Tables 2A-2D as well as FIGs. 5-6. The naming Scheme is “tRNA-Amino acid-natural codon -isodecoder identifiers-(edited anticodon).”

[0285] Table 2A wd-tRNA / WoBell Screen

[0286]

[0287]

[0288]

[0289]

[0290]

[0291]

[0292]

[0293]

[0294]

[0295]

[0296]

[0297]

[0298]

[0299]

[0300]

[0301] Table 2B CFTR Screen

[0302]

[0303]

[0304]

[0305]

[0306]

[0307]

[0308]

[0309] Table 2C wd-tRNA / Wo Bell Screen Top 10 Hits

[0310] Table 2D CFTR- wd-tRNA / WoBell Screen Top 10 Hit Plus Top Performing From Remaining Families Not Represented

[0311] It was found that a number of wd-tRNAs boosted hCFTR expression to levels greater than what was observed with nd-tRNAs. This one-codon-at-a-time approach using individual wd-tRNAs and nd-tRNAs enables one to further dissect the impact of individual codons on CFTR channel expression and function (i.e. folding and trafficking). Following the screen in 16HBE14o- cells with exogenous CFTR-NLuc cDNA delivery, lentivirus of the top 5 performing wd-tRNA sequences are generated and used to transduce basal primary hBE cells (MOI 4) and differentiate for 4 weeks on filters under ALI conditions. Then, the transepithelial Cl- current is measured in Ussing chambers as described herein. Total RNA is isolated and endogenous CFTR transcript abundance is quantified by qRT-PCRs. WB assays are also performed to determine the impact of wd-tRNAs on the proportion of C and B band populations of CFTR protein.

[0312] Example 4 Recode hCFTR lacking individual codons influenced most by nd-tRNA and wd-tRNAs expression.

[0313] In this example, assays are carried out to determine if the increased hCFTR expression / function occurs directly from nd-tRNA- and wd-tRNA-dependent changes on CFTR biogenesis processes.

[0314] Briefly, the hCFTR cDNA is recoded to eliminate the most sensitive codons over the entire CDS and replace with the most common eukaryotic codon for that amino acid, an approach used by CAI optimization. The codon optimized CFTR CDS is synthesized by Twist Biosciences. The top 10 single codon replacement (scr-) hCFTR cDNAs are stably introduced into the AAVS1 safe harbor locus of G542X 16HBEge- cells using a HITI all-in-one plasmid system. Scr-hCFTR-NLuc expression is determined by In-Gel Fluorescence (IGF) to determine the proportion of C and B band populations of CFTR protein as described in Ko, W., et al., Efficient suppression of endogenous CFTR nonsense mutations using anticodon- engineered transfer RNAs. Mol Ther Nucleic Acids 28, 685-701, doi: 10.1016 / j.omtn.2022.04.033 (2022), or Marquez Loza, L. I. et al. Increased CFTR expression and function from an optimized lentiviral vector for cystic fibrosis gene therapy. Mol Ther Methods Clin Dev 21, 94-106, (2021). The function is determined by Ussing chamber recordings and compared to WT hCFTR-NLuc.

[0315] Here inventors will determine the impact of one codon sequence on CFTR protein biogenesis in and function in isolation. The highest performing scr-hCFTR CDS sequences are then taken and combined to determine if they provide additive benefit to CFTR function. Results from this study are important for identifying a hCFTR CDS that has augmented function for use in super-exon and total gene replacement CF therapeutic approaches.

[0316] In sum, a number of nd-tRNA and wd-tRNA were identified to increase or decrease protein expression. Accordingly, related codon replacement in CFTR CDS can be beneficial and detrimental to CFTR channel function. In preliminary screens of nd-tRNAs, one nd-tRNA isotype was found to consistently reduce hCFTR-NLuc expression (FIG. 8A), which suggest that replacing those codons with a ‘rare’ codon for less efficient translation at those positions may be of benefit. It is possible that nd-tRNA and wd-tRNAs may have boost CFTR expression and function through indirect effects, such as altering the expression of proteins involved in trafficking, degradation, and post-translational modification. Future studies can be performed to determine cellular responses to nd-tRNA and wd-tRNA expression using RNA- seq and comparative mass spectrometry. The combination of PTC suppression and “boosted” translation will result in augments CFTR function and can be pursued as a possible therapeutic.

[0317] Example 5 Piggybac Transposase assembly and usage

[0318] In this example, assays are carried out to further determine if nd-tRNA and wd-tRNA lead to functional impact on protein of interest such as CFTR. As noted before, the nomenclature “AA-anticodon-#” is used for tRNA species. The followings are a couple of names using arginine as an example, where nucleotides in parenthesis denote mutated anticodon sequence.

[0319] • Natural decoding tRNA: Arg-TCT- 1-1

[0320] • Wobble decoding tRNA: Arg-TCT-l-l(GCG).

[0321] To explore the impact of overexpressing tRNA on a protein of interest (CFTR), a PiggyBac transposase was employed to integrate out designed tRNA expression sequence into the genome of 16HBE14o- cells for downstream assessment on CFTR mRNA transcript levels / stability, protein expression, and channel function. The tRNA expression sequences used were previously described in screens described above, and were inserted in four (4) sequential, duplicate copies proceeded by a separately expressed a selection marker containing a fluorescent protein (mScarlet) and hygromycin resistant gene into a circular vector. Expression cassettes are flanked by PiggyBac ITRs (Inverted Terminal Repeat sequences) that are recognized by the transposase and direct cargo integration into the genome; the transposase is expressed from the same plasmid. Separate plasmids were created for each tRNA hit as determined from the screens (described on slide 4). Stable cells were generated through transient transfection and 48hr incubation followed by application of hygromycin selection for 7 days. Proper integration of expression cassette was determined via survival post hygromycin selection and detection of fluorescent reporter mScarlet.

[0322] These expression cassettes were used to create stable cell lines expressing tRNA of interest in 16HBE14o- cells that endogenously express CFTR to measure impact on native channel expression, mRNA stability, and channel function. After the 16HBE14o- cells were transfected, the cells were incubated for 48-72 hours before apply hygromycin selection for 7 or more days. Secondary check such as basal mScarlet expression was carried out. Example 6 Transient transfection of 4x tRNA cassettes improves endogenous CFTR mRNA transcript stability; Stable integration of 4x tRNA expression cassettes improve endogenous CFTR mRNA transcript stability

[0323] Translation elongation is monitored by various pathways that regulate mRNA transcript abundance and ribosome activity. Two major pathways are No-Go Decay (NGD) and Codon Optimality Mediated Decay (COMD). NGD is triggered by stalled or colliding ribosomes along the transcript, recruiting endonucleases, exonucleases, and factors that either dissociate the ribosome for recycling or ubiquitinate for degradation. COMD is initiated by slow decoding that results in a vacant E-site, which is then bound by N0T5 (hCNOT3), recruiting the CCR4- NOT complex for deadenylation and subsequent 3 ’-5’ degradation.

[0324] In this example, assays were carried out to show that improving elongation with supplemented nd- & wd-tRNAs alleviates these hindrances in elongation and improves stability of the transcript in a similar manner to what has been shown in traditional codon optimized transcripts.

[0325] Stable tRNA-expressing cell lines generated from above methods were seeded in 6- well plates at3xl05cells / well and harvested 48hrs later for RNA extraction. RT-qPCR was performed using primers targeting a region of the CFTR spanning exon 22-23, relative expression normalized to TATA-Binding Protein. One-way ANOVA and Tukey’s post-hoc test performed; *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. The results are shown in Table 3 below and FIG. 9. The results indicate that stable tRNA supplementation manipulates CFTR mRNA transcript stability.

[0326] Table 3 Example 7 Stable integration of 4x tRNA expression cassettes manipulate endogenous CFTR protein expression

[0327] In this example, assays are carried out to assess the impact of overexpressing tRNA on protein expression of CFTR using western blotting targeting endogenous CFTR in the stable tRNA-expressing cell lines. Cells were seeded in 6-well plates at 3xl05cells / well and cell lysates were harvested 48hrs later in RIPA buffer. Protein concentration was normalized and 15ug were ran on 10-20% SDS-PAGE gel. Total protein (triplicates) was transferred to PVDF membrane, and CFTR was immunoblotted for with a mouse anti-CFTR antibody. For CFTR, mouse anti-CFTR and goat anti-mouse HRP conjugated were used. For Na+ / K+ATPase, rabbit anti-Na / K ATPase and anti-rabbit IRDye 680RD were used. Band intensities were quantified using ImageJ software and normalized to a total protein control Na+ / K+ ATPase (immunoblotted for with Rabbit anti- Na+ / K+ ATPase). One-way ANOVA and Tukey’s post- hoc test performed; *p < 0.05. The Quantified values relative to WT CFTR expression were determined and the results are shown in FIGs.10A and 10B. the results demonstrate that stable integration of 4x tRNA expression cassettes manipulate endogenous CFTR protein expression.

[0328] Example 8 Stable integration of 4x tRNA expression cassettes manipulate endogenous CFTR channel function

[0329] In this example, assays are carried out to assess the impact of overexpressing tRNA on CFTR channel function.

[0330] Briefly, stable tRNA-expressing cell lines were seeded on onto 6.5 mm Transwell Permeable Support with 0.4 pm Inserts (Corning; no. 3413) pre-coated with collagen from rat tail (Sigma- Aldrich; no. C7661-25MG) 7 days before assay. Cells were maintained in normal cell culture media at 37°C and 5% CO2 until the formation of electrically tight epithelial monolayer was confirmed by measuring transepithelial resistance. Short-circuit current ( / sc) was measured under voltage-clamp condition to determine CFTR channel function. Cell monolayers were mounted in Ussing chambers (Physiologic Instruments, San Diego, CA, USA) filled with Ringer’s solution at 37°C. After baseline recordings, the cells were treated from the apical side with 100 pM amiloride to block epithelial sodium channels and then with 100 pM 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS) to block Ca2+-activated chloride channels. The solution in the apical side was replaced with a low Cl" solution (135mM Na-gluconate, 5mMHEPES, 0.6mMKH2PO4, 2.4 K2HPO4, 1.2mMMgCl2, 1.2mM CaCl2, and 5mM D-glucose adjusted to pH 7.4). CFTR-mediated Cl" current was measured by adding CFTR activators, 10 pM forskolin and 100 pM 3-isobutyl-l-methlyxanthine (IBMX), and CFTR inhibitor, 20 pM CFTR inhibitor- 172 (CFTRinh-172), to the apical side. Data were acquired with Acquire & Analyze 2.3 software (Physiologic Instruments). The change in Iscin response to additions of CFTR activators and CFTR inhibitor were quantified as measures of functional CFTR CD transport activity. One-Way ANOVA and Tukey’s post-hoc test; *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. The results are shown in FIGs. 11, 12, and 13A-13B, and demonstrate that tRNA supplementation manipulates CFTR channel function.

[0331] The foregoing examples and description of the preferred embodiments should be taken as illustrating, rather than as limiting the present disclosure as defined by the claims. As will be readily appreciated, numerous variations and combinations of the features set forth above can be utilized without departing from the present disclosure as set forth in the claims. Such variations are not regarded as a departure from the scope of the disclosure, and all such variations are intended to be included within the scope of the following claims. All references cited herein are incorporated by reference in their entireties.

Claims

CLAIMSWHAT IS CLAIMED IS:

1. An isolated transfer RNA (tRNA) comprising an RNA sequence encoded by a nucleic acid or DNA sequence selected from the group consisting of SEQ ID NOs: 409, 1-408, and 410-442.

2. The isolated tRNA of claim 1, wherein the nucleic acid or DNA sequence is selected from(i) the group consisting of SEQ ID NOs: 1-216 or(ii) the group consisting of SEQ ID NOs: 1-30 or(iii) the group consisting of SEQ ID NOs: 409, 254-408, and 410-442.

3. The isolated tRNA of claim 2, wherein the nucleic acid or DNA sequence is selected from(A) the group consisting of SEQ ID NOs: 1-5, 7-9, 11, 13-14, 16-26, 28-31, 33-36, 39- 40, 43-47, 50-53, 55, 58-65, 67, 69, 71-73, 76-78, 80, 83, 87, 90-92, 97-98, 100, 107, 110-111, 113, 116, 118, 125, 127, 130, 133, 140, 159, and 179, or(B) the group consisting of SEQ ID NOs: 1-5, 7-9, 11, 13-14, 16-26, 28-30, or(C) the group consisting of SEQ ID NOs: 409, 282, 292, 293, 295, 372, 410, 412, 413, and 420, or(D) the group consisting of SEQ ID NOs: 409, 277, 286, 323, 336, 346, 355, 360, 361, 364, 372, 380, 382, 384, 389, 390, 398, 403, 411, 415, 420, 424, 425, 434, 435, and 437.

4. The isolated tRNA of claim 3, wherein the nucleic acid or DNA sequence is selected from the group (C).

5. The isolated tRNA of claim 3, wherein the nucleic acid or DNA sequence is selected from the group (D).

6. The isolated tRNA of any one of claims 1-5, comprising a T-arm, a D-arm, an anticodon-arm, and an acceptor arm comprising CCA at the 3’ end.

7. The isolated tRNA of any one of claims 1-6, further comprising a heterologous sequence or a modification.

8. The isolated tRNA of any one of claims 1-7, wherein the isolated tRNA is 70 to 100 nucleotides in length.

9. A nucleic acid molecule comprising a nucleic acid sequence encoding or comprising the isolated tRNA of any one of claims 1-8.

10. The nucleic acid molecule of claim 9, wherein the nucleic acid molecule is DNA.

11. An expression cassette comprising a promoter and a nucleic acid sequence encoding the isolated tRNA of any one of claims 1-8, wherein the promoter is operably linked to the nucleic acid sequence.

12. A vector comprising the nucleic acid molecule of claim 9 or 10, or the expression cassette of claim 11.

13. The vector of claim 12, wherein the vector is a viral vector, a plasmid vector, a closed end DNA thread (CEDT) vector, or a minicircle (MC) vector.

14. The vector of claim 12 or 13, wherein the vector further comprises one or more elements selected from the group consisting of a DNA nuclear targeting sequence (DTS), a transcription enhancing 5’ leader sequence (TELS), and a Barcoding Sequence (ABS).

15. A composition comprising (i) the isolated tRNA ofany one of claims 1-8, or the nucleic acid molecule of claim 9 or 10, or the expression cassette of claim 11, or the vector of any one of claims 12-14, and (ii) a pharmaceutically acceptable carrier.

16. The composition of claim 15, wherein the carrier comprises a liposome, or a nanoparticle or an exosome.

17. A cell or a progeny thereof, said cell comprising the isolated tRNA of any one of claims 1-8, the nucleic acid molecule of claim 9 or 10, or the expression cassette of claim 11, or the vector of any one of claims 12-14.

18. A method of modulating the production of a protein in a cell, comprising introducing into the cell the isolated tRNA of any one of claims 1-8, the nucleic acid molecule of claim 9 or 10, or the expression cassette of claim 11, or the vector of any one of claims 12-14.

19. The method of claim 18, wherein the modulating is increasing and wherein the nucleic acid or DNA sequence is selected from the group consisting of(B) SEQ ID NOs: 1-5, 7-9, 11, 13-14, 16-26, and 28-30, or(C) SEQ ID NOs: 282, 292, 293, 295, 372, 409, 410, 412, 413, and 420, or(D) SEQ ID NOs: 277, 286, 323, 336, 346, 355, 360, 361, 364, 372, 380, 382, 384, 389, 390, 398, 403, 409, 411, 415, 420, 424, 425, 434, 435, and 437.

20. The method of claim 19, wherein the protein is a cystic fibrosis transmembrane conductance regulator (CFTR) protein.

21. The method of claim 20, wherein the nucleic acid or DNA sequence is selected from the group (D).

22. A method of treating a disease or condition associated with an abnormal expression level of a protein in a subject in need thereof, the method comprising administering to the subject(a) the isolated tRNA of any one of claims 1-8, or(b) a nucleic acid molecule encoding or comprising the isolated tRNA, or(c) an expression cassette comprising the nucleic acid molecule, or(d) a vector comprising the nucleic acid molecule or the expression cassette, or(e) a composition comprising the isolated tRNA, or the nucleic acid molecule, or the expression cassette, or the vector, or(f) a cell comprising the isolated tRNA, or the nucleic acid molecule, or the expression cassette, or the vector.

23. The method of claim 22, wherein the abnormal expression level is a decreased expression level of the protein.

24. The method of any one of claims 18-24, wherein the protein is a CFTR protein.

25. The method of claim 22 or 23, wherein the disease or condition is a haploinsufficiency disorder.

26. The method of claim 25, wherein the protein is encoded by a gene selected from AGGF1, ARHGAP31, BMPR2, CHD7, C0L2A1, C0L3A1, CTLA4, CTNNB1, DLL4, EHMT1, ELN, ENG, FAS, FBN1, F0XG1, GATA3, GLI3, GRN, IRF6, JAG1, KCNQ4, LMX1B, MBD5, MED13L, MITF, MNX1, MYCN, NFIA, NFIX, N0TCH1, NSD1, PAX3, PHIP, PRKAR1 A, RAI1, RBPJ, RPS14, RUNX2, SALL4, SCN1 A, SETBP1, SHANK3, SHH, SHOX, SLC2A1 / GLUT1, SOXIO, SYNGAP1, TBX1, TBX3, TBX5, TCF4, TCOF1, TGIF1, TNXB, TRPS1, WT1, and ZIC2.

27. The method of claims 25 or 26, wherein the haploinsufficiency disorder is selected from 5q-syndrome, Adams-Oliver syndrome 1, Adams-Oliver syndrome 3, Adams-Oliver syndrome 5, Adams-Oliver syndrome 6, Alagille syndrome 1, Autoimmune lymphoproliferative syndrome type IA, Autoimmune lymphoproliferative syndrome type V, Autosomal dominant deafness-2A, Brain malformations with or without urinary tract defects (BRMUTD), Carney complex type 1, CHARGE syndrome, Cleidocranial dysplasia, Currarino syndrome, Denys- Drash syndrome / Frasier syndrome, Developmental delay, intellectual disability, obesity, and dysmorphic features (DIDOD), DiGeorge syndrome (TBX1 -associated), Dravet syndrome, Duane-radial ray syndrome, Ehlers-Danlos syndrome (classic-like), Ehlers-Danlos syndrome (vascular type), Feingold syndrome 1, Frontotemporal lobar degeneration with TDP43 inclusions (FTLD-TDP), GRN-related, GLUT1 deficiency syndrome, Greig cephalopoly syndactyly syndrome, Hereditary hemorrhagic telangiectasia type 1, Holoprosencephaly 3, Holoprosencephaly 4, Holoprosencephaly 5, Holt-Oram syndrome, Hypoparathyroidism, sensorineural deafness, and renal disease (HDR), Kleefstra syndrome 1, Klippel-Trenaunay syndrome (AAGF -related), Leri-Weill dyschondrosteosis, Marfan syndrome, Mental retardation and distinctive facial features with or without cardiac defects (MRFACD), Mental retardation, autosomal dominant 1, Mental retardation, autosomal dominant 19, Mental retardation, autosomal dominant 29, Nail-patella syndrome (NPS), Phelan-McDermid syndrome, Pitt-Hopkins syndrome, Primary pulmonary hypertension 1, Rett syndrome (congenital variant), Smith-Magenis syndrome (RAI 1 -associated), Sotos syndrome 1, Sotos syndrome 2, Stickler syndrome type I, Supravalvular aortic stenosis, SYNGAP1- related intellectual disability, Treacher Collins syndrome, Trichorhinophalangeal syndrometype I, Ulnar-mammary syndrome, van der Woude syndrome 1, Waardenburg syndrome type 1, Waardenburg syndrome type 2A, and Waardenburg syndrome type 4C.

28. The method of claim 22, wherein the abnormal expression level is an increased expression level of the protein.

29. The cell of claim 17 or the method of any one of claims 18-28, wherein the cell is a mammalian cell, a vertebrate cell, an inveterate cell, a plant cell, a yeast cell, a fungus cell, or a bacterial cell.

30. The cell of claim 17 or the method of any one of claims 18-28, wherein the cell is a human cell.

31. The cell of claim 17 or the method of any one of claims 18-28, wherein the cell is a bronchial epithelial cell.

32. The method of any one of claims 22-31, wherein the administering is carried out using a viral delivery, nanoparticle, polyethylenimine (PEI), receptor-targeted polyplex, liposome, exosome, electroporation or hydrodynamic injection.

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