WO2023220342A2 - Engineered tranfer rnas - Google Patents

Engineered tranfer rnas Download PDF

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Publication number
WO2023220342A2
WO2023220342A2 PCT/US2023/021991 US2023021991W WO2023220342A2 WO 2023220342 A2 WO2023220342 A2 WO 2023220342A2 US 2023021991 W US2023021991 W US 2023021991W WO 2023220342 A2 WO2023220342 A2 WO 2023220342A2
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Prior art keywords
seq
trna
engineered
variant
sequence
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PCT/US2023/021991
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French (fr)
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WO2023220342A3 (en
Inventor
Anupama Lakshmanan
Kevin Christopher STEIN
Adrian Wrangham Briggs
Jacob Michael TOME
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Shape Therapeutics Inc.
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Publication of WO2023220342A2 publication Critical patent/WO2023220342A2/en
Publication of WO2023220342A3 publication Critical patent/WO2023220342A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/50—Methods for regulating/modulating their activity
    • C12N2320/51—Methods for regulating/modulating their activity modulating the chemical stability, e.g. nuclease-resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2330/00—Production
    • C12N2330/50—Biochemical production, i.e. in a transformed host cell
    • C12N2330/51—Specially adapted vectors

Definitions

  • Premature stop codons leading to mutations in proteins have been implicated in many severe diseases and disorders.
  • Translation of a mRNA molecule that contains a premature stop codon also referred to as a premature termination codon, PTC
  • PTC premature termination codon
  • engineered tRNA variant(s) or novel regulatory elements may improve premature termination codon (PTC) readthrough, which may be used to treat diseases and disorders.
  • PTC premature termination codon
  • engineered tRNA variant(s) comprising one or more mutations at position(s) 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62, according to canonical numbering.
  • the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 79.
  • the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79.
  • the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79.
  • the engineered tRNA variant has at least 90% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79.
  • engineered tRNA variant(s) comprising SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, or SEQ ID NO: 187.
  • engineered tRNA variant(s) comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 254, SEQ ID NO: 255, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 261, SEQ ID NO: 262, SEQ ID NO: 263, SEQ ID NO: 264, SEQ ID NO:
  • the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 54.
  • the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
  • the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
  • the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 92; optionally, wherein the sequence is not SEQ ID NO: 92 or SEQ ID NO: 53.
  • Also described herein are engineered tRNA variant(s) comprising SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 191.
  • engineered tRNA variant(s) comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 260, SEQ ID NO: 265, SEQ ID NO: 266, or SEQ ID NO: 267.
  • polynucleic acid(s) encoding the engineered tRNA variant(s) described herein, optionally wherein the polynucleotide comprises at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 196, 197, 199-233, 176-179, 180-183, 272-295, 344-353, or 354-365.
  • polynucleic acid(s) comprising nucleic acid sequence(s) encoding a tRNA, optionally an engineered tRNA, and a regulatory region, wherein the regulatory region has at least at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to sequence identity to SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, or SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336,
  • the regulatory region comprises or consists of SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region. In some embodiments, the regulatory region is 5
  • the nucleic acid sequence encoding the tRNA is selected from SEQ ID NOs 3-48, 96-115, 136-155, 196, 197, 199-233, 176-179, 180-183, 272-295, 344-353, and 354-365.
  • expression vector(s) comprising polynucleic acid(s) described herein.
  • the expression vector further comprises a promoter.
  • the promoter is a polymerase III promoter.
  • the polymerase III promoter is a polymerase III type 3 promoter.
  • the polymerase III type 3 promoter is U6.
  • the U6 is human U6; optionally, wherein the human U6 comprises at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 388.
  • the expression vector further comprises a polynucleic acid encoding a reporter protein.
  • the reporter protein is a fluorescent protein.
  • the expression vector is a lentiviral expression vector.
  • cell(s) comprising the polynucleotide(s) described herein. Also described herein are cell(s) comprising the expression vector(s) described herein. Also described herein are cell(s) expressing the engineered tRNA variant(s) described herein. [0020] In some embodiments, the cell(s) express a broken reporter protein. In some embodiments, the broken reporter protein is a broken fluorescent protein. In some embodiments, the broken fluorescent protein is broken GFP.
  • the cell expresses an engineered tRNA or an engineered tRNA variant with improved PTC readthrough efficiency as compared to a cell expressing a reference tRNA.
  • the reference tRNA is selected from SEQ ID NO: 79 and SEQ ID NO: 54.
  • the cell comprises a single copy, two copies, three copies, four copies, five copies, six copies, seven copies, or eight copies of a polynucleotide described herein, an expression vector described herein, or an engineered tRNA variant described herein. In some embodiments, the cell comprises at least two or more copies of a polynucleotide described herein, an expression vector described herein, or an engineered tRNA variant described herein.
  • Also described herein are method(s) for identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency comprising: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding an engineered tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA; introducing the expression vectors into cells stably expressing a reporter protein having a PTC; incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells into bins based on expression levels of PTC-readthrough of reporter protein; identifying a sequence of an engineered tRNA variant and/or a regulatory region of a cell from one of the bins; and, based on the sequence, identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency.
  • the expression vector(s) further comprises a reporter protein.
  • the reporter protein is a fluorescent protein.
  • the fluorescent protein is mCherry.
  • the reporter protein is a fluorescent protein having a PTC.
  • the reporter protein is a GFP protein having a PTC.
  • introducing the expression vectors into cells expressing the reporter protein comprises transfecting the cells with the expression vectors at a multiplicity of infection (MOI) suitable to achieve single copy transduction per cell.
  • MOI multiplicity of infection
  • sorting the cells comprises fluorescence-activated cell sorting (FACS).
  • FACS fluorescence-activated cell sorting
  • identifying the sequence of the tRNA variant and/or regulatory region comprises single cell sequencing of the tRNA variant and/or regulatory region of the cell. In some embodiments, identifying the sequence of the tRNA variant and/or regulatory region comprises bulk amplicon sequencing of the tRNA variant and/or regulatory region of the cell. In some embodiments, identifying the sequence of the tRNA variant and/or regulatory region comprises next-generation sequencing of the tRNA variant and/or regulatory region of the cell. In some embodiments, one of the bins is a bin having the highest expression level of PTC-readthrough of the reporter protein compared to other bins. In some embodiments, the nucleic acid sequence encoding the engineered tRNA variant further comprises a nucleic acid sequence encoding an hU6 promoter 5’ of the engineered tRNA variant.
  • range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
  • the term “about” a number refers to that number plus or minus 10% of that number.
  • the term “about” a range refers to that range minus 10% of its lowest value and plus 10% of its greatest value.
  • FIG. 1 A is a schematic of the canonical structure and numbering scheme for tRNA.
  • FIG. IB is a schematic showing exemplary positions at which the canonical tRNA structure can be mutated (schematic adapted from trna.bioinf.uni-leipzig.de).
  • FIG. 2A is a schematic showing an example workflow for generating a cloned and amplified tRNA library using a lentiviral plasmid backbone.
  • the lentiviral plasmid backbone includes a promoter, such as a U6 promoter, e.g., between the 5’ LTR and BamHI site (bottom right schematic).
  • the lentiviral plasmid backbone includes a promoter, such as a U6 promoter, e.g., between the 3’ LTR and BamHI site (bottom left schematic).
  • FIG. 2B is a schematic showing a workflow for Next Generation Sequencing (NGS) verification of cloned plasmid and packaged lentiviral tRNA libraries for three different tRNA libraries (1 - no promoter tRNA library; 2 - hU6 tRNA library; and 3 - Upstream -tRNA library), and a graph confirming that library sequence diversity is preserved during lentivirus generation when compared to the sequence diversity of the cloned plasmid.
  • NGS Next Generation Sequencing
  • FIG. 3 is a schematic showing an example of a method for measuring PTC readthrough efficiency for individual clones, e.g., variants from the libraries.
  • FIG. 4A shows the percentage of GFP+ cells after dual transfection of a broken GFP plasmid and no promoter tRNA plasmid, hU6 tRNA plasmid, or upstream-tRNA plasmid, indicating readthrough efficiency of the broken GFP.
  • FIG. 4B shows the GFP+/mCherry+ mean fluorescent intensity (MFI) ratio of cells after dual transfection of a broken GFP plasmid and a no promoter tRNA plasmid, hU6 tRNA plasmid, or upstream-tRNA plasmid, indicating readthrough efficiency of the broken GFP.
  • MFI mean fluorescent intensity
  • FIG. 5 A shows the number of unique sequences for each of the tRNA variant plasmid library pools. Bars, from left to right within each category: A-box mutant library (“Abox”), B- box mutant library (“Bbox”), and Variable Region mutant library (“Var”).
  • Abox A-box mutant library
  • Bbox B- box mutant library
  • Var Variable Region mutant library
  • CCT2.10 variant libraries with hU6 promoter (“hU6-CCT2.10 Repl”), CCT4 variant libraries with hU6 promoter (“hU6-CCT4 Repl”), CCT2.10 variant libraries with U6 promoter (hU6-CCT2.10 Rep2”), CCT4 variant libraries with hU6 promoter (“hU6-CCT4 Rep2”), CCT2.10 variant libraries without U6 promoter (“noU6-CCT2.10 Repl”), CCT4 variant libraries without U6 promoter (“noU6-CCT4 Repl”), and CCT4 variant libraries without U6 promoter (“noU6-CCT4 Rep2”).
  • FIG. 5B shows percent library coverage for tRNA variant lentivirus libraries. Bars, from left to right within each category: A-box mutant library (“Abox”), B-box mutant library (“Bbox”), and Variable Region mutant library (“Var”). Categories (sets of three bars), from left to right: CCT2.10 variant libraries with U6 promoter (“hU6-CCT2.10”), CCT4 variant libraries with U6 promoter (“hU6-CCT4”), CCT2.10 variant libraries without U6 promoter (“noU6- CCT2.10”), and CCT4 variant libraries without U6 promoter (“noU6-CCT4”).
  • Abox A-box mutant library
  • Bbox B-box mutant library
  • Var Variable Region mutant library
  • FIG. 6A shows percent library coverage for plasmid pools of Upstream -tRNA libraries.
  • the libraries are, from left to right: CCT2.10 tRNA with a 227 bp putative regulatory region (“noU6-227prom-l”), CCT2.10 tRNA with a 227 bp putative regulatory region (“noU6- 227prom-2”); CCT2.10 tRNA with a 100 bp putative regulatory region (“noU6-100prom-l”); and CCT2.10 tRNA with a 100 bp putative regulatory region (“noU6-100prom-2”).
  • FIG. 6B shows percent library coverage for pools of Upstream-tRNA libraries.
  • the libraries are, from left to right, CCT2.10 tRNA with a 100 bp putative regulatory region (“promlOObp”); and CCT2.10 tRNA with a 227 bp putative regulatory region (“prom227bp”).
  • FIG. 7 is a schematic showing an example of a high-throughput screen workflow for identifying putative regulatory elements (tRNA 5’ regions) or tRNA variants with the hU6 promoter or without a promoter with high PTC readthrough efficiency.
  • FIG. 8A shows a histogram of GFP MFI, from, front to back, untransfected cells; cells transfected with a no promoter tRNA library; cells transfected with a hU6 tRNA library; and cells transfected with a novel Upstream-tRNA library.
  • the arrow shows the tail of GFP+ cells.
  • FIG. 8B shows normalized counts of tRNA variants after sorting on GFP expression.
  • FIG. 8C shows normalized counts of the subset of variants enriched in the top bin.
  • FIG. 9 shows fractions of reads from 100 bp Upstream-tRNA libraries (“promlOObp”), 227 bp Upstream-tRNA libraries (“prom227bp”), and a spiked-in control library (ctrl combo) after sorting on GFP expression.
  • FIG. 10A is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+.
  • HEK293 cells stably expressing a broken GFP (GFP with a R74X premature stop codon inserted into the sequence) were transduced with plasmids comprising tRNA variants (tRNA constructs 1-24) and corresponding controls (hU6-CCT2.10; noU6-CCT2.10; hU6- CCT4; hU6-CCT2.10-WT; noU6-CCT4-WT; or no U6-CCT2.10 WT).
  • FIG. 10B is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+.
  • HEK293 cells stably expressing a broken GFP (GFP with a R97X premature stop codon inserted into the sequence) were transduced with plasmids comprising tRNA variants (tRNA constructs 1-24) and corresponding controls (hU6-CCT4; hU6-CCT2.10; noU6- CCT2.10; hU6-CCT2.10-WT; noU6-CCT4-WT; or no U6-CCT2.10 WT).
  • FIG. 11 A is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+.
  • HEK293 cells stably expressing a broken GFP (GFP with a R74X premature stop codon inserted into the sequence) were transduced with plasmids comprising upstream-tRNA variants (1-24) and corresponding controls (noU6-CCT2.10; hU6-CCT4-WT; hU6-CCT2.10- WT; hU6-CCT2.10; hU6-CCT4; noU6CCT4-WT; and noU6-CCT2.10-WT).
  • FIG. 1 IB is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+.
  • HEK293 cells stably expressing a broken GFP (GFP with a R74X premature stop codon inserted into the sequence) were transduced with plasmids comprising upstream-tRNA variants (1-24) and corresponding controls (noU6-CCT2.10; hU6-CCT2.10; hU6-CCT4; hU6- CCT2.10-WT; hU6-CCT4-WT; noU6-CCT2.10-WT; and noU6-CCT4-WT).
  • FIG. 12 is a set of graphs showing the median GFP-A intensity of live singlet cells from single-copy integration cell lines and corresponding controls.
  • tRNA transfer RNA
  • mRNA template messenger RNA
  • suppressor tRNAs can comprise an engineered anticodon for recognition of a premature stop codon and at least partially transform translation of a premature stop codon into a sense codon, such as, for example by adding a corrective (e.g., non-disease-causing) amino acid to the growing peptide associated with premature stop codons.
  • engineered tRNAs show improved read through stop codons in primary neuronal cultures harvested from R225X Rett model mice. Additionally, engineered tRNA variants from WO 2021/113218 showed higher readthrough of Arg>opal PTCs in cells transfected with a dual plasmid broken reporter system compared to engineered tRNAs from WO 2021/113218, and a top-performing engineered tRNA variant from WO 2021/113218 showed higher readthrough of three different PTCs in stably integrated broken fluorescent reporter systems compared to a top- performing engineered tRNA variant from WO 2021/113218.
  • engineered tRNAs variants for PTC readthrough and associated methods.
  • the engineered tRNAs variants have improved PTC readthrough efficiency compared to a reference tRNA.
  • novel regulatory elements e.g., within a regulatory region, e.g., a putative regulatory region, e.g., as described herein
  • a novel regulatory element increases transcription of a tRNA.
  • a novel regulatory element increases transcription of a suppressor tRNA.
  • a novel regulatory element increases transcription of an engineered tRNA.
  • a novel regulatory element increases transcription of an engineered tRNA variant.
  • a novel regulatory element increases transcription of a suppressor tRNA, resulting in increased PTC readthrough compared to the suppressor tRNA lacking the novel regulatory element.
  • a novel regulatory element increases transcription of an engineered tRNA, resulting in increased PTC readthrough compared to the engineered tRNA lacking the novel regulatory element. In some cases, a novel regulatory element increases transcription of an engineered tRNA variant, resulting in increased PTC readthrough compared to the engineered tRNA variant lacking the novel regulatory element.
  • the high throughput screen of engineered tRNA variants and/or putative regulatory elements can be a lentiviral high throughput screen.
  • the methods for high throughput screening comprise inserting an engineered tRNA variant and/or a putative regulatory element into a lentiviral expression vector.
  • the engineered tRNA variants and/or the tRNA (e.g., engineered tRNA or engineered tRNA variant) downstream of the putative regulatory elements being screened were not cleaved from the lentiviral construct as would potentially be expected when using an RNA virus such as a lentivirus. Therefore, the diversity of the engineered tRNA variants and/or the putative regulatory elements in the screened libraries were unexpectedly preserved, allowing for these lentiviral library screens to be used for identifying engineered tRNA variants and/or novel regulatory elements that provide increased PTC readthrough efficiency in cells having a gene with a PTC.
  • the engineered tRNA variants described herein have an improved PTC readthrough efficiency relative to a reference tRNA.
  • an engineered tRNA variant that has been mutated relative to a parental tRNA has a higher PTC readthrough efficiency than the parental tRNA.
  • an engineered tRNA variant that includes a novel regulatory element has a higher PTC readthrough efficiency than the same tRNA sequence without the novel regulatory element, or with a different regulatory element or putative regulatory element.
  • the efficiency of PTC readthrough is an in vivo efficiency of PTC readthrough.
  • the in vivo efficiency of PTC readthrough can be determined by an increase in the abundance of full-length protein, or, conversely, of a reduction in the amount of truncated protein.
  • the increase or decrease can be determined relative to a control.
  • the increase or decrease can be determined by comparing a sample from the same patient before and after treatment.
  • the increase or decrease can also be measured by comparing a sample from one source (e.g., a treated sample) and a sample from a second source (e.g., an untreated reference sample).
  • in vivo efficiency of PTC readthrough can be determined by at least partially treating a disease or condition.
  • in vivo efficiency of PTC readthrough can be measured by at least partial improvement (following treatment) of one or more symptoms associated with the disease or condition being treated.
  • the in vivo efficiency of PTC readthrough is from 1% to 100% or more, e.g., from 10% to 100%, 20% to 100%, 30% to 100%, 40% to 100%, 50% to 100%, 60% to 100%, 70% to 100%, 75% to 100%, 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, 20% to 40%, 20% to 60%, or 10% to 70%.
  • the in vivo efficiency of PTC readthrough is at least 1%, e.g., at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100%.
  • the efficiency of PTC readthrough is an in vitro efficiency of PTC readthrough, such as an in vitro efficiency of PTC suppression readthrough as determined by: (a) transfecting a first vector encoding an engineered tRNA or variant thereof and a second vector encoding a screening mRNA encoding a first green fluorescent protein into a first human cell, where the screening mRNA encoding the first green fluorescent protein can comprise a premature stop codon (this can be referred to herein as a, e.g., “broken” GFP); (b) transfecting a third vector encoding a comparable screening mRNA encoding a second green fluorescent protein into a second human cell, wherein the comparable screening mRNA does not comprise a premature stop codon; and (c) comparing an amount of fluorescence emitted from the first human cell and the second human cell.
  • a green fluorescent protein can comprise at least two premature stop codons. In some instances, the premature stop codons can
  • the in vitro efficiency of PTC readthrough is from 1% to 100% or more, e.g., 10% to 100%, 20% to 100%, 30% to 100%, 40% to 100%, 50% to 100%, 60% to 100%, 70% to 100%, 75% to 100%, 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, 20% to 40%, 20% to 60%, or 10% to 70%.
  • the in vitro efficiency of PTC readthrough is at least 1%, e.g., at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.
  • an engineered tRNA or engineered tRNA variant can be acylated with a canonical amino acid. In some cases, an engineered tRNA or engineered tRNA variant can be acylated with a non-canonical amino acid.
  • a non-canonical amino acid can comprise p- Acetylphenylalanine, p-Propargyloxyphenylalanine, p-Azidophenylalanine, O-methyltyrosine, p- lodophenylalanine, 3-Iodotyrosine, Biphenylalanine, 2-Aminocaprylic acid, p- Benzoylphenylalanine, o-Nitrobenzylcysteine, o-Nitrobenzylserine, 4,5-Dimethoxy-2- nitrobenzylserine, o-Nitrobenzyllysine, Dansylalanine, Acetyllysine, Methylhistidine, 2- Aminononanoic acid, 2-Aminodecanoic acid, 2-Aminodecanoic acid, Cbz-lysine, Boc-lysine, or Allyloxy carbonyllysine.
  • an engineered tRNA or engineered tRNA variant can be acylated with an amino acid selected provided in Table 1.
  • an engineered tRNA or eng neered tRNA variant can be a lysyl-tRNA, an arginyl-tRNA, a histidyl-tRNA, a glycyl-tRNA, an alanyl-tRNA, a valyl-tRNA, a leucyl- tRNA, an isoleucyl-tRNA, methionyl-tRNA, a phenylalanyl-tRNA, a tryptophanyl-tRNA, a prolyl-tRNA, a seryl-tRNA, a threonyl-tRNA, a cysteinyl-tRNA, a tyrosyl-tRNA, an asparaginyl tRNA, a glutaminyl-tRNA, an aspartyl-tRNA, a pyrrolysyl tRNA, a selenocytstyl t
  • an engineered tRNA or engineered tRNA variant can include a designer tRNAs (such as hybrid tRNAs made from two different naturally occurring tRNAs) or orthogonal tRNAs from other species.
  • a synthetic or chimeric orthogonal tRNA-tRNA synthetase pair can be used or included.
  • synthetic tRNAs that can interact with naturally occurring tRNA synthetases are included or used.
  • a pyrrolysyl tRNA or a selenocytstyl tRNA can be used in genetic code expansion to incorporate non-canonical amino acids into an engineered tRNA or engineered tRNA variant.
  • an engineered tRNA or engineered tRNA variant can be a lysine- tRNA, an arginine-tRNA, a histidine-tRNA, a glycine-tRNA, an alanine-tRNA, a valine-tRNA, a leucine-tRNA, an isoleucine-tRNA, methionine-tRNA, a phenylalanine-tRNA, a tryptophan- tRNA, a proline-tRNA, a serine-tRNA, a threonine-tRNA, a cysteine-tRNA, a tyrosine-tRNA, an asparagine-tRNA, a glutamine-tRNA, an aspartic acid-tRNA, or a glutamic acid-tRNA.
  • an engineered tRNA or engineered tRNA variant can be derived from a human tRNA. In some cases, an engineered tRNA or engineered tRNA variant can be derived from a non-human tRNA. In some cases, an engineered tRNA or engineered tRNA variant can be derived from a tRNA that can be orthogonal to a human tRNA. An engineered tRNA or engineered tRNA variant can be acylated by an amino-acyl synthetase that can recognize the engineered tRNA or engineered tRNA variant and acylate the engineered tRNA or engineered tRNA variant with an amino acid.
  • the engineered tRNA or engineered tRNA variant can be an engineered pre-tRNA or an engineered pre-tRNA variant.
  • Such an engineered pre-tRNA or variant thereof can comprise an intronic sequence.
  • an intronic sequence can be spliced to produce a mature engineered tRNA or variant thereof.
  • an intronic sequence can be spliced within a cell containing an engineered tRNA or variant thereof.
  • the mature engineered tRNA or engineered tRNA variant can at least partially transform an interpretation of a premature stop codon into a sense codon.
  • an engineered pre-tRNA or variant thereof with an intron can be more efficient at transforming an interpretation of a premature stop codon into a sense codon as compared to an engineered pre-tRNA or variant thereof without an intron.
  • the efficiency can be measured by transforming a vector encoding an engineered suppressor pre- tRNA or variant thereof with an intron into a primary cell line comprising a premature stop codon to which the engineered suppressor pre-tRNA or variant thereof recognizes and comparing the level of premature stop codon readthrough against another comparable cell that has been transformed with a vector encoding an engineered suppressor pre-tRNA or variant thereof without an intron.
  • determining the amount of full-length protein can be used to measure premature stop codon readthrough.
  • An engineered tRNA or variant thereof can be engineered with an anticodon sequence that base pairs with a stop codon, instead of a codon encoding for the amino acid of interest.
  • an engineered Arg tRNA or variant thereof with an anticodon sequence that base pairs with the premature stop codon can base pair with the stop codon enabling the engineered tRNA or variant thereof charged with the Arg to add the Arg to the growing polypeptide molecule, thus, effecting readthrough of the premature stop codon.
  • an engineered tRNA or variant thereof targeting a premature stop codon at a position in the growing polypeptide in which a Glutamine (amino acid of interest) can be normal (e.g., not causing disease).
  • an engineered Gin tRNA or variant thereof with an anticodon sequence that base pairs with the premature stop codon can base pair with the stop codon enabling the engineered tRNA or variant thereof charged with the Gin to add the Gin to the growing polypeptide molecule, thus, effecting readthrough of the premature stop codon.
  • Engineered tRNAs or engineered tRNA variants of the present disclosure can be engineered to recognize and suppress an amber stop codon (UAG), an ochre stop codon (UAA), or an opal stop codon (UGA), or a combination thereof.
  • an engineered tRNA or variant thereof can be engineered to suppress an amber stop codon (UAG).
  • an engineered tRNA or variant thereof can be engineered to suppress an ochre stop codon (UAA).
  • an engineered tRNA or variant thereof can be engineered to suppress an opal stop codon (UGA).
  • the present disclosure provides for compositions of multiple tRNA, engineered tRNAs, or engineered tRNA variants capable of recognizing and suppressing more than one amber stop codon, ochre stop codon, and/or opal stop codon.
  • An engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can comprise an Arginine (Arg) tRNA isodecoder.
  • An engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can comprise a Glutamine (Gin) tRNA isodecoder.
  • An engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can comprise an Arginine (Arg) tRNA isodecoder.
  • An engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can comprise a Glutamine (Gin) tRNA isodecoder.
  • an engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Gin tRNA isodecoder. In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Gin tRNA isodecoder. In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Arg tRNA isodecoder. In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Arg tRNA isodecoder.
  • An engineered tRNA or variant thereof with an anticodon configured to base pair with any one of the stop codons described herein can be charged with any one of the amino acids (canonical or noncanonical) described herein.
  • RNAs can encode polypeptides. Some embodiments described herein relate to polypeptide(s). Polypeptide can include full-length polypeptides or fragments of full-length polypeptides. For example, a fragment of a full-length polypeptide can be encoded by an mRNA with a premature stop codon, whereas a full-length polypeptide can be encoded by an mRNA without a premature stop codon.
  • an mRNA targeted by the engineered tRNA or variant thereof can comprise one, two, three, four, or five premature stop codons. Accordingly, an engineered tRNA or variant thereof as described herein can produce readthrough of the one or more premature stop codons, at least partially restoring a substantially full-length polypeptide. In some cases, at least partially restoring a substantially full-length polypeptide can comprise at least partially treating a disease or condition.
  • an engineered tRNA or variant thereof can restore 30% to 99% of PTC readthroughs, e.g., 40% to 45%, 40% to 50%, 40% to 55%, 40% to 60%, 40% to 65%, 40% to 70%, 40% to 75%, 40% to 80%, 40% to 85%, 40% to 90%, 40% to 95%, 45% to 50%, 45% to 55%, 45% to 60%, 45% to 65%, 45% to
  • an engineered tRNA or variant thereof can restore at least 40% of PTC readthroughs.
  • two or more stop codons can be the same type of stop codon.
  • two or more stop codons can be different types of stop codons.
  • one type of engineered tRNA or variant thereof can be used to at least partially restore a full- length polypeptide when a target mRNA contains two or more stop codons that are the same type of stop codon.
  • more than one type of engineered tRNA or variant thereof can be used to at least partially restore a full-length polypeptide when a target mRNA contains two or more stop codons that are different types of stop codons.
  • the engineered tRNA or engineered tRNA variant can reduce or prevent nonsense-mediated decay of the target mRNA.
  • the engineered tRNAs disclosed herein can be modified to produce an engineered tRNA variant.
  • the engineered tRNAs disclosed herein can be modified relative to a reference tRNA.
  • the modification can be a mutation in a sequence of the engineered tRNA, such as an insertion or a substitution of a nucleotide.
  • the sequence that can be mutated can be a DNA sequence, a tRNA sequence or a pre-tRNA sequence.
  • the modification can be a chemical modification of a nucleotide in the sequence of the engineered tRNA.
  • the chemical modification can comprise a methyl group, a fluoro group, a methoxyethyl group, an ethyl group, a phosphate group, an amide group, an ester group, or any combination thereof.
  • the engineered tRNA or the variant thereof can comprise a chemical modification comprising a methyl group, a fluoro group, a methoxyethyl group, an ethyl group, a phosphate group, an amide group, an ester group, or any combination thereof.
  • the reference tRNA can be a wild-type tRNA or an engineered tRNA, such that the engineered tRNA has more than one mutation.
  • the wild-type tRNA or the engineered tRNA can be referred to as a “backbone” or “parental” tRNA.
  • Mutations can be made in any region of the engineered tRNA including, but not limited to, the acceptor stem, anticodon stem, D-loop, D stem, and T-loop, T-stem, or the variable region or loop to produce the engineered tRNA variants of the present disclosure.
  • substitutions of nucleotides in the acceptor stem and anticodon stem to increase Watson-Crick base pairing can stabilize the acceptor and anticodon stems of the engineered tRNA.
  • FIG. 1 A The canonical tRNA secondary structure and numbering scheme is shown FIG. 1 A. See Laslett and Canback, “ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences,” Nucleic Acids Research 32(1): 11-16 (2004).
  • the acceptor stem is encoded by residues 1-7 and 66-72.
  • the D-stem is encoded by residues 10-13 and 22-25.
  • the 8-11 residue D-loop is encoded by residues 14-21 (optionally comprising residues 17A, 20A, and 20B).
  • the anticodon stem is encoded by residues 27-31 and 39-43.
  • the anticodon loop is encoded by residues 32-38, with the anticodon being encoded by residues 34-36.
  • the variable region is encoded by residues 44-48.
  • the T-stem is encoded by residues 49-53 and 61-65.
  • the T-loop is encoded by residues 54-60.
  • the CCA end is encoded by residues 73+.
  • the A-box is encoded by residues 9-18.
  • the B-box is encoded by residues 53-61.
  • the engineered tRNA variant can comprise a mutation in a T-loop, a T-stem, a D-loop, a D-stem, a variable loop, an anticodon stem, or an anticodon loop.
  • the mutation can be relative to the nucleic acid sequence, e.g., of any of those in Table 2, Table 3, or Table 4.
  • the engineered tRNA variant comprises 1, 2, 3, 4, 5, 6, 7, 8, 9,
  • the engineered tRNA variant comprises from 1 to 15 mutations, e.g., 1 to 14, 1 to 13, 1 to 12, 1 to 11, 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6,
  • the engineered tRNA variant comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, or at least 15 mutations, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4.
  • the engineered tRNA variant comprises no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9, no more than 10, no more than 11, no more than 12, no more than 13, no more than 14, or no more than 15 mutations, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4.
  • the engineered tRNA variant comprises mutation(s) in a T- loop, a T-stem, a D-loop, a D-stem, a variable loop, an anticodon stem, an anticodon loop, or a combination thereof, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4.
  • the engineered tRNA variant comprises a mutation in the anticodon (e.g., nucleic acids 33-35 in any of the sequences in Table 2, Table 3, or Table 4. In some cases, the engineered tRNA variant does not comprise a mutation in the anticodon (e.g., nucleic acids 33-35 in any of the sequences in Table 2, Table 3, or Table 4.
  • an engineered tRNA or an engineered tRNA variant such as those provided in Table 2, Table 3, and Table 4.
  • a reference made herein to an engineered tRNA or engineered tRNA variant can include a DNA sequence, e.g., of Table 2, Table 3, and Table 4.
  • a reference made herein to an engineered tRNA or engineered tRNA variant can include an RNA sequence, e.g., of Table 2, Table 3, and Table 4, that is encoded by a polynucleotide comprising a DNA sequence, e.g., of Table 2, Table 3, and Table 4.
  • A can be a nucleobase comprising adenosine.
  • A can be a nucleoside comprising a ribose or a deoxyribose, and adenosine.
  • A can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and adenosine.
  • T can be a nucleobase comprising thymine. In some embodiments, T can be a nucleoside comprising a ribose or a deoxyribose, and thymine. In some embodiments, T can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and thymine. In some embodiments, U can be a nucleobase comprising uracil. In some embodiments, U can be a nucleoside comprising a ribose or a deoxyribose, and uracil.
  • U can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and uracil.
  • C can be a nucleobase comprising cytosine.
  • C can be a nucleoside comprising a ribose or a deoxyribose, and cytosine.
  • C can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and cytosine.
  • G can be a nucleobase comprising guanine.
  • G can be a nucleoside comprising a ribose or a deoxyribose, and guanine. In some embodiments, G can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and guanine.
  • the engineered tRNA or engineered tRNA variant comprises modifications, e.g., post-transcriptional modifications. See, e.g, Suzuki, “The Expanding World of tRNA Modifications and their Disease Relevance,” Nature Reviews Molecular Cell Biology 22:375-92 (2021), which is hereby incorporated by reference in its entirety.
  • the modification(s) are selected from ac 4 C ( ri-acetylcytidine), acp 3 U (3-(3-amino-3- carboxypropyl)uridine), Cm (2'- ⁇ -methylcytidine), cmnm 5 s 2 U (5-carboxymethylaminomethyl-2- thiouridine), cmnm 5 U (5-carboxymethylaminomethyluridine), D (dihydrouridine), EC (5- formylcytidine), CCm (5-formyl-2'-O-methylcytidine), galQ (galactosyl-queuosine), Gm (2'- ⁇ - methylguanosine), hm 5 C (5-hydroxymethylcytidine), hm 5 Cm (2'- ⁇ 9-methyl-5- hydroxymethylcytidine), I (inosine), i 6 A (A ⁇ -isopentenyladenosine), m 3 A (1 -methyladenos
  • engineered tRNAs and variants thereof for suppression of opal stop codon(s) are shown in Table 2.
  • the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5A termination signal).
  • the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail. Table 2.
  • Exemplary suppressor tRNA sequence for opal stop codons are shown in Table 2.
  • engineered tRNAs and variants thereof for suppression of ochre stop codon(s) are shown in Table 3.
  • the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5A termination signal).
  • the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail.
  • engineered tRNAs and variants thereof for suppression of ochre stop codon(s) are shown in Table 4.
  • the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5A termination signal).
  • the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail.
  • Mutations can be made in any region of the engineered tRNA that suppresses a stop codon including, but not limited to, the acceptor stem, anticodon stem, D-loop, D stem, and T- loop, T-stem, or the variable region or loop to produce the engineered tRNA variants of the present disclosure.
  • substitutions of nucleotides in the acceptor stem and anticodon stem to increase Watson-Crick base pairing can stabilize the acceptor and anticodon stems of the engineered tRNA.
  • an engineered tRNA or a variant thereof comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to a tRNA, engineered tRNA, or engineered tRNA variant sequence, e.g., as shown Table 2, Table 3, or Table 4.
  • an engineered tRNA or a variant thereof comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to a tRNA, engineered tRNA, or engineered tRNA variant sequence, e.g., as shown Table 2, Table 3, or Table 4.
  • an engineered tRNA or variant thereof comprises a sequence that has at least 70% identity to a tRNA, engineered tRNA, or engineered tRNA variant sequence in Table 2, Table 3, or Table 4, e.g., at least 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a tRNA, engineered tRNA, or engineered tRNA variant sequence in Table 2, Table 3, or Table 4.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, or 10, mutations in the A-box region (e.g., corresponding to residues 9-18 of FIG. 1A, or a corresponding region of a sequences in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, or 9, mutations in the B-box region (e.g., corresponding to residues 53-61 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14, mutations in the acceptor stem region (e.g., corresponding to residues 1-7 and 66-72 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, or 8, mutations in the D-arm region (e.g., corresponding to residues 10-13 and 22-25 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 1, or 11, mutations in the D-loop region (e.g., corresponding to residues 14- 21 of FIG. 1A, or a corresponding region of a sequences in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, mutations in the anti codon- stem region (e.g., corresponding to residues 27-31 and 39-43 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, or 7, mutations in the anticodon loop region (e.g., corresponding to residues 32-38 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • a reference sequence e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, or 3, mutations in the anticodon (e.g., corresponding to residues 34-36 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • the engineered tRNA or variant thereof does not comprise a mutation in the anticodon (e.g., corresponding to residues 34-36 of FIG.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, mutations in the variable region (e.g., corresponding to residues 44-48 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, mutations in the T-stem (e.g., corresponding to residues 49-53 and 61-65 of FIG.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, or 7, mutations in the T-loop (e.g., corresponding to residues 54-60 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
  • Exemplary mutations are set forth in Table 5.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 of the mutations shown in Table 5.
  • the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, of the A-box mutations shown in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, of the Variable Region mutations shown in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, of the B-box mutations shown in Table 5.
  • the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, but none of the Variable Region or B-box mutations in Table 5. [0109] In some cases, the engineered tRNA or variant thereof comprises one or more Variable Region mutations as shown in Table 5, but none of the A-box or B-box mutations in Table 5.
  • the engineered tRNA or variant thereof comprises one or more B-box mutations as shown in Table 5, but none of the Variable Region or A-box mutations in Table 5.
  • the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5 and one or more of the Variable Region mutations in Table 5.
  • the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, and one or more of the B-box mutations in Table 5.
  • the engineered tRNA or variant thereof comprises one or more B-box mutations as shown in Table 5, and one or more of the Variable Region mutations in Table 5.
  • the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, one or more of the Variable Region mutations in Table 5, and one or more of the B-box mutations in Table 5 [0112] In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5 and one or more of the Variable Region mutations in Table 5, but none of the B-box mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5 and one or more of the B-box mutations in Table 5, but none of the Variable Region mutations in Table 5.
  • the engineered tRNA or variant thereof comprises one or more B-box mutations as shown in Table 5 and one or more of the Variable Region mutations in Table 5, but none of the A-box mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, one or more of the Variable Region mutations in Table 5, and one or more of the B-box mutations in Table 5, but none of the mutations described herein.
  • the format Xi>X2 indicates that Xi can be substituted for X2.
  • the number preceding Xi>X2 indicates the nucleotide position with reference to the DNA sequence encoding the engineered tRNA.
  • Thymine (“T”) can be present in the DNA context, and when in reference to the tRNA sequence, should be understood to refer to uracil (“U”).
  • T Thymine
  • U uracil
  • the mutation can be a change from the reference residue to any residue other than the original residue in the reference sequence.
  • N could be a mutation to A, G, C, or T.
  • RNA sequence In the context of a RNA sequence, “N” could be a mutation to A, G, C, or U.
  • an engineered tRNA variant comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to an engineered tRNA variant sequence, e.g., as shown Tables 6A-6D.
  • an engineered tRNA variant comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to an engineered tRNA variant sequence, e.g., as shown Tables 6A-6D.
  • an engineered tRNA variant comprises a sequence that has at least 70% identity to an engineered tRNA variant sequence in Tables 6A-6D, e.g., at least 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an engineered tRNA variant sequence in Tables 6A-6D.
  • engineered tRNA variants are shown in Tables 6A-6D.
  • the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5 A termination signal).
  • the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail.
  • expression of the engineered tRNA and variants thereof described herein is driven by regulatory element(s) such as enhancer and/or promoter sequence(s).
  • regulatory element(s) such as enhancer and/or promoter sequence(s).
  • the engineered tRNA(s) or variant(s) thereof are on the same nucleic acid molecule(s) as the regulatory element(s). In some cases, the engineered tRNA(s) or variant(s) thereof are on different nucleic acid molecule(s) as the regulatory element(s).
  • the regulatory element is a known regulatory element, e.g., a promoter (e.g., as described herein).
  • the promoter is a Polymerase III promoter.
  • the promoter is a Polymerase III type 1 promoter.
  • the promoter is a Polymerase III type 2 promoter.
  • the promoter is a Polymerase III type 3 promoter.
  • the Polymerase III type 3 promoter is a 7SK, U6, or Hl promoter.
  • the promoter is a human promoter.
  • the regulatory element is a putative regulatory element, e.g., a tRNA upstream region (e.g., as described herein). In some cases, the putative regulatory element is in a putative regulatory region. In some cases, the putative regulatory element comprises a promoter or enhancer. In some cases, the putative regulatory element is a novel regulatory element. In some cases, the putative regulatory element comprises a novel promoter or enhancer.
  • the engineered tRNA and variants thereof described herein are driven by a putative regulatory element, e.g., within a region 5’ of a known tRNA sequence (a “putative regulatory region”).
  • a putative regulatory region comprises from 20 to 500 bp 5’ of a known tRNA sequence.
  • the putative regulatory region comprises from 20 nucleotides to 500 nucleotides 5’ of a known tRNA sequence.
  • the putative regulatory region is from 20 nucleotides to 500 nucleotides in length, e.g., 20 to 450, 20 to 400, 20 to 350, 20 to 300, 20 to 250, 20 to 200, 20 to 150, 20 to 100, 20 to 50, 50 to 500, 50 to 450, 50 to 400, 50 to 350, 50 to 300, 50 to 250, 50 to 200, 50 to 150, 50 to 100, 100 to 500, 100 to 450, 100 to 400, 100 to 350, 100 to 300, 100 to 250, 100 to 200, 100 to 150, 150 to 500, 150 to 450, 150 to 400, 150 to 350, 150 to 300, 150 to 250, 150 to 200, 200 to 500, 200 to 450, 200 to 400, 200 to 350, 200 to 300, 200 to 250, 250 to 500, 250 to 450, 250 to 400, 250 to 350, 250 to 300, 300 to 500, 300 to 450, 300 to 400, 300 to 350, 350 to 500, 350 to 450, 350 to 400, 400 to 500, 400, 400 to 500, 400, 300
  • the putative regulatory region comprises 100, or about 100, bases 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises 227, or about 227, bases 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises 100, or about 100, nucleotides 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises 227, or about 227, nucleotides 5’ of a polynucleotide encoding a known tRNA.
  • the putative regulatory region 5’ of a polynucleotide encoding a known tRNA is engineered to be 5’ of a polynucleotide encoding a different tRNA (e.g., a polynucleotide encoding a tRNA that is not that known tRNA).
  • the putative regulatory region comprises AGGCCATATGCTATTTTTGTACAGTAATCCTTTCCTTTTTTTCCCCATTTTTCTTAAAT CTTAAAAATAAGACTGAATTCTGATATCAAGAGTTAAGGTC (SEQ ID NO: 192), CTTTTAATTTATTTCTTAAACTTTATTTAGACTTAAACACTATTTACCTAGGATTTTAG CTGCATAATAGATTGATTGTTAAATGTTTGCTCTCTGTGGC (SEQ ID NO: 193), CTCTGGAGTGAGGCTTCATTGGTCCCAGGTGAGCGTTTCGTTGCCAGCTCGTTGCGC GAGGTCTGAATGCACAGTGGAAACAACTTAGGGTGGGTATGGGAAAAGAAGAAAC ATATTTCAGAAGCACTCGCCAATATAAATTTTTAAAAATAAAGATCTTAATACAGTA ATTTGACTAGAGCTAGTAGACTGAATGAGTATGGACACCAGAAATATGCTTTCGGCT G (SEQ ID NO: 194), or CAGGGGCAGA
  • the putative regulatory region comprises
  • TCTTTCCAGTTCCGAGAAGTTCAGAAAAGTTTCTTCGGTGATTGGAATAACGTTCGC CTTTAAACTTCTCAAGAGATTTAGGGTGGGTTTTAGTATGCGG SEQ ID NO: 330
  • TCCCCCCCCACCGCTCAGAGAGCAGGATGCTGAGATGGCTCGGTGATGCAGAAGGT ATGTGCTTTTTCAGTTCTGGTGCTGATGCTGTGTGTGTGGTGAG SEQ ID NO: 331
  • CAGCTTCAGTAGCGCAGAGGCGGCGGTGGCGAGAGGTGCGGCGAAGGAGGCAGAG GCACTTATGCTTGTCAGGTGGGTCACGGCAGTTTCTCATAGCACT (SEQ ID NO: 334); TGGAATTTTACTCAAGCTAACATCCTATTCAGTAGCCGGAATGCTAGGAGCATAACA TCAATCTATAAGATGAAAGGAAGAGAAACTAAAAGCAGACGAG (SEQ ID NO: 335); AATCGGAGTCTCCTCCTAGCTCTCTGCTCTGCTGGGTCCCCACCTCTGGCCACGAGGAC TCCACGAAGGCCACAAAGACAAGCCGGAGGCTACGGGGCGTGT (SEQ ID NO: 336); GCTTTAGCTGACTGTAGCCAGTGTTTCTTTGGTGGGACAACGCAACTATCACTGCAA CATTATCTCTATAGGAGAATTTAAAGAACCCTGACGCCTACCG (SEQ ID NO: 337); TTTAAATTCGAAAGGAATGTTAGACACCAAAGGT
  • the putative regulatory region comprises at least 25 bases (e.g., at least 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 bp) of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333
  • the putative regulatory region comprises at least 20 bases of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343.
  • the putative regulatory region comprises from 20 bases to 100 bases of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343.
  • the putative regulatory region comprises 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 bp, or any number of bp therebetween, of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 34
  • the putative regulatory region comprises at least 100 bases (e.g., at least 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, or 225 bp) of SEQ IDNO: 194 or SEQ ID NO: 195.
  • the putative regulatory region comprises from 20 bases to 100 bases of SEQ IDNO: 194 or SEQ ID NO: 195.
  • the putative regulatory region comprises 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, or 225 bp, or any number of bp therebetween, of SEQ IDNO: 194 or SEQ ID NO: 195.
  • the putative regulatory region comprises a sequence that has from 70% to 100% identity (e.g., 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, or 99% to 100% identity) to SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO:
  • the putative regulatory region is engineered to be 5’ of a polynucleotide coding for a tRNA. In some cases, the putative regulatory region is engineered to be 5’ of an engineered tRNA and variants thereof described herein. For example, the putative regulatory region is 5’ of an engineered tRNA or variant thereof comprising from 70% to 100% sequence identity (e.g., 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, or 99% to 100% identity) to any one of SEQ ID NOs: 3-48, 96-115, 136-155, 196, 197, 199-222, 227, 228, 229, 272-295, or 344-365.
  • 70% to 100% sequence identity e.g., 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, or 99% to 100% identity
  • the putative regulatory region engineered to 5’ of the polynucleotide coding for the tRNA is in a vector (e.g., a viral vector) as disclosed herein.
  • the method comprises: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding a tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA, e.g., as described herein and, optionally, an intact reporter protein; introducing the expression vectors into cells stably expressing a broken PTC readthrough reporter protein (e.g., a PTC readthrough reporter protein with engineered premature stop codons, e.g., a fluorescent protein with engineered premature stop codons, e.g., GFP with engineered premature stop codons); incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells based on expression levels of unbroken PTC readthrough reporter protein; identifying the sequence of the engineered tRNA variant(s) and/or regulatory regions of one or more of the
  • the library comprises from 200 to 100,000 lentiviral expression vectors to be screened. In some cases, the library comprises about 200, 500, 1,000, 5,000, 10,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, or 100,000 lentiviral expression vectors to be screened. In some cases, the library comprises 100,000 or more lentiviral expression vectors to be screened.
  • Reporter proteins can be used to identify, for example, cells that comprise a tRNA variant encoding sequence (e.g., plasmid).
  • PTC readthrough reporter protein e.g., when a cell expresses both an engineered tRNA variant and a “broken” reporter protein.
  • the reporter protein can be referred to as a “PTC readthrough reporter protein.”
  • the reporter protein or PTC readthrough reporter protein is a fluorescent protein.
  • the reporter protein is a green fluorescent protein, yellow fluorescent protein, or red fluorescent protein.
  • the reporter protein is EBFP, ECFP, EGFP, YFP, mHoneydew, mBanana, mOrange, tdTomato, mTangerine, mStrawberry, mCherry, mGrapel, mRaspberry, mGrape2, or mPlum.
  • the reporter protein and PTC readthrough reporter proteins are different, e.g., different fluorescent proteins.
  • lentiviral expression vectors comprising the engineered tRNA variants, e.g., as described herein (with a promoter, for example with a human U6 promoter, or without a promoter).
  • lentiviral expression vectors comprising putative regulatory region(s) 5’ upstream of a tRNA, such as a suppressor tRNA, engineered tRNA, or engineered tRNA variant.
  • An exemplary lentiviral expression vector is shown in FIG. 2A.
  • the lentiviral expression vector(s) comprise promoter(s).
  • the promoter is human U6.
  • the promoter is a Polymerase III promoter. In some cases, the promoter is a Polymerase III type 1 promoter. In some cases, the promoter is a Polymerase III type 2 promoter. In some cases, the promoter is a Polymerase III type 3 promoter. In some cases, the Polymerase III type 3 promoter is a 7SK, U6, or Hl promoter. In some cases, the promoter is a human promoter.
  • the lentiviral expression vector(s) comprise reporter protein(s), e.g., as described above.
  • the lentiviral expression vector(s) comprise selectable marker(s).
  • the selectable marker is an antibiotic resistance gene.
  • the selectable marker is a puromycin resistance gene.
  • cell(s) are selected using the selectable marker, for example, to confirm successful transduction.
  • the lentiviral expression vector(s) described herein are introduced into cell(s).
  • the cell(s) are mammalian cell(s).
  • the cell(s) are human cell(s).
  • the cell(s) are from a cultured cell line.
  • the cell(s) express a reporter protein.
  • the cell(s) express a reporter protein having a PTC, which is also referred to as a broken reporter protein.
  • the cell(s) stably express a broken reporter protein.
  • the broken reporter protein is a broken fluorescent protein.
  • the broken reporter protein is broken GFP (e.g., a GFP having a PTC).
  • the transduction is performed at a multiplicity of infection such that cells expressing, e.g., stably expressing, a single copy of the engineered tRNA or variant thereof per cell are obtained.
  • the cell(s) expressing the lentiviral expression vector(s) described herein are sorted, e.g., on PTC readthrough efficiency, e.g., based on expression level of an intact version of the protein that the cell(s) express, such expression of the full-length protein version of a broken reporter protein.
  • a subset of the sorted cell(s), e.g., those with high PTC readthrough efficiency, e.g., based on expression level of an intact version of the protein that the cell(s) express as a broken reporter protein, are identified by sequence.
  • the identification comprises sequencing the engineered tRNA and/or putative regulatory region sequence(s).
  • compositions comprising the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells. Also provided herein are compositions comprising putative regulatory regions 5’ upstream of tRNAs, such as the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells.
  • compositions comprising regulatory elements 5’ upstream of tRNAs, such as the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells.
  • compositions comprising U6 promoters 5’ upstream of tRNAs, such as the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells.
  • tRNA, engineered tRNAs, or engineered tRNA variants are methods of generating the tRNA, engineered tRNAs, or engineered tRNA variants, the polynucleotide encoding the tRNA, engineered tRNAs, or engineered tRNA variants, or the pharmaceutical compositions described herein.
  • putative regulatory regions, regulatory elements, and/or promoters such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants
  • the method can include aspects disclosed herein.
  • a vector can be produced that can comprise a plurality of promoters, a genetic sequence encoding one or more tRNA, engineered tRNAs, or engineered tRNA variants, and/or a genetic sequence encoding putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants.
  • the vector can comprise a first promoter (e.g., an hU6, or a mU6 promoter), a second promoter (e.g., an hU6, or a mU6 promoter), a third promoter (e.g., a human cytomegalovirus (CMV) promoter), a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide.
  • a first promoter e.g., an hU6, or a mU6 promoter
  • a second promoter e.g., an hU6, or a mU6 promoter
  • a third promoter e.g., a human cytomegalovirus (CMV) promoter
  • CMV human cytomegalovirus
  • the vector can comprise a putative regulatory region, regulatory element, and/or promoter, and a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide.
  • the polynucleotide can comprise a 5’ ITR upstream of the promoter. In some cases, the polynucleotide can comprise a 3’ ITR downstream of the reporter gene.
  • the reporter gene can comprise one or more genes encoding for mCherry, green fluorescent protein (GFP), or P-galactosidase.
  • the first promoter or the second promoter can comprise a U6 promoter (e.g., a human U6 (hU6)).
  • the U6 promoter can be a human U6 promoter or a mouse U6 promoter.
  • the hU6 promoter can comprise at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 388.
  • the U6 promoter can be methylated.
  • the third promoter can be a human cytomegalovirus (CMV) promoter.
  • the vector can be produced by purification or isolation.
  • the promoter can be a U7 promoter.
  • the promoter can be a PolIII promoter.
  • the present disclosure provides viral vectors packaging tRNA, engineered tRNAs, or engineered tRNA variants, putative regulatory regions, regulatory elements, promoters, stuffer sequences, and any combination thereof.
  • the viral vectors of the present disclosure can package one or more copies of the engineered tRNA or variant thereof.
  • the viral vectors of the present disclosure can package 2 copies of the tRNA, engineered tRNAs, or engineered tRNA variants.
  • the viral vectors of the present disclosure can package 3 copies of the tRNA, engineered tRNAs, or engineered tRNA variants.
  • the viral vectors of the present disclosure can package 4 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package 6 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package more than 6 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. Viral vectors of the present disclosure can package from 1 to 200, from 1 to 100, from 50 to 100, from 20 to 40, from 10 to 50, or from 1 to 70 copies of the tRNA, engineered tRNAs, or engineered tRNA variants.
  • the viral vectors of the present disclosure can package at least 1, 10, 20, 30, 40, 50, 70, 100, 200, 300, 400 or more copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package at most about 400, 300, 200, 100, 70, 50, 40, 30, 20, 10, 2, or less copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, a putative regulatory region is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants.
  • a regulatory element is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants.
  • a promoter is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants.
  • a hU6 promoter is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants.
  • One or more tRNA, engineered tRNAs, or engineered tRNA variants, and/or one or more putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants can be packaged in a vector, including but not limited to a plasmid, an AAV vector, a lentivirus vector, or any other vector system.
  • the vectors disclosed herein can also encode for a marker or a reporter gene, such as GFP or mCherry.
  • the vectors disclosed herein can also encode for an upstream promoter, such as human U6 (hU6).
  • engineered tRNA or variants thereof, markers, and/or stuffer sequences are packaged in a viral vector are under the control of a regulatory element, such as a promotor (e.g., a mouse U6 (mU6) or a human U6 (hU6) promoter).
  • a promotor e.g., a mouse U6 (mU6) or a human U6 (hU6) promoter.
  • engineered tRNAs suppressors or variants thereof, markers, regulatory elements, and/or stuffer sequences are packaged in a viral vector without a promoter.
  • a vector can comprise a plurality of promoters, a genetic sequence encoding one or more tRNA, engineered tRNAs, or engineered tRNA variants, and/or a genetic sequence encoding putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants.
  • the vector can comprise a first promoter (e.g., an hU6, or a mU6 promoter), a second promoter (e.g., an hU6, or a mU6 promoter), a third promoter (e.g., a human cytomegalovirus (CMV) promoter), a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide.
  • a first promoter e.g., an hU6, or a mU6 promoter
  • a second promoter e.g., an hU6, or a mU6 promoter
  • a third promoter e.g., a human cytomegalovirus (CMV) promoter
  • CMV human cytomegalovirus
  • the vector can comprise a putative regulatory region, regulatory element, and/or promoter, and a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide.
  • the polynucleotide can comprise a 5’ ITR upstream of the promoter. In some cases, the polynucleotide can comprise a 3’ ITR downstream of the reporter gene.
  • the reporter gene can comprise one or more genes encoding for mCherry, green fluorescent protein (GFP), or P-galactosidase.
  • the first promoter or the second promoter can comprise a U6 promoter (e.g., a human U6 (hU6).
  • the U6 promoter can be a human U6 promoter or a mouse U6 promoter.
  • the U6 promoter can be methylated.
  • the third promoter can be a human cytomegalovirus (CMV) promoter.
  • the vector can be purified or isolated.
  • the vectors of the present disclosure can also package a stuffer sequence, to ensure successful production of virus particles that package the entire genome to be delivered.
  • a naturally occurring stuffer sequence e.g., DNA from strawberry or lambda phage
  • the stuffer sequence can be a fully synthetic sequence.
  • vectors provided herein package from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence.
  • vectors provided herein package putative regulatory regions, from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence.
  • vectors provided herein package regulatory elements, from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence.
  • vectors provided herein package promoters, from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence.
  • vectors provided herein package a hU6 promoter, from 1 to 6 engineered tRNAs and a stuffer sequence.
  • a spacer sequence can include a stuffer sequence or a filler sequence.
  • a spacer sequence, a stuffer sequence, or a filler sequence can be referred to interchangeably in some embodiments.
  • the vector can comprise one or more spacer sequences to place a sequence of an engineered tRNA or a variant thereof in different distances from an ITR. In some cases, the vector can comprise one or more spacer sequences to place a sequence of putative regulatory region, regulatory element, and/or promoter upstream of an engineered tRNA or a variant thereof in different distances from an ITR.
  • the spacer sequence can comprise a 6 nucleotides (nts) long sequence.
  • the spacer sequence can comprise 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 1000 nucleotides or any number of nucleotides in between any of the two numbers of nucleotides mentioned herein.
  • the space sequence can comprise between about 10 nts to about 100 nts, about 100 nts to about 500 nts, about 50 to about 600 nts, or about 200 nts to about 1000 nts. In some cases, the spacer sequence can comprise less than 6 nts or more than 1000 nts. In some cases, the spacer sequence can comprise a stuffer sequence.
  • the stuffer sequence can be about 25, about 50, about 100, about 150, about 200, about 250, or about 300 nucleotides in length.
  • the stuffer sequence can be 25, 50, 100, 150, 200, 250, or 300 nucleotides in length, or a range of lengths encompassing any two of the aforementioned numbers of nucleotides.
  • the stuffer sequence can comprise at least 25 nucleotides, at least 50 nucleotides, at least 100 nucleotides, at least 150 nucleotides, at least 200 nucleotides, at least 250 nucleotides, or at least 300 nucleotides. In some embodiments, the stuffer sequence is at least about 50 nucleotides, at least about 100 nucleotides, at least about 150 nucleotides, or at least about 200 nucleotides.
  • the stuffer sequence can comprise at least 250 nucleotides, at least 300 nucleotides, at least 350 nucleotides, at least 400 nucleotides, at least 450 nucleotides, or at least 500 nucleotides. In some embodiments, the stuffer sequence can comprise no more than 25 nucleotides, no more than 50 nucleotides, no more than 100 nucleotides, no more than 150 nucleotides, no more than 200 nucleotides, no more than 250 nucleotides, or no more than 300 nucleotides.
  • the stuffer sequence is no more than about 50 nucleotides, no more than about 100 nucleotides, no more than about 150 nucleotides, or no more than about 200 nucleotides. In some embodiments, the stuffer sequence can comprise no more than 250 nucleotides, no more than 300 nucleotides, no more than 350 nucleotides, no more than 400 nucleotides, no more than 450 nucleotides, or no more than 500 nucleotides.
  • the stuffer sequence is 5’ of one or more copies of the engineered tRNA or engineered tRNA variant within the polynucleotide. In some embodiments, the stuffer sequence is 5’ of one or more copies of the putative regulatory region, regulatory element, and/or promoter that is upstream of the engineered tRNA or engineered tRNA variant within the polynucleotide. In some embodiments, the stuffer sequence is 3’ of one or more copies of the engineered tRNA or engineered tRNA variant within the polynucleotide.
  • the stuffer sequence separates two or more copies of the engineered tRNA or engineered tRNA variant within a polynucleotide or separates two or more copies of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant. In some embodiments, multiple stuffer sequences separate multiple copies of the engineered tRNA or engineered tRNA variant within a polynucleotide.
  • a polynucleotide encoding an engineered tRNA or engineered tRNA variant can comprise a first copy of the engineered tRNA or engineered tRNA variant, followed by a first stuffer sequence, followed by a second copy of the engineered tRNA or engineered tRNA variant, followed by a second stuffer sequence, followed by a third copy of the engineered tRNA or engineered tRNA variant (in a 5’ to 3’ direction). There also can be one or more stuffer sequences 5’ of the first copy of the engineered tRNA or engineered tRNA variant, or 3’ of the third copy of the engineered tRNA or engineered tRNA variant.
  • a polynucleotide encoding putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant can comprise a first copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant, followed by a first stuffer sequence, followed by a second copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant, followed by a second stuffer sequence, followed by a third copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant (in a 5’ to 3’ direction).
  • changing the distance of an engineered tRNA or a variant thereof from an ITR can increase an efficiency of a stop codon readthrough of the engineered tRNA or a variant thereof.
  • an orientation of a sequence of an engineered tRNA or a variant thereof in a vector construct can affect an efficiency of a stop codon readthrough of the engineered tRNA or a variant thereof.
  • a vector can comprise one or more engineered tRNA sequences or an engineered tRNA variant sequences in a vector placed in different orientations.
  • a vector can comprise one or more putative regulatory regions, regulatory elements, or promoter that are upstream of the engineered tRNA sequences or the engineered tRNA variant sequences in a vector placed in different orientations.
  • a kit can comprise a composition described herein for treating a disease or disorder, and a container.
  • a kit can comprise a composition described herein for treating Rett Syndrome, and a container.
  • a kit can comprise a composition described herein for treating Hurler Syndrome, and a container.
  • a kit can comprise a composition described herein for treating Cystic Fibrosis, and a container.
  • a kit can comprise a composition described herein for treating a kidney disease or disorder, and a container.
  • a kit can comprise a pharmaceutical composition, which can comprise an engineered tRNA or variant thereof, a polynucleotide (e.g., vector) encoding the engineered tRNA or variant thereof, or both.
  • a kit can comprise a pharmaceutical composition, which can comprise a regulatory element or a promoter upstream of an engineered tRNA or variant thereof, a polynucleotide (e.g., vector) encoding the regulatory element or a promoter upstream of the engineered tRNA or variant thereof, or both.
  • a container can be plastic, glass, metal, or any combination thereof.
  • a kit can comprise instructions for use, such as instructions for administration to a subject in need thereof.
  • a packaged product comprising a composition described herein can be properly labeled.
  • the pharmaceutical composition described herein can be manufactured according to good manufacturing practice (cGMP) and labeling regulations.
  • a pharmaceutical composition disclosed herein can be aseptic.
  • kits comprising an engineered tRNA or variant thereof and/or a regulatory element or promoter upstream of an engineered tRNA or variant thereof.
  • kits comprising an engineered tRNA variant.
  • kits comprising a regulatory element or a promoter upstream of an engineered tRNA variant.
  • the kits can comprise a pharmaceutical composition described herein (e.g.
  • the kit can comprise a packaging or a container. In some embodiments, the kit can comprise a packaging. In some embodiments, the kit can comprise a container.
  • kits can include contacting the composition with a packaging or container.
  • the method can include contacting the composition with a packaging.
  • the method can include contacting the composition with a container.
  • Premature stop codons leading to mutations in proteins have been implicated in many severe diseases and disorders, such as Rett Syndrome, Dravet Syndrome, and muscular dystrophies such as Duchenne Muscular Dystrophy. Translation of a mRNA molecule that contains a premature stop codon can cause premature termination of the translation process to produce a truncated polypeptide or protein.
  • premature stop codon can be used interchangeably with “premature termination codon” (PTC).
  • PTC premature termination codon
  • the stop codon can be opal (TGA; UGA), ochre (TAA; UAA), or an amber (TAG; UAG) stop codon.
  • the disease-causing mutation in the mRNA sequence can comprise an opal stop codon (TGA; UGA) in the place of a codon encoding Arg (e.g., CGU, CGC, CGA, CGG, AGA, or AAG).
  • the disease-causing mutation in the mRNA sequence can comprise an ochre (TAA; UAA) or an ochre (TAG; UAG) stop codon in the place of a codon encoding Glutamine (e.g., CCA, CAG).
  • the premature stop codon results in a truncated version of the polypeptide or protein.
  • the disease, disorder, or condition can be caused by an increased level of a truncated version of the polypeptide, or a decreased level of substantially full-length polypeptide.
  • a method of treating a subject having a disease associated with a premature stop codon comprises administering an engineered tRNA or variant thereof, e.g., as described herein.
  • a method of treating a subject having a disease associated with a premature stop codon comprises administering a regulatory element or promoter upstream of an engineered tRNA or variant thereof, e.g., as described herein.
  • the disease associated with a premature stop codon is Rett syndrome, autism, West syndrome, Lennox-Gastaut syndrome, epileptic encephalopathy (EEP), Pitt-Hopkins syndrome, or any combination thereof.
  • a disease or condition can comprise cystic fibrosis, deafness (e.g. autosomal dominant 17 deafness, autosomal dominant 13 deafness, autosomal dominant 11 deafness) retinitis pigmentosa or any combination thereof.
  • a disease or condition can comprise Tay-Sachs, Parkinson’s, Cystic Fibrosis, Usher syndrome, Wolman disease, a liver disease (Alpha-1 antitrypsin (AAT) deficiency), or any combination thereof.
  • a disease or condition can be a neurodegenerative disease, a muscular disorder, a metabolic disorder, an ocular disorder (e.g. an ocular disease), a cancer, or any combination thereof.
  • the disease associated with a premature stop codon is cystic fibrosis, albinism, Alzheimer disease, Amyotrophic lateral sclerosis, Asthma, P-thalassemia, Cadasil syndrome, Charcot-Marie-Tooth disease, Chronic Obstructive Pulmonary Disease (COPD), dementia, Distal Spinal Muscular Atrophy (DSMA), Dystrophic Epidermolysis bullosa, Epidermylosis bullosa, Fabry disease, Factor V Leiden associated disorders, Familial Adenomatous, Polyposis, Galactosemia, Gaucher's Disease, Glucose-6-phosphate dehydrogenase, Haemophilia, Hereditary Hematochromatosis, Hunter Syndrome, Huntington's disease, Hurler Syndrome, Inflammatory Bowel Disease (IBD), Inherited polyagglutination syndrome, Leber congenital amaurosis, Lesch-Nyhan syndrome, Lynch syndrome, Marfan syndrome, Mucopo
  • the disease associated with a premature stop codon can be a muscular dystrophy, an ornithine transcarbamylase deficiency, a breast cancer, an ovarian cancer, a prostate cancer, a lung cancer, a skin cancer, Stargardt macular dystrophy, Charcot-Marie-Tooth disease, or any combination thereof.
  • a disease associated with a premature stop codon can be a muscular dystrophy.
  • a muscular dystrophy can include myotonic, Duchenne, Becker, Limb-girdle, facioscapulohumeral, congenital, oculopharyngeal, distal, Emery-Dreifuss, or any combination thereof.
  • the disease associated with a premature stop codon can comprise pain, such as chronic pain. Pain can include neuropathic pain, nociceptive pain, or a combination thereof. Nociceptive pain can include visceral pain, somatic pain, or a combination thereof.
  • a method of treating a subject having Rett syndrome comprises administering an engineered tRNA or engineered tRNA variant as disclosed herein to the subject. In some aspects, a method of treating a subject having Rett syndrome comprises administering a regulatory element or promoter upstream of an engineered tRNA or engineered tRNA variant as disclosed herein to the subject. In some embodiments, the subject is a human.
  • percent “identity,” in the context of two or more nucleic acid or polypeptide sequences, refers to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection.
  • sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection.
  • the percent “identity” can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.
  • test sequence identity For sequence comparison, typically one sequence acts as a reference sequence (also called the subject sequence) to which test sequences (also called query sequences) are compared.
  • the percent sequence identity is defined as a test sequence’s percent identity to a reference sequence. For example, when stated “Sequence A having a sequence identity of 50% to Sequence B,” Sequence A is the test sequence and Sequence B is the reference sequence.
  • sequence comparison algorithm When using a sequence comparison algorithm, test and reference sequences are input into a computer program, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then aligns the sequences to achieve the maximum alignment, based on the designated program parameters, introducing gaps in the alignment if necessary. The percent sequence identity for the test sequence(s) relative to the reference sequence can then be determined from the alignment of the test sequence to the reference sequence.
  • the equation for percent sequence identity from the aligned sequence is as follows:
  • percent identity and sequence similarity calculations are performed using the BLAST algorithm for sequence alignment, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990).
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/).
  • the BLAST algorithm uses a test sequence (also called a query sequence) and a reference sequence (also called a subject sequence) to search against, or in some cases, a database of multiple reference sequences to search against.
  • the BLAST algorithm performs sequence alignment by finding high-scoring alignment regions between the test and the reference sequences by scoring alignment of short regions of the test sequence (termed “words”) to the reference sequence.
  • the scoring of each alignment is determined by the BLAST algorithm and takes factors into account, such as the number of aligned positions, as well as whether introduction of gaps between the test and the reference sequences would improve the alignment.
  • the alignment scores for nucleic acids can be scored by set match/mismatch scores.
  • the alignment scores can be scored using a substitution matrix to evaluate the significance of the sequence alignment, for example, the similarity between aligned amino acids based on their evolutionary probability of substitution.
  • the substitution matrix used is the BLOSUM62 matrix.
  • the public default values of April 6, 2023 are used when using the BLASTN and BLASTP algorithms.
  • the BLASTN and BLASTP algorithms then output a “Percent Identity” output value and a “Query Coverage” output value.
  • the overall percent sequence identity as used herein can then be calculated from the BLASTN or BLASTP output values as follows:
  • Percent Sequence Identity (“Percent Identity” output value) x (“Query Coverage” output value)
  • the following non-limiting examples illustrate the calculation of percent identity between two nucleic acids sequences.
  • Test sequence 1 has 50% sequence identity to reference sequence 2.
  • the following non-limiting examples illustrate the calculation of percent identity between two protein sequences.
  • Test sequence 7 has 50% sequence identity to reference sequence 8.
  • Test sequence 9 has 50% sequence identity to reference sequence 10.
  • Test sequence 11 has 100% sequence identity to reference sequence 12.
  • CCT2.10 SEQ ID NO: 32
  • CCT4 SEQ ID NO: 7
  • Table 7 The sequences of these tRNAs, along with the positions selected for degeneracies in the variant library and the sequences are shown in Table 7 below.
  • degenerate bases degenerate bases (denoted ‘N’, meaning A, C, G, or T in DNA and A, C, G, or U in RNA) were introduced in the DNA oligonucleotides encoding the tRNA sequences as shown in the table below.
  • each of the six libraries were designed to contain 4 A 5 (1,024) variants.
  • tRNA variants were contained within a synthetic oligonucleotide comprising, from 5’ to 3’, the tRNA sequence and a polyT, and inserted into a lentiviral expression vector either with the hU6 promoter sequence (GAGggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattagaattaatttgactgtaaacacaaaga tattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagttttgcagtttttaaaattatgtttttaaaatggactatcatatgcttaccgtaa cttgaaagtatttcgatttcttggctttggctttggctttggctttggctttggctttggcttttgg
  • Additional oligonucleotide pools were prepared with CCT2.10, adding 5’ sequences that were either 227 bp upstream or 100 bp upstream of bioinformatically mined known human tRNA sequences (“Upstream -tRNA” libraries), in which the 227 bp upstream sequence and 100 bp upstream sequences are putative regulatory regions that may comprise regulatory elements, such as promoters.
  • High-throughput screening approaches for tRNA variants and putative regulatory regions enables systematic identification of global patterns in tRNA sequences and putative regulatory regions (Upstream-tRNA) that can, for example, enhance or influence nonsense suppression efficiency.
  • Upstream-tRNA putative regulatory regions
  • An exemplary approach to screening different libraries is shown in FIG.
  • the cloned and amplified tRNA library (in a lentiviral backbone) is introduced into cells stably expressing broken GFP (i.e., with an engineered premature stop codon) at a low MOI, to achieve single copy transduction.
  • PTC readthrough generates intact GFP.
  • Cells are FACS-sorted on GFP expression and NGS libraries are prepared from each sorting group. This includes preparing an NGS library from the sorting group of cells with high GFP mean fluorescence intensity (MFI) in order to identify top-performing library candidates by sequencing.
  • MFI mean fluorescence intensity
  • Example 1 The libraries described in Example 1 were cloned into a lentiviral backbone with CMV-mCherry as the transduction marker (FIG. 2A). Read through of 44 clones randomly selected from across the different libraries was tested as shown in FIG. 3. Each of the variants was co-transfected with broken GFP constructs into HEK293 cells. After 48 hours, the read- through capacity of each library candidate clone was quantified by GFP expression through flow cytometry. As mCherry is driven by the CMV promoter directly off the plasmid containing the library candidate clone, one would expect to see mCherry expression from this transfection.
  • mCherry and GFP expression was measured to identify transfected cells with GFP read-through rescue.
  • FIG. 4A percentage of mCherry+ cells that are GFP+
  • FIG. 4B GFP MFI normalized to mCherry MFI
  • a subset of library candidate clones from each of the libraries had GFP expression comparable to or greater than CCT2.10.
  • library candidate clones from the Upstream-tRNA libraries 100 bp prom and 227 bp prom
  • the library candidate clones demonstrating GFP expression comparable to or greater than CCT2.10 are shown in Tables 9A, 9B, and 9C, below. Sequences in Table 9C were engineered 5’ of the sequence encoding CCT2.10 (SEQ ID NO: 32) in the tested constructs.
  • High-Throughput Screening was carried out on the libraries described in Example 2 as shown in FIG. 7. Briefly, cells were transduced at low MOI to facilitate single-copy integration of library variants and then expanded in puromycin (puro) media for about two weeks before FACS sorting into bins of GFP expression. As shown in FIG. 8A, the highest number of GFP+ cells were seen in the Upstream-tRNA libraries, followed by the U6 tRNA variant libraries, and the lowest number of GFP+ cells were seen in the no promoter tRNA variant libraries.
  • the sorted cells were used to prepare NGS libraries and sequenced to identify variants.
  • FIG. 8B the abundance distribution of CCT2.10 hU6 tRNA variants in the high GFP expressing bin shifted relative to cells in the lower and no GFP-expression bins
  • FIG. 8C the abundance of the CCT2.10 hU6 tRNA variants in the high GFP bin was increased compared to the other bins, demonstrating the high bin selection for topperforming candidates.
  • the frequency of lOObp and 227bp Upstream-tRNA was the highest in the high GFP expressing bins, also demonstrating selection for top-performing candidates.
  • Top-performing tRNA variants from the high-throughput screening as described in the previous examples were identified using differential expression analysis. These top performing tRNA variants (Table 10) and corresponding controls (hu6-CCT2.10 (CCT2.10 with hU6 promoter); noU6-CCT2.10 (CCT2.10 without hU6 promoter); hU6-CCT4 (CCT4 with hU6 promoter); noU6-CCT4WT (CCT4 having a WT anti-codon, and without hU6 promoter); and noU6CCT2.10 WT (CCT2.10 having a WT anti-codon, and without hU6 promoter)) were cloned into a pUC backbone with the CMV-Thyl.l transduction marker.
  • HEK293 cells stably expressing either the R74X or R97X broken GFP reporter were transfected with 200 ng of plasmid comprising the tRNA variant and a CMV-Thyl. l transfection reporter cassette. After 48 hours, cells were stained with a NIR viability dye and a BV421- Thyl.l dye at room temperature for 15 minutes. Cells were assessed for transfection and read- through efficiency by flow cytometry quantifying Thy 1.1 and GFP expression. Dead cells were excluded from analysis.
  • variants identified by the HTS screen performed similarly or better than the control noU6-CCT2.10 in both HEK293 R74X-GFP expressing cells (FIG. 10A) and in R97X-GFP expressing cells (FIG. 10B).
  • Top-performing Upstream-tRNA variants (comprising a putative regulatory region) from the Upstream-tRNA library HTS screen as described in the previous examples were identified using differential expression analysis. These top-performing Upstream-tRNA variants (putative regulatory region and a tRNA sequence) (Table 11) and corresponding controls were cloned into a pUC backbone with the CMV-Thyl.l transduction marker.
  • the tRNA insert sequences either rely on their intrinsic promoter for tRNA expression or include an external promoter for additional expression.
  • HEK293T cell lines were generated in duplicate, with each tRNA insert sequence cloned in either the forward or reverse orientations and with one of two different GFP reporters (R97X broken GFP-FLAG (“broken GFP reporter”) or Intact GFP-FLAG (“intact GFP reporter”)).
  • R97X broken GFP-FLAG (“broken GFP reporter”) or Intact GFP-FLAG (“intact GFP reporter”)
  • a no tRNA control was also generated. Therefore, a total of 26 cell lines were generated.
  • GFP fluoresence was assessed for each of the generated cell lines, as shown in FIG. 12. Except for the negative control cell line and untransfected control cell line, reproducible GFP readthrough was observed at day 20 post transfection for the single-copy integrations in all the broken GFP reporter cell lines.
  • An engineered tRNA variant comprising one or more mutations at position(s) 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62, according to canonical numbering.
  • engineered tRNA variant of embodiment 3 wherein the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 73 or SEQ ID NO: 79.
  • engineered tRNA variant of embodiment 4 wherein the engineered tRNA variant has at least 90% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 73 or SEQ ID NO: 79.
  • An engineered tRNA variant comprising SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, or SEQ ID NO: 187.
  • An engineered tRNA variant comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 254, SEQ ID NO: 255, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 296, SEQ ID NO: 297, SEQ ID NO: 298, SEQ ID NO: 299, SEQ ID NO: 300, SEQ ID NO:
  • engineered tRNA variant of embodiment 2 wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
  • An engineered tRNA variant comprising SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 191.
  • An engineered tRNA variant comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 260, SEQ ID NO: 266, SEQ ID NO: 267, or SEQ ID NO: 268.
  • the regulatory region comprises or consists of SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region.
  • nucleic acid sequence encoding the tRNA is selected from SEQ ID NOs 3-48, 96-115, 136-155, 196, 197, 199-222, 227-229, 176-179, 180-183, 272-295, 344-353, and 354-365.
  • An expression vector comprising the polynucleic acid of any one of embodiments 14-18.
  • a cell comprising the polynucleotide of any one of embodiments 14-18.
  • a cell comprising the expression vector of any one of embodiments 19-27.
  • a method for identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency comprising: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding a tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA; introducing the expression vectors into cells stably expressing a reporter protein having a PTC; incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells into bins based on expression levels of the reporter protein; identifying a sequence of a tRNA variant and/or a regulatory region of a cell from one of the bins; and, based on the sequence, identifying engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency.
  • introducing the expression vectors into cells expressing the reporter protein comprises transfecting the cells with the expression vectors at a multiplicity of infection (MOI) suitable to achieve single copy transduction per cell.
  • MOI multiplicity of infection
  • sorting the cells comprises fluorescence-activated cell sorting (FACS).
  • identifying the sequence of the tRNA variant and/or regulatory region comprises single cell sequencing of the tRNA variant and/or regulatory region of the cell.

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Abstract

Described herein are, among other things, engineered tRNA variant(s) or novel regulatory elements, as well as high-throughput methods for identifying the same. The engineered tRNA variants and novel regulatory elements may improve premature termination codon (PTC) readthrough, which may be used to treat diseases and disorders.

Description

ENGINEERED TRANFER RNAS
CLAIM OF PRIORITY
[0001] This application claims the benefit of U.S. Provisional Application Serial Nos. 63/341,688, filed on May 13, 2022, and 63/438,141, filed on January 10, 2023. The entire contents of the foregoing are incorporated herein by reference.
BACKGROUND
[0002] Premature stop codons leading to mutations in proteins have been implicated in many severe diseases and disorders. Translation of a mRNA molecule that contains a premature stop codon (also referred to as a premature termination codon, PTC) can cause premature termination of the translation process to produce a truncated polypeptide or protein, which can cause these severe diseases or disorders.
[0003] There is a need for effective treatments for diseases and disorders associated with premature stop codons, including effective production and delivery of these treatments.
SUMMARY
[0004] Described herein are, among other things, engineered tRNA variant(s) or novel regulatory elements, as well as high-throughput methods for identifying the same. The engineered tRNA variants and novel regulatory elements may improve premature termination codon (PTC) readthrough, which may be used to treat diseases and disorders.
[0005] Also described herein are engineered tRNA variant(s) comprising one or more mutations at position(s) 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62, according to canonical numbering.
[0006] In some embodiments, the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 79. In some embodiments, the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79. In some embodiments, the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79. In some embodiments, the engineered tRNA variant has at least 90% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79. [0007] Also described herein are engineered tRNA variant(s) comprising SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, or SEQ ID NO: 187.
[0008] Also described herein are engineered tRNA variant(s) comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 254, SEQ ID NO: 255, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 261, SEQ ID NO: 262, SEQ ID NO: 263, SEQ ID NO: 264, SEQ ID NO: 268, SEQ ID NO: 269, SEQ ID NO: 270, SEQ ID NO: 271, SEQ ID NO: 296, SEQ ID NO: 297, SEQ ID NO: 298, SEQ ID NO: 299, SEQ ID NO: 300, SEQ ID NO: 301, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 304, SEQ ID NO: 305, SEQ ID NO: 306, SEQ ID NO: 307, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 315, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 319, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 370, SEQ ID NO: 371, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 385, SEQ ID NO: 386, or SEQ ID NO: 387.
[0009] In some embodiments, the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 54. In some embodiments, the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54. In some embodiments, the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54. In some embodiments, the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 92; optionally, wherein the sequence is not SEQ ID NO: 92 or SEQ ID NO: 53. [0010] Also described herein are engineered tRNA variant(s) comprising SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 191.
[0011] Also described herein are engineered tRNA variant(s) comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 260, SEQ ID NO: 265, SEQ ID NO: 266, or SEQ ID NO: 267.
[0012] Also described herein are polynucleic acid(s) encoding the engineered tRNA variant(s) described herein, optionally wherein the polynucleotide comprises at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 196, 197, 199-233, 176-179, 180-183, 272-295, 344-353, or 354-365. [0013] Also described herein are polynucleic acid(s) comprising nucleic acid sequence(s) encoding a tRNA, optionally an engineered tRNA, and a regulatory region, wherein the regulatory region has at least at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to sequence identity to SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, or SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region. In some embodiments, the regulatory region comprises or consists of SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region. In some embodiments, the regulatory region is 5’ of the nucleic acid sequence encoding the tRNA.
[0014] In some embodiments, the nucleic acid sequence encoding the tRNA is selected from SEQ ID NOs 3-48, 96-115, 136-155, 196, 197, 199-233, 176-179, 180-183, 272-295, 344-353, and 354-365.
[0015] Also described herein are expression vector(s) comprising polynucleic acid(s) described herein.
[0016] In some embodiments, the expression vector further comprises a promoter. In some embodiments, the promoter is a polymerase III promoter. In some embodiments, the polymerase III promoter is a polymerase III type 3 promoter. In some embodiments, the polymerase III type 3 promoter is U6. In some embodiments, the U6 is human U6; optionally, wherein the human U6 comprises at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 388.
[0017] In some embodiments, the expression vector further comprises a polynucleic acid encoding a reporter protein. In some embodiments, the reporter protein is a fluorescent protein. [0018] In some embodiments, the expression vector is a lentiviral expression vector.
[0019] Also described herein are cell(s) comprising the polynucleotide(s) described herein. Also described herein are cell(s) comprising the expression vector(s) described herein. Also described herein are cell(s) expressing the engineered tRNA variant(s) described herein. [0020] In some embodiments, the cell(s) express a broken reporter protein. In some embodiments, the broken reporter protein is a broken fluorescent protein. In some embodiments, the broken fluorescent protein is broken GFP.
[0021] In some embodiments, the cell expresses an engineered tRNA or an engineered tRNA variant with improved PTC readthrough efficiency as compared to a cell expressing a reference tRNA. In some embodiments, the reference tRNA is selected from SEQ ID NO: 79 and SEQ ID NO: 54.
[0022] In some embodiments, the cell comprises a single copy, two copies, three copies, four copies, five copies, six copies, seven copies, or eight copies of a polynucleotide described herein, an expression vector described herein, or an engineered tRNA variant described herein. In some embodiments, the cell comprises at least two or more copies of a polynucleotide described herein, an expression vector described herein, or an engineered tRNA variant described herein. Also described herein are method(s) for identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency, the method comprising: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding an engineered tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA; introducing the expression vectors into cells stably expressing a reporter protein having a PTC; incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells into bins based on expression levels of PTC-readthrough of reporter protein; identifying a sequence of an engineered tRNA variant and/or a regulatory region of a cell from one of the bins; and, based on the sequence, identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency.
[0023] In some embodiments, the expression vector(s) further comprises a reporter protein. In some embodiments, the reporter protein is a fluorescent protein. In some embodiments, the fluorescent protein is mCherry. In some embodiments, the reporter protein is a fluorescent protein having a PTC. In some embodiments, the reporter protein is a GFP protein having a PTC.
[0024] In some embodiments, introducing the expression vectors into cells expressing the reporter protein comprises transfecting the cells with the expression vectors at a multiplicity of infection (MOI) suitable to achieve single copy transduction per cell.
[0025] In some embodiments, sorting the cells comprises fluorescence-activated cell sorting (FACS).
[0026] In some embodiments, identifying the sequence of the tRNA variant and/or regulatory region comprises single cell sequencing of the tRNA variant and/or regulatory region of the cell. In some embodiments, identifying the sequence of the tRNA variant and/or regulatory region comprises bulk amplicon sequencing of the tRNA variant and/or regulatory region of the cell. In some embodiments, identifying the sequence of the tRNA variant and/or regulatory region comprises next-generation sequencing of the tRNA variant and/or regulatory region of the cell. In some embodiments, one of the bins is a bin having the highest expression level of PTC-readthrough of the reporter protein compared to other bins. In some embodiments, the nucleic acid sequence encoding the engineered tRNA variant further comprises a nucleic acid sequence encoding an hU6 promoter 5’ of the engineered tRNA variant.
[0027] Throughout this application, various embodiments may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
[0028] As used in the specification and claims, the singular forms “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a sample” includes a plurality of samples, including mixtures thereof.
[0029] As used herein, the term “about” a number refers to that number plus or minus 10% of that number. The term “about” a range refers to that range minus 10% of its lowest value and plus 10% of its greatest value.
[0030] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.
[0031] Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims. DESCRIPTION OF DRAWINGS
[0032] FIG. 1 A is a schematic of the canonical structure and numbering scheme for tRNA. [0033] FIG. IB is a schematic showing exemplary positions at which the canonical tRNA structure can be mutated (schematic adapted from trna.bioinf.uni-leipzig.de).
[0034] FIG. 2A is a schematic showing an example workflow for generating a cloned and amplified tRNA library using a lentiviral plasmid backbone. In some cases, the lentiviral plasmid backbone includes a promoter, such as a U6 promoter, e.g., between the 5’ LTR and BamHI site (bottom right schematic). In some cases, the lentiviral plasmid backbone includes a promoter, such as a U6 promoter, e.g., between the 3’ LTR and BamHI site (bottom left schematic).
[0035] FIG. 2B is a schematic showing a workflow for Next Generation Sequencing (NGS) verification of cloned plasmid and packaged lentiviral tRNA libraries for three different tRNA libraries (1 - no promoter tRNA library; 2 - hU6 tRNA library; and 3 - Upstream -tRNA library), and a graph confirming that library sequence diversity is preserved during lentivirus generation when compared to the sequence diversity of the cloned plasmid.
[0036] FIG. 3 is a schematic showing an example of a method for measuring PTC readthrough efficiency for individual clones, e.g., variants from the libraries.
[0037] FIG. 4A shows the percentage of GFP+ cells after dual transfection of a broken GFP plasmid and no promoter tRNA plasmid, hU6 tRNA plasmid, or upstream-tRNA plasmid, indicating readthrough efficiency of the broken GFP.
[0038] FIG. 4B shows the GFP+/mCherry+ mean fluorescent intensity (MFI) ratio of cells after dual transfection of a broken GFP plasmid and a no promoter tRNA plasmid, hU6 tRNA plasmid, or upstream-tRNA plasmid, indicating readthrough efficiency of the broken GFP.
[0039] FIG. 5 A shows the number of unique sequences for each of the tRNA variant plasmid library pools. Bars, from left to right within each category: A-box mutant library (“Abox”), B- box mutant library (“Bbox”), and Variable Region mutant library (“Var”). Categories (boxed set of three bars), from left to right: CCT2.10 variant libraries with hU6 promoter (“hU6-CCT2.10 Repl”), CCT4 variant libraries with hU6 promoter (“hU6-CCT4 Repl”), CCT2.10 variant libraries with U6 promoter (hU6-CCT2.10 Rep2”), CCT4 variant libraries with hU6 promoter (“hU6-CCT4 Rep2”), CCT2.10 variant libraries without U6 promoter (“noU6-CCT2.10 Repl”), CCT4 variant libraries without U6 promoter (“noU6-CCT4 Repl”), and CCT4 variant libraries without U6 promoter (“noU6-CCT4 Rep2”).
[0040] FIG. 5B shows percent library coverage for tRNA variant lentivirus libraries. Bars, from left to right within each category: A-box mutant library (“Abox”), B-box mutant library (“Bbox”), and Variable Region mutant library (“Var”). Categories (sets of three bars), from left to right: CCT2.10 variant libraries with U6 promoter (“hU6-CCT2.10”), CCT4 variant libraries with U6 promoter (“hU6-CCT4”), CCT2.10 variant libraries without U6 promoter (“noU6- CCT2.10”), and CCT4 variant libraries without U6 promoter (“noU6-CCT4”).
[0041] FIG. 6A shows percent library coverage for plasmid pools of Upstream -tRNA libraries. The libraries are, from left to right: CCT2.10 tRNA with a 227 bp putative regulatory region (“noU6-227prom-l”), CCT2.10 tRNA with a 227 bp putative regulatory region (“noU6- 227prom-2”); CCT2.10 tRNA with a 100 bp putative regulatory region (“noU6-100prom-l”); and CCT2.10 tRNA with a 100 bp putative regulatory region (“noU6-100prom-2”).
[0042] FIG. 6B shows percent library coverage for pools of Upstream-tRNA libraries. The libraries are, from left to right, CCT2.10 tRNA with a 100 bp putative regulatory region (“promlOObp”); and CCT2.10 tRNA with a 227 bp putative regulatory region (“prom227bp”). [0043] FIG. 7 is a schematic showing an example of a high-throughput screen workflow for identifying putative regulatory elements (tRNA 5’ regions) or tRNA variants with the hU6 promoter or without a promoter with high PTC readthrough efficiency.
[0044] FIG. 8A shows a histogram of GFP MFI, from, front to back, untransfected cells; cells transfected with a no promoter tRNA library; cells transfected with a hU6 tRNA library; and cells transfected with a novel Upstream-tRNA library. The arrow shows the tail of GFP+ cells.
[0045] FIG. 8B shows normalized counts of tRNA variants after sorting on GFP expression.
[0046] FIG. 8C shows normalized counts of the subset of variants enriched in the top bin.
[0047] FIG. 9 shows fractions of reads from 100 bp Upstream-tRNA libraries (“promlOObp”), 227 bp Upstream-tRNA libraries (“prom227bp”), and a spiked-in control library (ctrl combo) after sorting on GFP expression.
[0048] FIG. 10A is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+. HEK293 cells stably expressing a broken GFP (GFP with a R74X premature stop codon inserted into the sequence) were transduced with plasmids comprising tRNA variants (tRNA constructs 1-24) and corresponding controls (hU6-CCT2.10; noU6-CCT2.10; hU6- CCT4; hU6-CCT2.10-WT; noU6-CCT4-WT; or no U6-CCT2.10 WT).
[0049] FIG. 10B is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+. HEK293 cells stably expressing a broken GFP (GFP with a R97X premature stop codon inserted into the sequence) were transduced with plasmids comprising tRNA variants (tRNA constructs 1-24) and corresponding controls (hU6-CCT4; hU6-CCT2.10; noU6- CCT2.10; hU6-CCT2.10-WT; noU6-CCT4-WT; or no U6-CCT2.10 WT).
[0050] FIG. 11 A is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+. HEK293 cells stably expressing a broken GFP (GFP with a R74X premature stop codon inserted into the sequence) were transduced with plasmids comprising upstream-tRNA variants (1-24) and corresponding controls (noU6-CCT2.10; hU6-CCT4-WT; hU6-CCT2.10- WT; hU6-CCT2.10; hU6-CCT4; noU6CCT4-WT; and noU6-CCT2.10-WT).
[0051] FIG. 1 IB is a graph showing the percentage of transduced HEK293 cells (Thy 1.1+) that are GFP+. HEK293 cells stably expressing a broken GFP (GFP with a R74X premature stop codon inserted into the sequence) were transduced with plasmids comprising upstream-tRNA variants (1-24) and corresponding controls (noU6-CCT2.10; hU6-CCT2.10; hU6-CCT4; hU6- CCT2.10-WT; hU6-CCT4-WT; noU6-CCT2.10-WT; and noU6-CCT4-WT).
[0052] FIG. 12 is a set of graphs showing the median GFP-A intensity of live singlet cells from single-copy integration cell lines and corresponding controls.
DETAILED DESCRIPTION
[0053] Translation of a mRNA molecule that contains a premature stop codon can cause premature termination of the translation process to produce a truncated polypeptide or protein. These premature stop codons and subsequent truncated proteins are associated with many severe diseases and disorders, such as Cystic Fibrosis, Cystinosis, MPS I Syndrome, Rett Syndrome, Dravet Syndrome, and muscular dystrophies such as Duchenne Muscular Dystrophy, cancers, Hemophilia, P -thalassemia, Spinal Muscular Atrophy, Hurler’s Syndrome, Hailey -Hailey disease, and Recessive Retinal Dystrophies. There is a need for effective treatments for these diseases and disorders.
[0054] One exemplary treatment for diseases and disorders associated with premature stop codons is administration of transfer RNA (tRNA) molecules that suppress premature stop codons to enable readthrough of the premature stop codon in a template messenger RNA (mRNA), which are referred to herein as “suppressor tRNA.” These suppressor tRNAs can comprise an engineered anticodon for recognition of a premature stop codon and at least partially transform translation of a premature stop codon into a sense codon, such as, for example by adding a corrective (e.g., non-disease-causing) amino acid to the growing peptide associated with premature stop codons.
[0055] As described, e.g., in WO 2021/113218, which is hereby incorporated by reference in its entirety, engineered tRNAs show improved read through stop codons in primary neuronal cultures harvested from R225X Rett model mice. Additionally, engineered tRNA variants from WO 2021/113218 showed higher readthrough of Arg>opal PTCs in cells transfected with a dual plasmid broken reporter system compared to engineered tRNAs from WO 2021/113218, and a top-performing engineered tRNA variant from WO 2021/113218 showed higher readthrough of three different PTCs in stably integrated broken fluorescent reporter systems compared to a top- performing engineered tRNA variant from WO 2021/113218. However, further testing demonstrated that AAV delivery showed lower readthrough (< -10% of transfected cells at lx dose and < -20% of transfected cells at 2x dose) than transient plasmid delivery (-20-60% of transfected cells), indicating that dosing and tRNA expression levels have a significant impact on PTC readthrough. Therefore, as described herein, further engineering and high throughput screening of tRNAs was performed in order to further increase potency of engineered tRNAs and increase PTC readthrough after in vivo dosing and delivery.
[0056] Thus, provided herein are, among other things, engineered tRNAs variants for PTC readthrough, and associated methods. In some cases, the engineered tRNAs variants have improved PTC readthrough efficiency compared to a reference tRNA.
[0057] Additionally provided herein are novel regulatory elements (e.g., within a regulatory region, e.g., a putative regulatory region, e.g., as described herein) for modulating transcription of a tRNA. In some cases, a novel regulatory element increases transcription of a tRNA. In some cases, a novel regulatory element increases transcription of a suppressor tRNA. In some cases, a novel regulatory element increases transcription of an engineered tRNA. In some cases, a novel regulatory element increases transcription of an engineered tRNA variant. In some cases, a novel regulatory element increases transcription of a suppressor tRNA, resulting in increased PTC readthrough compared to the suppressor tRNA lacking the novel regulatory element. In some cases, a novel regulatory element increases transcription of an engineered tRNA, resulting in increased PTC readthrough compared to the engineered tRNA lacking the novel regulatory element. In some cases, a novel regulatory element increases transcription of an engineered tRNA variant, resulting in increased PTC readthrough compared to the engineered tRNA variant lacking the novel regulatory element.
[0058] Also provided herein are methods for high throughput screening of engineered tRNA variants, e.g., for improved PTC readthrough efficiency. Further provided herein are methods for high throughput screening for novel regulatory element, e.g., for modulating tRNA transcription. The high throughput screen of engineered tRNA variants and/or putative regulatory elements can be a lentiviral high throughput screen. In some embodiments, the methods for high throughput screening comprise inserting an engineered tRNA variant and/or a putative regulatory element into a lentiviral expression vector. Surprisingly, when using this method, the engineered tRNA variants and/or the tRNA (e.g., engineered tRNA or engineered tRNA variant) downstream of the putative regulatory elements being screened were not cleaved from the lentiviral construct as would potentially be expected when using an RNA virus such as a lentivirus. Therefore, the diversity of the engineered tRNA variants and/or the putative regulatory elements in the screened libraries were unexpectedly preserved, allowing for these lentiviral library screens to be used for identifying engineered tRNA variants and/or novel regulatory elements that provide increased PTC readthrough efficiency in cells having a gene with a PTC.
ENGINEERED TRNA AND VARIANTS THEREOF
[0059] Provided herein, among other things, are engineered tRNA variants and novel regulatory elements.
[0060] In some cases, the engineered tRNA variants described herein have an improved PTC readthrough efficiency relative to a reference tRNA. For example, in some cases, an engineered tRNA variant that has been mutated relative to a parental tRNA has a higher PTC readthrough efficiency than the parental tRNA. In some cases, an engineered tRNA variant that includes a novel regulatory element has a higher PTC readthrough efficiency than the same tRNA sequence without the novel regulatory element, or with a different regulatory element or putative regulatory element.
[0061] In some cases, the efficiency of PTC readthrough is an in vivo efficiency of PTC readthrough. In some cases, the in vivo efficiency of PTC readthrough can be determined by an increase in the abundance of full-length protein, or, conversely, of a reduction in the amount of truncated protein. The increase or decrease can be determined relative to a control. For example, the increase or decrease can be determined by comparing a sample from the same patient before and after treatment. The increase or decrease can also be measured by comparing a sample from one source (e.g., a treated sample) and a sample from a second source (e.g., an untreated reference sample). In some cases, in vivo efficiency of PTC readthrough can be determined by at least partially treating a disease or condition. For example, in vivo efficiency of PTC readthrough can be measured by at least partial improvement (following treatment) of one or more symptoms associated with the disease or condition being treated.
[0062] In some cases, the in vivo efficiency of PTC readthrough is from 1% to 100% or more, e.g., from 10% to 100%, 20% to 100%, 30% to 100%, 40% to 100%, 50% to 100%, 60% to 100%, 70% to 100%, 75% to 100%, 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, 20% to 40%, 20% to 60%, or 10% to 70%. In some cases, the in vivo efficiency of PTC readthrough is at least 1%, e.g., at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100%.
[0063] In some cases, the efficiency of PTC readthrough is an in vitro efficiency of PTC readthrough, such as an in vitro efficiency of PTC suppression readthrough as determined by: (a) transfecting a first vector encoding an engineered tRNA or variant thereof and a second vector encoding a screening mRNA encoding a first green fluorescent protein into a first human cell, where the screening mRNA encoding the first green fluorescent protein can comprise a premature stop codon (this can be referred to herein as a, e.g., “broken” GFP); (b) transfecting a third vector encoding a comparable screening mRNA encoding a second green fluorescent protein into a second human cell, wherein the comparable screening mRNA does not comprise a premature stop codon; and (c) comparing an amount of fluorescence emitted from the first human cell and the second human cell. In some cases, a green fluorescent protein can comprise at least two premature stop codons. In some instances, the premature stop codons can be the same stop codons, or different stop codons.
[0064] In some cases, the in vitro efficiency of PTC readthrough is from 1% to 100% or more, e.g., 10% to 100%, 20% to 100%, 30% to 100%, 40% to 100%, 50% to 100%, 60% to 100%, 70% to 100%, 75% to 100%, 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, 20% to 40%, 20% to 60%, or 10% to 70%. In some cases, the in vitro efficiency of PTC readthrough is at least 1%, e.g., at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.
[0065] In some cases, an engineered tRNA or engineered tRNA variant can be acylated with a canonical amino acid. In some cases, an engineered tRNA or engineered tRNA variant can be acylated with a non-canonical amino acid. A non-canonical amino acid can comprise p- Acetylphenylalanine, p-Propargyloxyphenylalanine, p-Azidophenylalanine, O-methyltyrosine, p- lodophenylalanine, 3-Iodotyrosine, Biphenylalanine, 2-Aminocaprylic acid, p- Benzoylphenylalanine, o-Nitrobenzylcysteine, o-Nitrobenzylserine, 4,5-Dimethoxy-2- nitrobenzylserine, o-Nitrobenzyllysine, Dansylalanine, Acetyllysine, Methylhistidine, 2- Aminononanoic acid, 2-Aminodecanoic acid, 2-Aminodecanoic acid, Cbz-lysine, Boc-lysine, or Allyloxy carbonyllysine.
[0066] In some embodiments, an engineered tRNA or engineered tRNA variant can be acylated with an amino acid selected provided in Table 1.
Table 1. Amino Acids, one and three letter codes
Figure imgf000013_0001
Figure imgf000014_0001
[0067] In some cases, an engineered tRNA or eng neered tRNA variant can be a lysyl-tRNA, an arginyl-tRNA, a histidyl-tRNA, a glycyl-tRNA, an alanyl-tRNA, a valyl-tRNA, a leucyl- tRNA, an isoleucyl-tRNA, methionyl-tRNA, a phenylalanyl-tRNA, a tryptophanyl-tRNA, a prolyl-tRNA, a seryl-tRNA, a threonyl-tRNA, a cysteinyl-tRNA, a tyrosyl-tRNA, an asparaginyl tRNA, a glutaminyl-tRNA, an aspartyl-tRNA, a pyrrolysyl tRNA, a selenocytstyl tRNA, or a glutamyl-tRNA.
[0068] This disclosure contemplates incorporating specific hybrid tRNAs or orthogonal tRNA/tRNA synthetase pairs. In some cases, an engineered tRNA or engineered tRNA variant can include a designer tRNAs (such as hybrid tRNAs made from two different naturally occurring tRNAs) or orthogonal tRNAs from other species. In some cases, a synthetic or chimeric orthogonal tRNA-tRNA synthetase pair can be used or included. In some cases, synthetic tRNAs that can interact with naturally occurring tRNA synthetases are included or used. In some cases, a pyrrolysyl tRNA or a selenocytstyl tRNA can be used in genetic code expansion to incorporate non-canonical amino acids into an engineered tRNA or engineered tRNA variant.
[0069] In some cases, an engineered tRNA or engineered tRNA variant can be a lysine- tRNA, an arginine-tRNA, a histidine-tRNA, a glycine-tRNA, an alanine-tRNA, a valine-tRNA, a leucine-tRNA, an isoleucine-tRNA, methionine-tRNA, a phenylalanine-tRNA, a tryptophan- tRNA, a proline-tRNA, a serine-tRNA, a threonine-tRNA, a cysteine-tRNA, a tyrosine-tRNA, an asparagine-tRNA, a glutamine-tRNA, an aspartic acid-tRNA, or a glutamic acid-tRNA.
[0070] In some cases, an engineered tRNA or engineered tRNA variant can be derived from a human tRNA. In some cases, an engineered tRNA or engineered tRNA variant can be derived from a non-human tRNA. In some cases, an engineered tRNA or engineered tRNA variant can be derived from a tRNA that can be orthogonal to a human tRNA. An engineered tRNA or engineered tRNA variant can be acylated by an amino-acyl synthetase that can recognize the engineered tRNA or engineered tRNA variant and acylate the engineered tRNA or engineered tRNA variant with an amino acid. In some cases, the engineered tRNA or engineered tRNA variant can be an engineered pre-tRNA or an engineered pre-tRNA variant. Such an engineered pre-tRNA or variant thereof can comprise an intronic sequence. In some cases, an intronic sequence can be spliced to produce a mature engineered tRNA or variant thereof. In some cases, an intronic sequence can be spliced within a cell containing an engineered tRNA or variant thereof. In some cases, once the intronic sequence is spliced the mature engineered tRNA or engineered tRNA variant can at least partially transform an interpretation of a premature stop codon into a sense codon. In some cases, an engineered pre-tRNA or variant thereof with an intron can be more efficient at transforming an interpretation of a premature stop codon into a sense codon as compared to an engineered pre-tRNA or variant thereof without an intron. The efficiency can be measured by transforming a vector encoding an engineered suppressor pre- tRNA or variant thereof with an intron into a primary cell line comprising a premature stop codon to which the engineered suppressor pre-tRNA or variant thereof recognizes and comparing the level of premature stop codon readthrough against another comparable cell that has been transformed with a vector encoding an engineered suppressor pre-tRNA or variant thereof without an intron. In some cases, determining the amount of full-length protein can be used to measure premature stop codon readthrough.
[0071] An engineered tRNA or variant thereof can be engineered with an anticodon sequence that base pairs with a stop codon, instead of a codon encoding for the amino acid of interest. For example, an engineered tRNA or variant thereof targeting a premature stop codon at a position in the growing polypeptide in which an Arginine (amino acid of interest) can be normal (e.g., not causing disease). In some cases, an engineered Arg tRNA or variant thereof with an anticodon sequence that base pairs with the premature stop codon can base pair with the stop codon enabling the engineered tRNA or variant thereof charged with the Arg to add the Arg to the growing polypeptide molecule, thus, effecting readthrough of the premature stop codon. For example, an engineered tRNA or variant thereof targeting a premature stop codon at a position in the growing polypeptide in which a Glutamine (amino acid of interest) can be normal (e.g., not causing disease). In some cases, an engineered Gin tRNA or variant thereof with an anticodon sequence that base pairs with the premature stop codon can base pair with the stop codon enabling the engineered tRNA or variant thereof charged with the Gin to add the Gin to the growing polypeptide molecule, thus, effecting readthrough of the premature stop codon.
[0072] Engineered tRNAs or engineered tRNA variants of the present disclosure can be engineered to recognize and suppress an amber stop codon (UAG), an ochre stop codon (UAA), or an opal stop codon (UGA), or a combination thereof. In some cases, an engineered tRNA or variant thereof can be engineered to suppress an amber stop codon (UAG). In some cases, an engineered tRNA or variant thereof can be engineered to suppress an ochre stop codon (UAA). In some cases, an engineered tRNA or variant thereof can be engineered to suppress an opal stop codon (UGA).
[0073] In some cases, the present disclosure provides for compositions of multiple tRNA, engineered tRNAs, or engineered tRNA variants capable of recognizing and suppressing more than one amber stop codon, ochre stop codon, and/or opal stop codon. An engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can comprise an Arginine (Arg) tRNA isodecoder. An engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can comprise a Glutamine (Gin) tRNA isodecoder. An engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can comprise an Arginine (Arg) tRNA isodecoder. An engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can comprise a Glutamine (Gin) tRNA isodecoder.
[0074] In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Gin tRNA isodecoder. In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Gin tRNA isodecoder. In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an amber stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Arg tRNA isodecoder. In some embodiments, an engineered tRNA or variant thereof that can recognize and suppress an ochre stop codon can have a sequence similarity of about 70% to about 100% to a naturally occurring Arg tRNA isodecoder.
[0075] An engineered tRNA or variant thereof with an anticodon configured to base pair with any one of the stop codons described herein can be charged with any one of the amino acids (canonical or noncanonical) described herein.
[0076] Messenger RNAs (mRNAs) can encode polypeptides. Some embodiments described herein relate to polypeptide(s). Polypeptide can include full-length polypeptides or fragments of full-length polypeptides. For example, a fragment of a full-length polypeptide can be encoded by an mRNA with a premature stop codon, whereas a full-length polypeptide can be encoded by an mRNA without a premature stop codon.
[0077] In some embodiments, an mRNA targeted by the engineered tRNA or variant thereof can comprise one, two, three, four, or five premature stop codons. Accordingly, an engineered tRNA or variant thereof as described herein can produce readthrough of the one or more premature stop codons, at least partially restoring a substantially full-length polypeptide. In some cases, at least partially restoring a substantially full-length polypeptide can comprise at least partially treating a disease or condition. In some cases, an engineered tRNA or variant thereof can restore 30% to 99% of PTC readthroughs, e.g., 40% to 45%, 40% to 50%, 40% to 55%, 40% to 60%, 40% to 65%, 40% to 70%, 40% to 75%, 40% to 80%, 40% to 85%, 40% to 90%, 40% to 95%, 45% to 50%, 45% to 55%, 45% to 60%, 45% to 65%, 45% to
70%, 45% to 75%, 45% to 80%, 45% to 85%, 45% to 90%, 45% to 95%, 50% to 55%, 50% to 60%, 50% to 65%, 50% to 70%, 50% to 75%, 50% to 80%, 50% to 85%, 50% to 90%, 50% to 95%, 55% to 60%, 55% to 65%, 55% to 70%, 55% to 75%, 55% to 80%, 55% to 85%, 55% to 90%, 55% to 95%, 60% to 65%, 60% to 70%, 60% to 75%, 60% to 80%, 60% to 85%, 60% to 90%, 60% to 95%, 65% to 70%, 65% to 75%, 65% to 80%, 65% to 85%, 65% to 90%, 65% to 95%, 70% to 75%, 70% to 80%, 70% to 85%, 70% to 90%, 70% to 95%, 75% to 80%, 75% to 85%, 75% to 90%, 75% to 95%, 80% to 85%, 80% to 90%, 80% to 95%, 85% to 90%, 85% to 95%, or 90% to 95% of PTC readthroughs
In some cases, an engineered tRNA or variant thereof can restore at least 40% of PTC readthroughs. In some cases, two or more stop codons can be the same type of stop codon. In some cases, two or more stop codons can be different types of stop codons. In some instances, one type of engineered tRNA or variant thereof can be used to at least partially restore a full- length polypeptide when a target mRNA contains two or more stop codons that are the same type of stop codon. In some instances, more than one type of engineered tRNA or variant thereof can be used to at least partially restore a full-length polypeptide when a target mRNA contains two or more stop codons that are different types of stop codons. In some cases, the engineered tRNA or engineered tRNA variant can reduce or prevent nonsense-mediated decay of the target mRNA. [0078] The engineered tRNAs disclosed herein can be modified to produce an engineered tRNA variant. For example, the engineered tRNAs disclosed herein can be modified relative to a reference tRNA. In some cases, the modification can be a mutation in a sequence of the engineered tRNA, such as an insertion or a substitution of a nucleotide. In some cases, the sequence that can be mutated can be a DNA sequence, a tRNA sequence or a pre-tRNA sequence. In some cases, the modification can be a chemical modification of a nucleotide in the sequence of the engineered tRNA. The chemical modification can comprise a methyl group, a fluoro group, a methoxyethyl group, an ethyl group, a phosphate group, an amide group, an ester group, or any combination thereof. In some cases, the engineered tRNA or the variant thereof can comprise a chemical modification comprising a methyl group, a fluoro group, a methoxyethyl group, an ethyl group, a phosphate group, an amide group, an ester group, or any combination thereof. [0079] The reference tRNA can be a wild-type tRNA or an engineered tRNA, such that the engineered tRNA has more than one mutation. In this context, the wild-type tRNA or the engineered tRNA can be referred to as a “backbone” or “parental” tRNA.
[0080] Mutations can be made in any region of the engineered tRNA including, but not limited to, the acceptor stem, anticodon stem, D-loop, D stem, and T-loop, T-stem, or the variable region or loop to produce the engineered tRNA variants of the present disclosure. For example, substitutions of nucleotides in the acceptor stem and anticodon stem to increase Watson-Crick base pairing can stabilize the acceptor and anticodon stems of the engineered tRNA.
[0081] The canonical tRNA secondary structure and numbering scheme is shown FIG. 1 A. See Laslett and Canback, “ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences,” Nucleic Acids Research 32(1): 11-16 (2004). As shown in FIG. 1 A, the acceptor stem is encoded by residues 1-7 and 66-72. The D-stem is encoded by residues 10-13 and 22-25. The 8-11 residue D-loop is encoded by residues 14-21 (optionally comprising residues 17A, 20A, and 20B). The anticodon stem is encoded by residues 27-31 and 39-43. The anticodon loop is encoded by residues 32-38, with the anticodon being encoded by residues 34-36. The variable region is encoded by residues 44-48. The T-stem is encoded by residues 49-53 and 61-65. The T-loop is encoded by residues 54-60. The CCA end is encoded by residues 73+. The A-box is encoded by residues 9-18. The B-box is encoded by residues 53-61. [0082] Disclosed herein, in some embodiments, are engineered tRNA variants. The engineered tRNA variant can comprise a mutation in a T-loop, a T-stem, a D-loop, a D-stem, a variable loop, an anticodon stem, or an anticodon loop. The mutation can be relative to the nucleic acid sequence, e.g., of any of those in Table 2, Table 3, or Table 4.
[0083] In some embodiments, the engineered tRNA variant comprises 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, or 15 mutations, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4. In some embodiments, the engineered tRNA variant comprises from 1 to 15 mutations, e.g., 1 to 14, 1 to 13, 1 to 12, 1 to 11, 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6,
1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 15, 2 to 14, 2 to 13, 2 to 12, 2 to 11, 2 to 10, 2 to 9, 2 to 8, 2 to 7,
2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 15, 3 to 14, 3 to 13, 3 to 12, 3 to 11, 3 to 10, 3 to 9, 3 to 8, 3 to 7,
3 to 6, 3 to 5, 3 to 4, 4 to 15, 4 to 14, 4 to 13, 4 to 12, 4 to 11, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to ,
4 to 5, 5 to 15, 5 to 14, 5 to 13, 5 to 12, 5 to 11, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 15, 6 to
14, 6 to 13, 6 to 12, 6 to 11, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 15, 7 to 14, 7 to 13, 7 to 12, 7 to
11, 7 to 10, 7 to 9, 7 to 8, 8 to 15, 8 to 14, 8 to 13, 8 to 12, 8 to 11, 8 to 10, 8 to 9, 9 to 15, 9 to 14, 9 to 13, 9 to 12, 9 to 11, 9 to 10, 10 to 15, 10 to 14, 10 to 13, 10 to 12, 10 to 11, 11 to 15, 11 to 14, 11 to 13, 11 to 12, 12 to 15, 12 to 14, 12 to 13, 13 to 15, 13 to 14, or 14 to 15 mutations, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4. In some embodiments, the engineered tRNA variant comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, or at least 15 mutations, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4. In some embodiments, the engineered tRNA variant comprises no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9, no more than 10, no more than 11, no more than 12, no more than 13, no more than 14, or no more than 15 mutations, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4.
[0084] In some embodiments, the engineered tRNA variant comprises mutation(s) in a T- loop, a T-stem, a D-loop, a D-stem, a variable loop, an anticodon stem, an anticodon loop, or a combination thereof, e.g., relative to a reference sequence, e.g., any of those in Table 2, Table 3, or Table 4.
[0085] In some cases, the engineered tRNA variant comprises a mutation in the anticodon (e.g., nucleic acids 33-35 in any of the sequences in Table 2, Table 3, or Table 4. In some cases, the engineered tRNA variant does not comprise a mutation in the anticodon (e.g., nucleic acids 33-35 in any of the sequences in Table 2, Table 3, or Table 4.
[0086] In some cases, reference is made to the DNA sequence of an engineered tRNA or an engineered tRNA variant, such as those provided in Table 2, Table 3, and Table 4. In some cases, reference is made to an RNA sequence of an engineered tRNA or an engineered tRNA variant, such as those provided in Table 2, Table 3, and Table 4. In some cases, a reference made herein to an engineered tRNA or engineered tRNA variant can include a DNA sequence, e.g., of Table 2, Table 3, and Table 4. In some cases, a reference made herein to an engineered tRNA or engineered tRNA variant can include an RNA sequence, e.g., of Table 2, Table 3, and Table 4, that is encoded by a polynucleotide comprising a DNA sequence, e.g., of Table 2, Table 3, and Table 4. In some embodiments, A can be a nucleobase comprising adenosine. In some embodiments, A can be a nucleoside comprising a ribose or a deoxyribose, and adenosine. In some embodiments, A can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and adenosine. In some embodiments, T can be a nucleobase comprising thymine. In some embodiments, T can be a nucleoside comprising a ribose or a deoxyribose, and thymine. In some embodiments, T can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and thymine. In some embodiments, U can be a nucleobase comprising uracil. In some embodiments, U can be a nucleoside comprising a ribose or a deoxyribose, and uracil. In some embodiments, U can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and uracil. In some embodiments, C can be a nucleobase comprising cytosine. In some embodiments, C can be a nucleoside comprising a ribose or a deoxyribose, and cytosine. In some embodiments, C can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and cytosine. In some embodiments, G can be a nucleobase comprising guanine. In some embodiments, G can be a nucleoside comprising a ribose or a deoxyribose, and guanine. In some embodiments, G can be a nucleotide comprising a phosphate, a ribose or a deoxyribose, and guanine.
[0087] In some cases, the engineered tRNA or engineered tRNA variant comprises modifications, e.g., post-transcriptional modifications. See, e.g, Suzuki, “The Expanding World of tRNA Modifications and their Disease Relevance,” Nature Reviews Molecular Cell Biology 22:375-92 (2021), which is hereby incorporated by reference in its entirety. In some cases, the modification(s) are selected from ac4C ( ri-acetylcytidine), acp3U (3-(3-amino-3- carboxypropyl)uridine), Cm (2'-< -methylcytidine), cmnm5s2U (5-carboxymethylaminomethyl-2- thiouridine), cmnm5U (5-carboxymethylaminomethyluridine), D (dihydrouridine), EC (5- formylcytidine), CCm (5-formyl-2'-O-methylcytidine), galQ (galactosyl-queuosine), Gm (2'-< - methylguanosine), hm5C (5-hydroxymethylcytidine), hm5Cm (2'-<9-methyl-5- hydroxymethylcytidine), I (inosine), i6A (A^-isopentenyladenosine), m3A (1 -methyladenosine), manQ (mannosyl-queuosine), m3C (3 -methylcytidine), m5C (5-methylcytidine), mchm5U (5- (carboxyhydroxymethyl)uridine methyl ester), mcm5s2U (5-methoxycarbonylmethyl-2- thiouridine), mcm5U (5-methoxycarbonylmethyluridine), mxG (1 -methylguanosine), m2G (A2- methylguanosine), m2,2G (A2,A2-dimethylguanosine), m7G (7-methylguanosine), m1! (1- methylinosine), mpG (5 '-methylphosphoguanosine), ms2i6A (2-methylthio-A6- isopentenyladenosine), ms2t6A (2-methylthio-A6-threonylcarbamoyladenosine), m6t6A (N6- methyl-A6 -threonylcarbamoyladenosine), m5U (5-methyluridine), m5Um (2'-<9-methyl-5- methyluridine), ncm5U (5-carbamoylmethyluridine), OHyW (hydroxywybutosine), O2yW (peroxywybutosine), Q (queuosine), t6A (A^-threonylcarbamoyladenosine), Um (2'-O- methyluridine), rm5U (5-taurinomethyluridine), rm5s2U (5-taurinomethyl-2-thiouridine), (pseudouridine), 'Em (2'-<9-methylpseudouridine), and combinations thereof.
Engineered tRNAs for Suppression of Opal Stop Codons
[0088] Examples of engineered tRNAs and variants thereof for suppression of opal stop codon(s) are shown in Table 2. In some embodiments, the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5A termination signal). Thus, in some embodiments, the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail. Table 2. Exemplary suppressor tRNA sequence for opal stop codons
Figure imgf000021_0001
Figure imgf000022_0001
Figure imgf000023_0001
Figure imgf000024_0001
Engineered tRNAs for Suppression of Ochre Stop Codons
[0089] Examples of engineered tRNAs and variants thereof for suppression of ochre stop codon(s) are shown in Table 3. In some embodiments, the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5A termination signal). Thus, in some embodiments, the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail.
Table 3. Exemplary suppressor tRNA sequence for ochre stop codons
Figure imgf000024_0002
Figure imgf000025_0001
Figure imgf000026_0001
Engineered tRNAs for Suppression of Amber Stop Codons
[0090] Examples of engineered tRNAs and variants thereof for suppression of ochre stop codon(s) are shown in Table 4. In some embodiments, the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5A termination signal). Thus, in some embodiments, the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail.
Table 4. Exemplary suppressor tRNA sequence for amber stop codons
Figure imgf000026_0002
Figure imgf000027_0001
Figure imgf000028_0001
Mutations in engineered tRNA for Suppression of Stop Codons
[0091] Mutations can be made in any region of the engineered tRNA that suppresses a stop codon including, but not limited to, the acceptor stem, anticodon stem, D-loop, D stem, and T- loop, T-stem, or the variable region or loop to produce the engineered tRNA variants of the present disclosure. For example, substitutions of nucleotides in the acceptor stem and anticodon stem to increase Watson-Crick base pairing can stabilize the acceptor and anticodon stems of the engineered tRNA.
[0092] In some cases, an engineered tRNA or a variant thereof comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to a tRNA, engineered tRNA, or engineered tRNA variant sequence, e.g., as shown Table 2, Table 3, or Table 4.
[0093] In some cases, an engineered tRNA or a variant thereof comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to a tRNA, engineered tRNA, or engineered tRNA variant sequence, e.g., as shown Table 2, Table 3, or Table 4.
[0094] In some cases, an engineered tRNA or variant thereof comprises a sequence that has at least 70% identity to a tRNA, engineered tRNA, or engineered tRNA variant sequence in Table 2, Table 3, or Table 4, e.g., at least 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to a tRNA, engineered tRNA, or engineered tRNA variant sequence in Table 2, Table 3, or Table 4.
[0095] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, or 10, mutations in the A-box region (e.g., corresponding to residues 9-18 of FIG. 1A, or a corresponding region of a sequences in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0096] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, or 9, mutations in the B-box region (e.g., corresponding to residues 53-61 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54). [0097] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14, mutations in the acceptor stem region (e.g., corresponding to residues 1-7 and 66-72 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0098] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, or 8, mutations in the D-arm region (e.g., corresponding to residues 10-13 and 22-25 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0099] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 1, or 11, mutations in the D-loop region (e.g., corresponding to residues 14- 21 of FIG. 1A, or a corresponding region of a sequences in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0100] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, mutations in the anti codon- stem region (e.g., corresponding to residues 27-31 and 39-43 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0101] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, or 7, mutations in the anticodon loop region (e.g., corresponding to residues 32-38 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0102] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, or 3, mutations in the anticodon (e.g., corresponding to residues 34-36 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54). [0103] In some cases, the engineered tRNA or variant thereof does not comprise a mutation in the anticodon (e.g., corresponding to residues 34-36 of FIG. 1A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e g., SEQ ID NO: 32, 79, 7, or 54).
[0104] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, mutations in the variable region (e.g., corresponding to residues 44-48 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54). [0105] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, mutations in the T-stem (e.g., corresponding to residues 49-53 and 61-65 of FIG. 1A, as well as a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54).
[0106] In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, or 7, mutations in the T-loop (e.g., corresponding to residues 54-60 of FIG. 1 A, or a corresponding region of a sequence in Table 2, Table 3, or Table 4), relative to a reference sequence (e.g., a sequence in Table 2, Table 3, or Table 4, e.g., SEQ ID NO: 32, 79, 7, or 54). [0107] Exemplary mutations are set forth in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 of the mutations shown in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, of the A-box mutations shown in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, of the Variable Region mutations shown in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more, e.g., 1, 2, 3, 4, or 5, of the B-box mutations shown in Table 5.
[0108] In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, but none of the Variable Region or B-box mutations in Table 5. [0109] In some cases, the engineered tRNA or variant thereof comprises one or more Variable Region mutations as shown in Table 5, but none of the A-box or B-box mutations in Table 5.
[0110] In some cases, the engineered tRNA or variant thereof comprises one or more B-box mutations as shown in Table 5, but none of the Variable Region or A-box mutations in Table 5. [OHl] In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5 and one or more of the Variable Region mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, and one or more of the B-box mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more B-box mutations as shown in Table 5, and one or more of the Variable Region mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, one or more of the Variable Region mutations in Table 5, and one or more of the B-box mutations in Table 5 [0112] In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5 and one or more of the Variable Region mutations in Table 5, but none of the B-box mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5 and one or more of the B-box mutations in Table 5, but none of the Variable Region mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more B-box mutations as shown in Table 5 and one or more of the Variable Region mutations in Table 5, but none of the A-box mutations in Table 5. In some cases, the engineered tRNA or variant thereof comprises one or more A-box mutations as shown in Table 5, one or more of the Variable Region mutations in Table 5, and one or more of the B-box mutations in Table 5, but none of the mutations described herein.
Table 5. Exemplary Mutations to Engineered tRNA to produce Engineered tRNA variants
Figure imgf000031_0001
[0113] As shown in Table 5, the format Xi>X2 indicates that Xi can be substituted for X2. The number preceding Xi>X2 indicates the nucleotide position with reference to the DNA sequence encoding the engineered tRNA. Thymine (“T”) can be present in the DNA context, and when in reference to the tRNA sequence, should be understood to refer to uracil (“U”). When X2 is N, the mutation can be a change from the reference residue to any residue other than the original residue in the reference sequence. In the context of a DNA sequence, “N” could be a mutation to A, G, C, or T. In the context of a RNA sequence, “N” could be a mutation to A, G, C, or U. [0114] In some cases, an engineered tRNA variant comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to an engineered tRNA variant sequence, e.g., as shown Tables 6A-6D.
[0115] In some cases, an engineered tRNA variant comprises a sequence that has from 70% to 100% identity, e.g., 70% to 99% identity, to an engineered tRNA variant sequence, e.g., as shown Tables 6A-6D.
[0116] In some cases, an engineered tRNA variant comprises a sequence that has at least 70% identity to an engineered tRNA variant sequence in Tables 6A-6D, e.g., at least 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to an engineered tRNA variant sequence in Tables 6A-6D.
[0117] Examples of engineered tRNA variants are shown in Tables 6A-6D. In some embodiments, the engineered tRNA or variant thereof comprises a poly-A termination signal (e.g., a 5 A termination signal). Thus, in some embodiments, the DNA sequence encoding the engineered tRNA or variant thereof comprises a poly-T tail.
Table 6A. Exemplary Mutations to Engineered tRNA to produce Engineered tRNA variants
Figure imgf000032_0001
Figure imgf000033_0001
Figure imgf000034_0001
Figure imgf000035_0001
Table 6B. Exemplary Mutations to Engineered tRNA to produce Engineered tRNA variants
Figure imgf000035_0002
Figure imgf000036_0001
Table 6C. Exemplary Mutations to Engineered tRNA to produce Engineered tRNA variants
Figure imgf000036_0002
Figure imgf000037_0001
Table 6D. Exemplary Mutations to Engineered tRNA to produce Engineered tRNA variants
Figure imgf000037_0002
Figure imgf000038_0001
REGULATORY ELEMENTS / REGIONS
[0118] In some cases, expression of the engineered tRNA and variants thereof described herein is driven by regulatory element(s) such as enhancer and/or promoter sequence(s). Thus, also described herein are nucleic acid sequence(s) encoding the regulatory element(s).
[0119] In some cases, the engineered tRNA(s) or variant(s) thereof are on the same nucleic acid molecule(s) as the regulatory element(s). In some cases, the engineered tRNA(s) or variant(s) thereof are on different nucleic acid molecule(s) as the regulatory element(s).
[0120] In some cases, the regulatory element is a known regulatory element, e.g., a promoter (e.g., as described herein). In some cases, the promoter is a Polymerase III promoter. In some cases, the promoter is a Polymerase III type 1 promoter. In some cases, the promoter is a Polymerase III type 2 promoter. In some cases, the promoter is a Polymerase III type 3 promoter. In some cases, the Polymerase III type 3 promoter is a 7SK, U6, or Hl promoter. In some cases, the promoter is a human promoter.
[0121] In some cases, the regulatory element is a putative regulatory element, e.g., a tRNA upstream region (e.g., as described herein). In some cases, the putative regulatory element is in a putative regulatory region. In some cases, the putative regulatory element comprises a promoter or enhancer. In some cases, the putative regulatory element is a novel regulatory element. In some cases, the putative regulatory element comprises a novel promoter or enhancer.
[0122] In some cases, the engineered tRNA and variants thereof described herein are driven by a putative regulatory element, e.g., within a region 5’ of a known tRNA sequence (a “putative regulatory region”). In some cases, the putative regulatory region comprises from 20 to 500 bp 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises from 20 nucleotides to 500 nucleotides 5’ of a known tRNA sequence. In some cases, the putative regulatory region is from 20 nucleotides to 500 nucleotides in length, e.g., 20 to 450, 20 to 400, 20 to 350, 20 to 300, 20 to 250, 20 to 200, 20 to 150, 20 to 100, 20 to 50, 50 to 500, 50 to 450, 50 to 400, 50 to 350, 50 to 300, 50 to 250, 50 to 200, 50 to 150, 50 to 100, 100 to 500, 100 to 450, 100 to 400, 100 to 350, 100 to 300, 100 to 250, 100 to 200, 100 to 150, 150 to 500, 150 to 450, 150 to 400, 150 to 350, 150 to 300, 150 to 250, 150 to 200, 200 to 500, 200 to 450, 200 to 400, 200 to 350, 200 to 300, 200 to 250, 250 to 500, 250 to 450, 250 to 400, 250 to 350, 250 to 300, 300 to 500, 300 to 450, 300 to 400, 300 to 350, 350 to 500, 350 to 450, 350 to 400, 400 to 500, 400 to 450, or 450 to 500 nucleotides in length.
[0123] In some cases, the putative regulatory region comprises 100, or about 100, bases 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises 227, or about 227, bases 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises 100, or about 100, nucleotides 5’ of a known tRNA sequence. In some cases, the putative regulatory region comprises 227, or about 227, nucleotides 5’ of a polynucleotide encoding a known tRNA. In some cases, the putative regulatory region 5’ of a polynucleotide encoding a known tRNA is engineered to be 5’ of a polynucleotide encoding a different tRNA (e.g., a polynucleotide encoding a tRNA that is not that known tRNA).
[0124] In some cases, the putative regulatory region comprises AGGCCATATGCTATTTTTGTACAGTAATCCTTTCCTTTTTTTCCCCATTTTTCTTAAAT CTTAAAAATAAGACTGAATTCTGATATCAAGAGTTAAGGTC (SEQ ID NO: 192), CTTTTAATTTATTTCTTAAACTTTATTTAGACTTAAACACTATTTACCTAGGATTTTAG CTGCATAATAGATTGATTGTTAAATGTTTGCTCTCTGTGGC (SEQ ID NO: 193), CTCTGGAGTGAGGCTTCATTGGTCCCAGGTGAGCGTTTCGTTGCCAGCTCGTTGCGC GAGGTCTGAATGCACAGTGGAAACAACTTAGGGTGGGTATGGGAAAAGAAGAAAC ATATTTCAGAAGCACTCGCCAATATAAATTTTTAAAAATAAAGATCTTAATACAGTA ATTTGACTAGAGCTAGCAGACTGAATGAGTATGGACACCAGAAATATGCTTTCGGCT G (SEQ ID NO: 194), or CAGGGGCAGAGGGGCGGGGGCGGGTGAGAACTGAGGGGCCACAGGATTGGTGTGA GGGGTGCAGGGGCCTCTCCCCACTTTGTGCGGTGCGGAGAGGGGCCGGGGCGCTGG CCCACCCACTGAGTCTGCAATCCCAGTCTCCTGTCACTTTGCTTTCGCAGGCTTGAGC TTTATCGCTCCAAGTACTCCACGGCTGCCACAAAGAAAAGTAAAGGGCCTGCTGCTG T (SEQ ID NO: 195).
[0125] In some cases, the putative regulatory region comprises
TGTTAGCTTTTAGTCGACACTTGAAAAAACCGCTTGGAACGGTTTCTAAGTCTTTGT GGATACTCTTTTCTGTTATCCTCCAGGCGGTAGTTACGCAGAG (SEQ ID NO: 320);
GCTGGAGTGCAGTGGTGCGATCTTGGATTTGGAAACTATAATAGAAACGGCTGATCT AAGATTTTCATGGTTATGTTTTGCCGCGCAGGTTCCGCGTGTG (SEQ ID NO: 321);
AATCAGCAAAAAGACTCAGAATTGTAATCGCGAAGGGAAAGAATGCGGCCACGTG
GCCTATTTTCCTGTGGATAGACTAAGCAAACGCTTTTCTTCAGGG (SEQ ID NO: 322);
GTGGAGGGGCAGAGAGTAAATGGAAGAGAAAGACTGGTACCCCTGGAAGAAACGC CATTTACTGGTGTCCTAAGAAACTGCGCGAGCCACAGCCCAGCAG (SEQ ID NO: 323);
CGGAAGGACCGGCCTCCCCTCACTCTAAGCATGCGCGTTAAAGCGACAGCATAGGC
TATAGAAAGCTTTATGAGAATAGCTGGGAGCCATACAGCCGCAG (SEQ ID NO: 324);
CATACCCGGCCATCGCCAGCAGTCAATGGAATGTGAGTGCCTTAGAGGTCTTGGGG CCGAAACGATCTCAACCTATTCTCAAACTTTAAATGGGCAAGAA (SEQ ID NO: 325);
TCTGCGATGCCCTGTGGATTCGCCTCGACGCCTTGTTGGCCCGGGGACCCTGGGGAT GTTTTATAAGGAAGGAAAAGATGTAGGTGAAGCCCAGAAGGAG (SEQ ID NO: 326); TTCTTTCCAACTCCAAGAACTTCAGAAAAGTTTCTTTGGTGATTGGAATAACGTTCG CCTTTAAACTTCTCAAGAGAGGTAGGGTCCGTTCCGCCGGCGG (SEQ ID NO: 327);
ATAATTTACTGAAAGGAAAGGCCAATCAACTCGATGTTACCAAAGCTGAAACAGAA AAATTTAATTCTCCCTTAACGAAGGAAGCCAACGCAGCACACAG (SEQ ID NO: 328); AGGAAACCATTTTTACCGTATTTTGTTCTTTTGACCGTTTCTTGTCAGTTAGCTGGTG TAAATTCTGTTTAAAGATGTGAAGGGAGCCTTCTCCATTCGT (SEQ ID NO: 329);
TCTTTCCAGTTCCGAGAAGTTCAGAAAAGTTTCTTCGGTGATTGGAATAACGTTCGC CTTTAAACTTCTCAAGAGATTTAGGGTGGGTTTTAGTATGCGG (SEQ ID NO: 330); TCCCCCCCCACCGCTCAGAGAGCAGGATGCTGAGATGGCTCGGTGATGCAGAAGGT ATGTGCTTTTTCAGTTCTGGTGCTGATGCTGTGTGTGTGGTGAG (SEQ ID NO: 331);
GCTGTGGGTGGCCCGCCCGGGTACTTTTCTCGTGGGTCAGAGACACAGTGGTGAGCC TCTGACTTTTCAGAGTCATTTGTGGAAAACCTGCCACCGCCTG (SEQ ID NO: 332);
GTTTTGTGGGAAATACAAGATACTTAATTCTTTGGAAAGTGTTTAGGGAAAGCTACG TTTACCTTAAAACAGTCTCTTGAAGAACCTGTTTTATGGGCGG (SEQ ID NO: 333);
CAGCTTCAGTAGCGCAGAGGCGGCGGTGGCGAGAGGTGCGGCGAAGGAGGCAGAG GCACTTATGCTTGTCAGGTGGGTCACGGCAGTTTCTCATAGCACT (SEQ ID NO: 334); TGGAATTTTACTCAAGCTAACATCCTATTCAGTAGCCGGAATGCTAGGAGCATAACA TCAATCTATAAGATGAAAGGAAGAGAAACTAAAAGCAGACGAG (SEQ ID NO: 335); AATCGGAGTCTCCTCCTAGCTCTGCTCTGCTGGGTCCCCACCTCTGGCCACGAGGAC TCCACGAAGGCCACAAAGACAAGCCGGAGGCTACGGGGCGTGT (SEQ ID NO: 336); GCTTTAGCTGACTGTAGCCAGTGTTTCTTTGGTGGGACAACGCAACTATCACTGCAA CATTATCTCTATAGGAGAATTTAAAGAACCCTGACGCCTACCG (SEQ ID NO: 337); TTTAAATTCGAAAGGAATGTTAGACACCAAAGGTATTTATGAGGTGTTTTGCAGGTC ATAAAAATGGAATAAATGGTTTTTTGAAGGTTATTGGCATCAA (SEQ ID NO: 338);
TGGGCATAAACTAAGGATTTTTGCTTTGATACATTAAATGCGTTTAGTAGAATGCCT ATAACCCAGCATGAGCAATATTTGGGTGAAGCGTACCAAGAGG (SEQ ID NO: 339); TTGTGAAGTCACCTAACAAACTAGTTGCTGGGATTGTTGCAAATTACGGAAGTGTGA AATAGTTTTCAAGTAGTATACGATCGAGGGCTTTCTCGGCTGT (SEQ ID NO: 340);
TCATGTCATATAAGTAGAACCATACAATATATATATAAAATCCAGGTTAATAGCCAA TCTTACAACATTTCTCATATTTTTTGCAGTTGCTAAGCCATGG (SEQ ID NO: 341);
CTTGTAACTCAGAAACCCATCCTGAAGCGGAATCTAGGACAGCAGGTCTGGGTGTG GCTGCACAGGGAAAGGTTGTTAATTGGACCTTACTAATGTAACT (SEQ ID NO: 342); or
ATTACATAACTCCACACTCTGGAGACAGAGTGGCCAGAGCGTAGCTTGTGAATGAC TGTGATTATTAATATATCTTTATTGAAAGAAGATGAGTACCTTG (SEQ ID NO: 343). [0126] In some cases, the putative regulatory region comprises at least 25 bases (e.g., at least 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 bp) of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343. In some cases, the putative regulatory region comprises at least 20 bases of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343. In some cases, the putative regulatory region comprises from 20 bases to 100 bases of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343. In some cases, the putative regulatory region comprises 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 bp, or any number of bp therebetween, of SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343.
[0127] In some cases, the putative regulatory region comprises at least 100 bases (e.g., at least 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, or 225 bp) of SEQ IDNO: 194 or SEQ ID NO: 195. In some cases, the putative regulatory region comprises from 20 bases to 100 bases of SEQ IDNO: 194 or SEQ ID NO: 195. In some cases, the putative regulatory region comprises 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, or 225 bp, or any number of bp therebetween, of SEQ IDNO: 194 or SEQ ID NO: 195.
[0128] In some cases, the putative regulatory region comprises a sequence that has from 70% to 100% identity (e.g., 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, or 99% to 100% identity) to SEQ ID NO: 192, SEQ ID NO: 193, SEQ IDNO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343.
[0129] In some cases, the putative regulatory region is engineered to be 5’ of a polynucleotide coding for a tRNA. In some cases, the putative regulatory region is engineered to be 5’ of an engineered tRNA and variants thereof described herein. For example, the putative regulatory region is 5’ of an engineered tRNA or variant thereof comprising from 70% to 100% sequence identity (e.g., 80% to 100%, 85% to 100%, 90% to 100%, 95% to 100%, or 99% to 100% identity) to any one of SEQ ID NOs: 3-48, 96-115, 136-155, 196, 197, 199-222, 227, 228, 229, 272-295, or 344-365. In some cases, the putative regulatory region engineered to 5’ of the polynucleotide coding for the tRNA is in a vector (e.g., a viral vector) as disclosed herein. METHODS FOR HIGH THROUGHPUT LENTIVIRAL SCREENING
[0130] A need exists for methods of screening and identifying tRNA variants and/or putative regulatory regions that can provide improved PTC readthrough efficiency compared to current suppressor tRNAs. Provided herein are methods for generating and screening engineered tRNA variant libraries to identify engineered tRNA variants that provide improved PTC readthrough efficiency. Provided herein are methods for generating and screening putative regulatory region libraries to identify novel regulatory elements that provide improved PTC readthrough efficiency when upstream of a suppressor tRNA (e.g., an engineered tRNA or engineered tRNA variant). [0131] In some cases, the method comprises: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding a tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA, e.g., as described herein and, optionally, an intact reporter protein; introducing the expression vectors into cells stably expressing a broken PTC readthrough reporter protein (e.g., a PTC readthrough reporter protein with engineered premature stop codons, e.g., a fluorescent protein with engineered premature stop codons, e.g., GFP with engineered premature stop codons); incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells based on expression levels of unbroken PTC readthrough reporter protein; identifying the sequence of the engineered tRNA variant(s) and/or regulatory regions of one or more of the cell(s) in one or more of the bin(s); and, based on the sequence, identifying engineered tRNA variants with improved PTC readthrough efficiency.
[0132] In some cases, the library comprises from 200 to 100,000 lentiviral expression vectors to be screened. In some cases, the library comprises about 200, 500, 1,000, 5,000, 10,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, or 100,000 lentiviral expression vectors to be screened. In some cases, the library comprises 100,000 or more lentiviral expression vectors to be screened.
Reporter Proteins
[0133] Reporter proteins can be used to identify, for example, cells that comprise a tRNA variant encoding sequence (e.g., plasmid).
[0134] They can also be used to identify PTC readthrough (e.g., when a cell expresses both an engineered tRNA variant and a “broken” reporter protein). In this case, the reporter protein can be referred to as a “PTC readthrough reporter protein.”
[0135] In some cases, the reporter protein or PTC readthrough reporter protein is a fluorescent protein. In some cases, the reporter protein is a green fluorescent protein, yellow fluorescent protein, or red fluorescent protein. In some cases the reporter protein is EBFP, ECFP, EGFP, YFP, mHoneydew, mBanana, mOrange, tdTomato, mTangerine, mStrawberry, mCherry, mGrapel, mRaspberry, mGrape2, or mPlum.
[0136] In some cases, the reporter protein and PTC readthrough reporter proteins are different, e.g., different fluorescent proteins.
Lentiviral Expression Vectors
[0137] Described herein are lentiviral expression vectors comprising the engineered tRNA variants, e.g., as described herein (with a promoter, for example with a human U6 promoter, or without a promoter). Described herein are lentiviral expression vectors comprising putative regulatory region(s) 5’ upstream of a tRNA, such as a suppressor tRNA, engineered tRNA, or engineered tRNA variant. An exemplary lentiviral expression vector is shown in FIG. 2A.
Promoters
[0138] In some cases, the lentiviral expression vector(s) comprise promoter(s). In some cases, for example, the promoter is human U6.
[0139] In some cases, the promoter is a Polymerase III promoter. In some cases, the promoter is a Polymerase III type 1 promoter. In some cases, the promoter is a Polymerase III type 2 promoter. In some cases, the promoter is a Polymerase III type 3 promoter. In some cases, the Polymerase III type 3 promoter is a 7SK, U6, or Hl promoter. In some cases, the promoter is a human promoter.
Reporter Proteins
[0140] In some cases, the lentiviral expression vector(s) comprise reporter protein(s), e.g., as described above.
Selectable Markers
[0141] In some cases, the lentiviral expression vector(s) comprise selectable marker(s). In some cases, the selectable marker is an antibiotic resistance gene. In some cases, the selectable marker is a puromycin resistance gene. In some cases of the methods described herein, cell(s) are selected using the selectable marker, for example, to confirm successful transduction.
Cells and Transduction
[0142] In some cases, the lentiviral expression vector(s) described herein are introduced into cell(s). In some cases, the cell(s) are mammalian cell(s). In some cases, the cell(s) are human cell(s). In some cases, the cell(s) are from a cultured cell line. [0143] In some cases, the cell(s) express a reporter protein. In some cases, the cell(s) express a reporter protein having a PTC, which is also referred to as a broken reporter protein. In some cases, the cell(s) stably express a broken reporter protein. In some cases, the broken reporter protein is a broken fluorescent protein. In some cases, the broken reporter protein is broken GFP (e.g., a GFP having a PTC).
[0144] In some cases, the transduction is performed at a multiplicity of infection such that cells expressing, e.g., stably expressing, a single copy of the engineered tRNA or variant thereof per cell are obtained.
Sorting
[0145] In some cases, the cell(s) expressing the lentiviral expression vector(s) described herein are sorted, e.g., on PTC readthrough efficiency, e.g., based on expression level of an intact version of the protein that the cell(s) express, such expression of the full-length protein version of a broken reporter protein.
Variant Identification
[0146] In some cases, a subset of the sorted cell(s), e.g., those with high PTC readthrough efficiency, e.g., based on expression level of an intact version of the protein that the cell(s) express as a broken reporter protein, are identified by sequence. In some cases, the identification comprises sequencing the engineered tRNA and/or putative regulatory region sequence(s).
COMPOSITIONS COMPRISING THE ENGINEERED TRNA AND VARIANTS THEREOF
[0147] Also provided herein are compositions comprising the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells. Also provided herein are compositions comprising putative regulatory regions 5’ upstream of tRNAs, such as the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells. Also provided herein are compositions comprising regulatory elements 5’ upstream of tRNAs, such as the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells. Also provided herein are compositions comprising U6 promoters 5’ upstream of tRNAs, such as the engineered tRNAs and variants thereof described herein, e.g., oligonucleotide libraries, plasmid libraries, vector libraries, and/or cells. METHODS OF MANUFACTURE
[0148] Provided herein are methods of generating the tRNA, engineered tRNAs, or engineered tRNA variants, the polynucleotide encoding the tRNA, engineered tRNAs, or engineered tRNA variants, or the pharmaceutical compositions described herein. Provided herein are methods of generating putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants, the polynucleotide encoding the putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants, or the pharmaceutical compositions described herein. The method can include aspects disclosed herein. In some cases, a vector can be produced that can comprise a plurality of promoters, a genetic sequence encoding one or more tRNA, engineered tRNAs, or engineered tRNA variants, and/or a genetic sequence encoding putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants. The vector can comprise a first promoter (e.g., an hU6, or a mU6 promoter), a second promoter (e.g., an hU6, or a mU6 promoter), a third promoter (e.g., a human cytomegalovirus (CMV) promoter), a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide. The vector can comprise a putative regulatory region, regulatory element, and/or promoter, and a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide. The polynucleotide can comprise a 5’ ITR upstream of the promoter. In some cases, the polynucleotide can comprise a 3’ ITR downstream of the reporter gene. In some cases, the reporter gene can comprise one or more genes encoding for mCherry, green fluorescent protein (GFP), or P-galactosidase. The first promoter or the second promoter can comprise a U6 promoter (e.g., a human U6 (hU6)). The U6 promoter can be a human U6 promoter or a mouse U6 promoter. The hU6 promoter can comprise at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 388. The U6 promoter can be methylated. The third promoter can be a human cytomegalovirus (CMV) promoter. In some cases, the vector can be produced by purification or isolation. In some cases, the promoter can be a U7 promoter. In some cases, the promoter can be a PolIII promoter.
PACKAGING
[0149] The present disclosure provides viral vectors packaging tRNA, engineered tRNAs, or engineered tRNA variants, putative regulatory regions, regulatory elements, promoters, stuffer sequences, and any combination thereof. In some embodiments, the viral vectors of the present disclosure can package one or more copies of the engineered tRNA or variant thereof. In some embodiments, the viral vectors of the present disclosure can package 2 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package 3 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package 4 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package 6 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package more than 6 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. Viral vectors of the present disclosure can package from 1 to 200, from 1 to 100, from 50 to 100, from 20 to 40, from 10 to 50, or from 1 to 70 copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package at least 1, 10, 20, 30, 40, 50, 70, 100, 200, 300, 400 or more copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, the viral vectors of the present disclosure can package at most about 400, 300, 200, 100, 70, 50, 40, 30, 20, 10, 2, or less copies of the tRNA, engineered tRNAs, or engineered tRNA variants. In some embodiments, a putative regulatory region is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants. In some embodiments, a regulatory element is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants. In some embodiments, a promoter is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants. In some embodiments, a hU6 promoter is upstream each or some the copies of the tRNAs, engineered tRNAs, or engineered tRNA variants.
[0150] One or more tRNA, engineered tRNAs, or engineered tRNA variants, and/or one or more putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants can be packaged in a vector, including but not limited to a plasmid, an AAV vector, a lentivirus vector, or any other vector system. The vectors disclosed herein can also encode for a marker or a reporter gene, such as GFP or mCherry. The vectors disclosed herein can also encode for an upstream promoter, such as human U6 (hU6). In some embodiments, engineered tRNA or variants thereof, markers, and/or stuffer sequences are packaged in a viral vector are under the control of a regulatory element, such as a promotor (e.g., a mouse U6 (mU6) or a human U6 (hU6) promoter). In some embodiments, engineered tRNAs suppressors or variants thereof, markers, regulatory elements, and/or stuffer sequences are packaged in a viral vector without a promoter. In some cases, a vector can comprise a plurality of promoters, a genetic sequence encoding one or more tRNA, engineered tRNAs, or engineered tRNA variants, and/or a genetic sequence encoding putative regulatory regions, regulatory elements, and/or promoters, such as hU6, upstream of tRNAs, engineered tRNAs, or engineered tRNA variants. The vector can comprise a first promoter (e.g., an hU6, or a mU6 promoter), a second promoter (e.g., an hU6, or a mU6 promoter), a third promoter (e.g., a human cytomegalovirus (CMV) promoter), a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide. The vector can comprise a putative regulatory region, regulatory element, and/or promoter, and a transgene comprising a polynucleotide encoding an engineered tRNA or a variant thereof, and a reporter gene encoding a detectable polypeptide. The polynucleotide can comprise a 5’ ITR upstream of the promoter. In some cases, the polynucleotide can comprise a 3’ ITR downstream of the reporter gene. In some cases, the reporter gene can comprise one or more genes encoding for mCherry, green fluorescent protein (GFP), or P-galactosidase. The first promoter or the second promoter can comprise a U6 promoter (e.g., a human U6 (hU6). The U6 promoter can be a human U6 promoter or a mouse U6 promoter. The U6 promoter can be methylated. The third promoter can be a human cytomegalovirus (CMV) promoter. In some cases, the vector can be purified or isolated.
[0151] The vectors of the present disclosure can also package a stuffer sequence, to ensure successful production of virus particles that package the entire genome to be delivered. For example, a naturally occurring stuffer sequence (e.g., DNA from strawberry or lambda phage) can be included in the vector. In some embodiments, the stuffer sequence can be a fully synthetic sequence. In some embodiments, vectors provided herein package from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence. In some embodiments, vectors provided herein package putative regulatory regions, from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence. In some embodiments, vectors provided herein package regulatory elements, from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence. In some embodiments, vectors provided herein package promoters, from 1 to 6 tRNA, engineered tRNAs, or engineered tRNA variants and a stuffer sequence. In some embodiments, vectors provided herein package a hU6 promoter, from 1 to 6 engineered tRNAs and a stuffer sequence. A spacer sequence can include a stuffer sequence or a filler sequence. A spacer sequence, a stuffer sequence, or a filler sequence can be referred to interchangeably in some embodiments. In some cases, the vector can comprise one or more spacer sequences to place a sequence of an engineered tRNA or a variant thereof in different distances from an ITR. In some cases, the vector can comprise one or more spacer sequences to place a sequence of putative regulatory region, regulatory element, and/or promoter upstream of an engineered tRNA or a variant thereof in different distances from an ITR. The spacer sequence can comprise a 6 nucleotides (nts) long sequence. The spacer sequence can comprise 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 1000 nucleotides or any number of nucleotides in between any of the two numbers of nucleotides mentioned herein. For example, the space sequence can comprise between about 10 nts to about 100 nts, about 100 nts to about 500 nts, about 50 to about 600 nts, or about 200 nts to about 1000 nts. In some cases, the spacer sequence can comprise less than 6 nts or more than 1000 nts. In some cases, the spacer sequence can comprise a stuffer sequence. The stuffer sequence can be about 25, about 50, about 100, about 150, about 200, about 250, or about 300 nucleotides in length. The stuffer sequence can be 25, 50, 100, 150, 200, 250, or 300 nucleotides in length, or a range of lengths encompassing any two of the aforementioned numbers of nucleotides. In some embodiments, the stuffer sequence can comprise at least 25 nucleotides, at least 50 nucleotides, at least 100 nucleotides, at least 150 nucleotides, at least 200 nucleotides, at least 250 nucleotides, or at least 300 nucleotides. In some embodiments, the stuffer sequence is at least about 50 nucleotides, at least about 100 nucleotides, at least about 150 nucleotides, or at least about 200 nucleotides. In some embodiments, the stuffer sequence can comprise at least 250 nucleotides, at least 300 nucleotides, at least 350 nucleotides, at least 400 nucleotides, at least 450 nucleotides, or at least 500 nucleotides. In some embodiments, the stuffer sequence can comprise no more than 25 nucleotides, no more than 50 nucleotides, no more than 100 nucleotides, no more than 150 nucleotides, no more than 200 nucleotides, no more than 250 nucleotides, or no more than 300 nucleotides. In some embodiments, the stuffer sequence is no more than about 50 nucleotides, no more than about 100 nucleotides, no more than about 150 nucleotides, or no more than about 200 nucleotides. In some embodiments, the stuffer sequence can comprise no more than 250 nucleotides, no more than 300 nucleotides, no more than 350 nucleotides, no more than 400 nucleotides, no more than 450 nucleotides, or no more than 500 nucleotides.
[0152] In some embodiments, the stuffer sequence is 5’ of one or more copies of the engineered tRNA or engineered tRNA variant within the polynucleotide. In some embodiments, the stuffer sequence is 5’ of one or more copies of the putative regulatory region, regulatory element, and/or promoter that is upstream of the engineered tRNA or engineered tRNA variant within the polynucleotide. In some embodiments, the stuffer sequence is 3’ of one or more copies of the engineered tRNA or engineered tRNA variant within the polynucleotide. In some embodiments, the stuffer sequence separates two or more copies of the engineered tRNA or engineered tRNA variant within a polynucleotide or separates two or more copies of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant. In some embodiments, multiple stuffer sequences separate multiple copies of the engineered tRNA or engineered tRNA variant within a polynucleotide. For example, a polynucleotide encoding an engineered tRNA or engineered tRNA variant can comprise a first copy of the engineered tRNA or engineered tRNA variant, followed by a first stuffer sequence, followed by a second copy of the engineered tRNA or engineered tRNA variant, followed by a second stuffer sequence, followed by a third copy of the engineered tRNA or engineered tRNA variant (in a 5’ to 3’ direction). There also can be one or more stuffer sequences 5’ of the first copy of the engineered tRNA or engineered tRNA variant, or 3’ of the third copy of the engineered tRNA or engineered tRNA variant. For example, a polynucleotide encoding putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant can comprise a first copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant, followed by a first stuffer sequence, followed by a second copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant, followed by a second stuffer sequence, followed by a third copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant (in a 5’ to 3’ direction). There also can be one or more stuffer sequences 5’ of the first copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant, or 3’ of the third copy of the putative regulatory region, regulatory element, or promoter that is upstream of the engineered tRNA or engineered tRNA variant.
[0153] In some cases, changing the distance of an engineered tRNA or a variant thereof from an ITR can increase an efficiency of a stop codon readthrough of the engineered tRNA or a variant thereof. In some cases, an orientation of a sequence of an engineered tRNA or a variant thereof in a vector construct can affect an efficiency of a stop codon readthrough of the engineered tRNA or a variant thereof. In some cases, a vector can comprise one or more engineered tRNA sequences or an engineered tRNA variant sequences in a vector placed in different orientations. In some cases, changing the distance of a putative regulatory region, regulatory element, or promoter that is upstream of an engineered tRNA or a variant thereof from an ITR can increase an efficiency of a stop codon readthrough of the engineered tRNA or a variant thereof. In some cases, an orientation of a sequence of a putative regulatory region, regulatory element, or promoter that is upstream of an engineered tRNA or a variant thereof in a vector construct can affect an efficiency of a stop codon readthrough of the engineered tRNA or a variant thereof. In some cases, a vector can comprise one or more putative regulatory regions, regulatory elements, or promoter that are upstream of the engineered tRNA sequences or the engineered tRNA variant sequences in a vector placed in different orientations. KITS
[0154] In some embodiments, a kit can comprise a composition described herein for treating a disease or disorder, and a container. In some embodiments, a kit can comprise a composition described herein for treating Rett Syndrome, and a container. In some embodiments, a kit can comprise a composition described herein for treating Hurler Syndrome, and a container. In some embodiments, a kit can comprise a composition described herein for treating Cystic Fibrosis, and a container. In some embodiments, a kit can comprise a composition described herein for treating a kidney disease or disorder, and a container. For example, a kit can comprise a pharmaceutical composition, which can comprise an engineered tRNA or variant thereof, a polynucleotide (e.g., vector) encoding the engineered tRNA or variant thereof, or both. For example, a kit can comprise a pharmaceutical composition, which can comprise a regulatory element or a promoter upstream of an engineered tRNA or variant thereof, a polynucleotide (e.g., vector) encoding the regulatory element or a promoter upstream of the engineered tRNA or variant thereof, or both. In some instances, a container can be plastic, glass, metal, or any combination thereof. In some cases, a kit can comprise instructions for use, such as instructions for administration to a subject in need thereof.
[0155] In some instances, a packaged product comprising a composition described herein can be properly labeled. In some instances, the pharmaceutical composition described herein can be manufactured according to good manufacturing practice (cGMP) and labeling regulations. In some cases, a pharmaceutical composition disclosed herein can be aseptic.
[0156] Disclosed herein, in some embodiments, are kits comprising an engineered tRNA or variant thereof and/or a regulatory element or promoter upstream of an engineered tRNA or variant thereof. Disclosed herein, in some embodiments, are kits comprising an engineered tRNA variant. Disclosed herein, in some embodiments, are kits comprising a regulatory element or a promoter upstream of an engineered tRNA variant. In some embodiments, the kits can comprise a pharmaceutical composition described herein (e.g. an engineered tRNA or variant thereof and a pharmaceutically acceptable excipient, carrier or diluent, optionally in a dose unit form, or an regulatory element or promoter upstream of an engineered tRNA or variant thereof and a pharmaceutically acceptable excipient, carrier or diluent, optionally in a dose unit form). In some embodiments, the kit can comprise a packaging or a container. In some embodiments, the kit can comprise a packaging. In some embodiments, the kit can comprise a container.
[0157] Some embodiments relate to methods of making the kit. The method can include contacting the composition with a packaging or container. The method can include contacting the composition with a packaging. The method can include contacting the composition with a container. METHODS OF TREATMENT
[0158] Premature stop codons leading to mutations in proteins have been implicated in many severe diseases and disorders, such as Rett Syndrome, Dravet Syndrome, and muscular dystrophies such as Duchenne Muscular Dystrophy. Translation of a mRNA molecule that contains a premature stop codon can cause premature termination of the translation process to produce a truncated polypeptide or protein. As used herein, “premature stop codon” can be used interchangeably with “premature termination codon” (PTC). The unintended truncation of proteins vital to neurodevelopment, particularly in children, can cause severe and life-altering diseases or disorders.
[0159] In some cases, the stop codon can be opal (TGA; UGA), ochre (TAA; UAA), or an amber (TAG; UAG) stop codon. In some cases, the disease-causing mutation in the mRNA sequence can comprise an opal stop codon (TGA; UGA) in the place of a codon encoding Arg (e.g., CGU, CGC, CGA, CGG, AGA, or AAG). In some cases, the disease-causing mutation in the mRNA sequence can comprise an ochre (TAA; UAA) or an ochre (TAG; UAG) stop codon in the place of a codon encoding Glutamine (e.g., CCA, CAG). In some cases, the premature stop codon results in a truncated version of the polypeptide or protein. In some cases, the disease, disorder, or condition can be caused by an increased level of a truncated version of the polypeptide, or a decreased level of substantially full-length polypeptide.
[0160] In some aspects, a method of treating a subject having a disease associated with a premature stop codon comprises administering an engineered tRNA or variant thereof, e.g., as described herein. In some aspects, a method of treating a subject having a disease associated with a premature stop codon comprises administering a regulatory element or promoter upstream of an engineered tRNA or variant thereof, e.g., as described herein. In some embodiments, the disease associated with a premature stop codon is Rett syndrome, autism, West syndrome, Lennox-Gastaut syndrome, epileptic encephalopathy (EEP), Pitt-Hopkins syndrome, or any combination thereof. In some cases, a disease or condition can comprise cystic fibrosis, deafness (e.g. autosomal dominant 17 deafness, autosomal dominant 13 deafness, autosomal dominant 11 deafness) retinitis pigmentosa or any combination thereof. In some cases, a disease or condition can comprise Tay-Sachs, Parkinson’s, Cystic Fibrosis, Usher syndrome, Wolman disease, a liver disease (Alpha-1 antitrypsin (AAT) deficiency), or any combination thereof. A disease or condition can be a neurodegenerative disease, a muscular disorder, a metabolic disorder, an ocular disorder (e.g. an ocular disease), a cancer, or any combination thereof.
[0161] In some cases, the disease associated with a premature stop codon is cystic fibrosis, albinism, Alzheimer disease, Amyotrophic lateral sclerosis, Asthma, P-thalassemia, Cadasil syndrome, Charcot-Marie-Tooth disease, Chronic Obstructive Pulmonary Disease (COPD), dementia, Distal Spinal Muscular Atrophy (DSMA), Dystrophic Epidermolysis bullosa, Epidermylosis bullosa, Fabry disease, Factor V Leiden associated disorders, Familial Adenomatous, Polyposis, Galactosemia, Gaucher's Disease, Glucose-6-phosphate dehydrogenase, Haemophilia, Hereditary Hematochromatosis, Hunter Syndrome, Huntington's disease, Hurler Syndrome, Inflammatory Bowel Disease (IBD), Inherited polyagglutination syndrome, Leber congenital amaurosis, Lesch-Nyhan syndrome, Lynch syndrome, Marfan syndrome, Mucopolysaccharidosis, Myotonic dystrophy types I and II, neurofibromatosis, Niemann-Pick disease type A, B and C, NY-esol related cancer, Parkinson's disease, Peutz- Jeghers Syndrome, Phenylketonuria, Pompe's disease, Primary Ciliary Disease, Prothrombin mutation related disorders, such as the Prothrombin G20210A mutation, Pulmonary Hypertension, Retinitis Pigmentosa, Sandhoff Disease, Severe Combined Immune Deficiency Syndrome (SCID), Sickle Cell Anemia, Spinal Muscular Atrophy, Stargardt's Disease, X-linked immunodeficiency, various forms of cancer (e.g., BRCA1 and 2 linked breast cancer and ovarian cancer), or a combination thereof.
[0162] The disease associated with a premature stop codon can be a muscular dystrophy, an ornithine transcarbamylase deficiency, a breast cancer, an ovarian cancer, a prostate cancer, a lung cancer, a skin cancer, Stargardt macular dystrophy, Charcot-Marie-Tooth disease, or any combination thereof. A disease associated with a premature stop codon can be a muscular dystrophy. A muscular dystrophy can include myotonic, Duchenne, Becker, Limb-girdle, facioscapulohumeral, congenital, oculopharyngeal, distal, Emery-Dreifuss, or any combination thereof. The disease associated with a premature stop codon can comprise pain, such as chronic pain. Pain can include neuropathic pain, nociceptive pain, or a combination thereof. Nociceptive pain can include visceral pain, somatic pain, or a combination thereof.
[0163] In some aspects, a method of treating a subject having Rett syndrome comprises administering an engineered tRNA or engineered tRNA variant as disclosed herein to the subject. In some aspects, a method of treating a subject having Rett syndrome comprises administering a regulatory element or promoter upstream of an engineered tRNA or engineered tRNA variant as disclosed herein to the subject. In some embodiments, the subject is a human. [0164] The term percent “identity,” in the context of two or more nucleic acid or polypeptide sequences, refers to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection. Depending on the application, the percent “identity” can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.
[0165] For sequence comparison, typically one sequence acts as a reference sequence (also called the subject sequence) to which test sequences (also called query sequences) are compared. The percent sequence identity is defined as a test sequence’s percent identity to a reference sequence. For example, when stated “Sequence A having a sequence identity of 50% to Sequence B,” Sequence A is the test sequence and Sequence B is the reference sequence. When using a sequence comparison algorithm, test and reference sequences are input into a computer program, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then aligns the sequences to achieve the maximum alignment, based on the designated program parameters, introducing gaps in the alignment if necessary. The percent sequence identity for the test sequence(s) relative to the reference sequence can then be determined from the alignment of the test sequence to the reference sequence. The equation for percent sequence identity from the aligned sequence is as follows:
[0166] [(Number of Identical Positions)/(Total Number of Positions in the Test Sequence)] x 100%
[0167] For purposes herein, percent identity and sequence similarity calculations are performed using the BLAST algorithm for sequence alignment, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/). The BLAST algorithm uses a test sequence (also called a query sequence) and a reference sequence (also called a subject sequence) to search against, or in some cases, a database of multiple reference sequences to search against. The BLAST algorithm performs sequence alignment by finding high-scoring alignment regions between the test and the reference sequences by scoring alignment of short regions of the test sequence (termed “words”) to the reference sequence. The scoring of each alignment is determined by the BLAST algorithm and takes factors into account, such as the number of aligned positions, as well as whether introduction of gaps between the test and the reference sequences would improve the alignment. The alignment scores for nucleic acids can be scored by set match/mismatch scores. For protein sequences, the alignment scores can be scored using a substitution matrix to evaluate the significance of the sequence alignment, for example, the similarity between aligned amino acids based on their evolutionary probability of substitution. For purposes herein, the substitution matrix used is the BLOSUM62 matrix. For purposes herein, the public default values of April 6, 2023 are used when using the BLASTN and BLASTP algorithms. The BLASTN and BLASTP algorithms then output a “Percent Identity” output value and a “Query Coverage” output value. The overall percent sequence identity as used herein can then be calculated from the BLASTN or BLASTP output values as follows:
[0168] Percent Sequence Identity = (“Percent Identity” output value) x (“Query Coverage” output value)
[0169] The following non-limiting examples illustrate the calculation of percent identity between two nucleic acids sequences. The percent identity is calculated as follows: [(number of identical nucleotide positions)/(total number of nucleotides in the test sequence)] x 100%. Percent identity is calculated to compare test sequence 1: AAAAAGGGGG (SEQ ID NO: 389, length = 10 nucleotides) to reference sequence 2: AAAAAAAAAA (SEQ ID NO: 390, length = 10 nucleotides). The percent identity between test sequence 1 and reference sequence 2 would be [(5)/(10)] x ioo% = 50%. Test sequence 1 has 50% sequence identity to reference sequence 2. In another example, percent identity is calculated to compare test sequence 3: CCCCCGGGGGGGGGGCCCCC (SEQ ID NO: 391, length = 20 nucleotides) to reference sequence 4: GGGGGGGGGG (SEQ ID NO: 392, length = 10 nucleotides). The percent identity between test sequence 3 and reference sequence 4 would be [(10)/(20)] x ioo% = 50%. Test sequence 3 has 50% sequence identity to reference sequence 4. In another example, percent identity is calculated to compare test sequence 5: GGGGGGGGGG (SEQ ID NO: 393, length = 10 nucleotides) to reference sequence 6: CCCCCGGGGGGGGGGCCCCC (SEQ ID NO: 394, length = 20 nucleotides). The percent identity between test sequence 5 and reference sequence 6 would be [(10)/(10)J x ioo% = 100%. Test sequence 5 has 100% sequence identity to reference sequence 6.
[0170] The following non-limiting examples illustrate the calculation of percent identity between two protein sequences. The percent identity is calculated as follows: [(number of identical amino acid positions)/(total number of amino acids in the test sequence)] x 100%. Percent identity is calculated to compare test sequence 7: FFFFFYYYYY (SEQ ID NO: 395, length = 10 amino acids) to reference sequence 8: YYYYYYYYYY (SEQ ID NO: 396, length = 10 amino acids). The percent identity between test sequence 7 and reference sequence 8 would be [(5)/(10)] x ioo% = 50%. Test sequence 7 has 50% sequence identity to reference sequence 8. In another example, percent identity is calculated to compare test sequence 9: LLLLLFFFFFYYYYYLLLLL (SEQ ID NO: 397, length = 20 amino acids) to reference sequence 10: FFFFFYYYYY (SEQ ID NO: 398, length = 10 amino acids). The percent identity between test sequence 9 and reference sequence 10 would be [(10)/(20)] x 100% = 50%. Test sequence 9 has 50% sequence identity to reference sequence 10. In another example, percent identity is calculated to compare test sequence 11 : FFFFFYYYYY (SEQ ID NO: 399, length = 10 amino acids) to reference sequence 12: LLLLLFFFFFYYYYYLLLLL (SEQ ID NO: 400, length = 20 amino acids). The percent identity between test sequence 11 and reference sequence
12 would be [( 10)/(l 0)] * 100% = 100%. Test sequence 11 has 100% sequence identity to reference sequence 12.
EXAMPLES
[0171] The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
Example 1: tRNA Variants and High-Throughput Sequencing Libraries
[0172] Two suppressor tRNA sequences for opal stop codons, CCT2.10 (SEQ ID NO: 32) and CCT4 (SEQ ID NO: 7) were chosen for the production of engineered tRNA variant libraries. The sequences of these tRNAs, along with the positions selected for degeneracies in the variant library and the sequences are shown in Table 7 below. During synthesis, degenerate bases (denoted ‘N’, meaning A, C, G, or T in DNA and A, C, G, or U in RNA) were introduced in the DNA oligonucleotides encoding the tRNA sequences as shown in the table below. Three variant libraries were designed for each CCT2.10 and CCT4, one containing degeneracies in the A-box at residues 9, 12, 13, 15, and 16; one containing degeneracies in the B-box at residues 52, 57, 59, 60, and 62, and one containing degeneracies in the variable region at residues 44-48. Thus, each of the six libraries were designed to contain 4A5 (1,024) variants.
Table 7. Sequences of engineered tRNAs and variant libraries.
Figure imgf000056_0001
Figure imgf000057_0001
[0173] These tRNA variants were contained within a synthetic oligonucleotide comprising, from 5’ to 3’, the tRNA sequence and a polyT, and inserted into a lentiviral expression vector either with the hU6 promoter sequence (GAGggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattagaattaatttgactgtaaacacaaaga tattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagttttaaaattatgttttaaaatggactatcatatgcttaccgtaa cttgaaagtatttcgatttcttggctttatatatcttGTGGAAAGGACGAAACACC (SEQ ID NO: 388)) or no promoter sequence upstream of the tRNA insertion. [0174] Additional oligonucleotide pools were prepared with CCT2.10, adding 5’ sequences that were either 227 bp upstream or 100 bp upstream of bioinformatically mined known human tRNA sequences (“Upstream -tRNA” libraries), in which the 227 bp upstream sequence and 100 bp upstream sequences are putative regulatory regions that may comprise regulatory elements, such as promoters.
[0175] These oligonucleotides were cloned into vectors to create high-throughput screening (HTS) libraries, as shown in Table 8, below.
Table 8. HTS libraries
Figure imgf000058_0001
[0176] These libraries were prepared as shown by the workflow schematic in FIG. 2A.
Initial sequencing checks of these libraries showed high coverage with low background.
Example 2: High-Throughput Screening Approaches for tRNA Variants and Putative
Regulatory Regions
[0177] High-throughput screening approaches for tRNA variants and putative regulatory regions enables systematic identification of global patterns in tRNA sequences and putative regulatory regions (Upstream-tRNA) that can, for example, enhance or influence nonsense suppression efficiency. An exemplary approach to screening different libraries is shown in FIG.
7. In this example, the cloned and amplified tRNA library (in a lentiviral backbone) is introduced into cells stably expressing broken GFP (i.e., with an engineered premature stop codon) at a low MOI, to achieve single copy transduction. PTC readthrough generates intact GFP. Cells are FACS-sorted on GFP expression and NGS libraries are prepared from each sorting group. This includes preparing an NGS library from the sorting group of cells with high GFP mean fluorescence intensity (MFI) in order to identify top-performing library candidates by sequencing.
Example 3: Lentivirus Library Singleplex Testing
[0178] The libraries described in Example 1 were cloned into a lentiviral backbone with CMV-mCherry as the transduction marker (FIG. 2A). Read through of 44 clones randomly selected from across the different libraries was tested as shown in FIG. 3. Each of the variants was co-transfected with broken GFP constructs into HEK293 cells. After 48 hours, the read- through capacity of each library candidate clone was quantified by GFP expression through flow cytometry. As mCherry is driven by the CMV promoter directly off the plasmid containing the library candidate clone, one would expect to see mCherry expression from this transfection.
[0179] mCherry and GFP expression was measured to identify transfected cells with GFP read-through rescue. As shown in FIG. 4A (percentage of mCherry+ cells that are GFP+) and FIG. 4B (GFP MFI normalized to mCherry MFI), a subset of library candidate clones from each of the libraries had GFP expression comparable to or greater than CCT2.10. In particular, library candidate clones from the Upstream-tRNA libraries (100 bp prom and 227 bp prom) showed GFP expression higher than the original CCT2.10 suppressor tRNA. The library candidate clones demonstrating GFP expression comparable to or greater than CCT2.10 are shown in Tables 9A, 9B, and 9C, below. Sequences in Table 9C were engineered 5’ of the sequence encoding CCT2.10 (SEQ ID NO: 32) in the tested constructs.
Table 9A. Randomly Selected Constructs from the “hU6-tRNA” Group of Table 8 Demonstrating GFP expression comparable to or greater than CCT2.10
Figure imgf000059_0001
Figure imgf000060_0001
Figure imgf000061_0001
Table 9B. Randomly Selected Constructs from the “no promoter-tRNA” Group of Table 8
Demonstrating GFP expression comparable to or greater than CCT2.10
Figure imgf000061_0002
Figure imgf000062_0001
Figure imgf000063_0001
Table 9C. Randomly Selected Constructs Demonstrating GFP expression comparable to or greater than CCT2.10, from “Upstream-tRNA” Group of Table 8
Figure imgf000063_0002
Figure imgf000064_0001
Example 4: Packaging and NGS Analysis of Lentivirus Libraries for High-Throughput Screening
[0180] Next generation sequencing was carried out on the plasmid and lentivirus libraries to verify that the diversity of the libraries is preserved post cloning and packaging (See schematic and graph of FIG. 2B). As shown in FIG. 5 A and FIG. 5B, nearly all of the tRNA variants were detected in the plasmid and viral libraries, with the exception of the CCT4 variable region, which was underrepresented. Likewise, as shown in FIG. 6A and 6B, nearly all of the Upstream-tRNA variants were detected. The frequency of the variants matched expectation in plasmid pools and lentivirus libraries with the exception of tRNA variants with mutations in the variable regions of CCT2.10 and CCT4, which were less abundant in the packaged viral libraries than the plasmid pools, which was most likely due to a synthesis error and/or insufficient packaging. Example 5: Lentivirus High-Throughput Screening Demonstrates Enrichment for Particular tRNA Variants
[0181] High-Throughput Screening was carried out on the libraries described in Example 2 as shown in FIG. 7. Briefly, cells were transduced at low MOI to facilitate single-copy integration of library variants and then expanded in puromycin (puro) media for about two weeks before FACS sorting into bins of GFP expression. As shown in FIG. 8A, the highest number of GFP+ cells were seen in the Upstream-tRNA libraries, followed by the U6 tRNA variant libraries, and the lowest number of GFP+ cells were seen in the no promoter tRNA variant libraries.
[0182] The sorted cells were used to prepare NGS libraries and sequenced to identify variants. As shown in FIG. 8B, the abundance distribution of CCT2.10 hU6 tRNA variants in the high GFP expressing bin shifted relative to cells in the lower and no GFP-expression bins, and as shown in FIG. 8C, the abundance of the CCT2.10 hU6 tRNA variants in the high GFP bin was increased compared to the other bins, demonstrating the high bin selection for topperforming candidates. As shown in FIG. 9, the frequency of lOObp and 227bp Upstream-tRNA was the highest in the high GFP expressing bins, also demonstrating selection for top-performing candidates.
Example 6: Singleplex Testing of HTS Identified tRNA Variants
[0183] Top-performing tRNA variants from the high-throughput screening as described in the previous examples were identified using differential expression analysis. These top performing tRNA variants (Table 10) and corresponding controls (hu6-CCT2.10 (CCT2.10 with hU6 promoter); noU6-CCT2.10 (CCT2.10 without hU6 promoter); hU6-CCT4 (CCT4 with hU6 promoter); noU6-CCT4WT (CCT4 having a WT anti-codon, and without hU6 promoter); and noU6CCT2.10 WT (CCT2.10 having a WT anti-codon, and without hU6 promoter)) were cloned into a pUC backbone with the CMV-Thyl.l transduction marker.
Table 10. Constructs Containing Top Performing tRNA Variants and Corresponding Controls.
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
[0184] Singleplex testing of these constructs was carried out using a broken GFP assay. Briefly, HEK293 cells stably expressing either the R74X or R97X broken GFP reporter were transfected with 200 ng of plasmid comprising the tRNA variant and a CMV-Thyl. l transfection reporter cassette. After 48 hours, cells were stained with a NIR viability dye and a BV421- Thyl.l dye at room temperature for 15 minutes. Cells were assessed for transfection and read- through efficiency by flow cytometry quantifying Thy 1.1 and GFP expression. Dead cells were excluded from analysis.
[0185] As shown in FIG. 10A and FIG. 10B, variants identified by the HTS screen performed similarly or better than the control noU6-CCT2.10 in both HEK293 R74X-GFP expressing cells (FIG. 10A) and in R97X-GFP expressing cells (FIG. 10B).
Example 7: Singleplex Testing of HTS Identified tRNA Variants
[0186] Top-performing Upstream-tRNA variants (comprising a putative regulatory region) from the Upstream-tRNA library HTS screen as described in the previous examples were identified using differential expression analysis. These top-performing Upstream-tRNA variants (putative regulatory region and a tRNA sequence) (Table 11) and corresponding controls were cloned into a pUC backbone with the CMV-Thyl.l transduction marker.
Table 11. Constructs of Containing Top-Performing Upstream-tRNA Variants and Corresponding Controls.
Figure imgf000068_0002
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
[0187] Singleplex testing was carried out using a broken GFP assay, as described in Example 6. As shown in FIG. 11 A and FIG. 1 IB, variants from Upstream-tRNA library with 100 bp upstream sequences (e.g., 100 bp putative regulatory region) identified by the HTS screen performed similarly or better than the control noU6-CCT2.10 in HEK293 R74X-GFP expressing cells (FIG. 11 A), and certain variants also performed similarly or better than the control noU6- CCT2.10 in HEK293 R97X-GFP expressing cells (FIG. 11B). Example 8: Improved in vivo PTC Readthrough with Engineered tRNA Variants and/or
Novel Regulatory Elements
[0188] In vivo rescue of a pathogenic mutation in a disease model is carried out using tRNA variants and/or putative regulatory regions identified in Example 6.
Example 9: Single-Copy Integration for Screening tRNA Variants and/or Regulatory Elements
[0189] To allow for direct comparison of the stop codon read-through levels for various tRNA variants and/or regulatory elements, stop codon read-through at a single copy per cell was assessed. Single-copy integration cell lines were generated having a tRNA insert sequence comprising construct 3 (“CCT2.10 GCTAT GGGTC ATCAT #3”) from Table 10 (Example 6), construct 9 (“CCT2.10 GCTAT GGGTC TGGTT #9”) from Table 10 (Example 6), construct 7 (“CCT2.10 tRNA-Leu-AAG-1-2 promoter #7”) from Table 11 (Example 7), construct 12 (“CCT2.10 tRNA-Arg-TCT-4-1 promoter #12”) from Table 11 (Example 7), CCT5 (negative control), or CCT2.10 (positive control). The tRNA insert sequences either rely on their intrinsic promoter for tRNA expression or include an external promoter for additional expression. For each tRNA insert sequence, HEK293T cell lines were generated in duplicate, with each tRNA insert sequence cloned in either the forward or reverse orientations and with one of two different GFP reporters (R97X broken GFP-FLAG (“broken GFP reporter”) or Intact GFP-FLAG (“intact GFP reporter”)). A no tRNA control was also generated. Therefore, a total of 26 cell lines were generated.
[0190] GFP fluoresence was assessed for each of the generated cell lines, as shown in FIG. 12. Except for the negative control cell line and untransfected control cell line, reproducible GFP readthrough was observed at day 20 post transfection for the single-copy integrations in all the broken GFP reporter cell lines.
OTHER EMBODIMENTS
[0191] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. NUMBERED EMBODIMENTS
1. An engineered tRNA variant comprising one or more mutations at position(s) 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62, according to canonical numbering.
2. The engineered tRNA variant of embodiment 1, wherein the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 79.
3. The engineered tRNA variant of embodiment 2, wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 73 or SEQ ID NO: 79.
4. The engineered tRNA variant of embodiment 3, wherein the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 73 or SEQ ID NO: 79.
5. The engineered tRNA variant of embodiment 4, wherein the engineered tRNA variant has at least 90% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 73 or SEQ ID NO: 79.
6. An engineered tRNA variant comprising SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, or SEQ ID NO: 187.
7. An engineered tRNA variant comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 254, SEQ ID NO: 255, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 296, SEQ ID NO: 297, SEQ ID NO: 298, SEQ ID NO: 299, SEQ ID NO: 300, SEQ ID NO: 301, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 304, SEQ ID NO: 305, SEQ ID NO: 306, SEQ ID NO: 307, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 315, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 319, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 370, SEQ ID NO: 371, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 385, SEQ ID NO: 386, or SEQ ID NO: 387.
8. The engineered tRNA variant of embodiment 1, wherein the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 54.
9. The engineered tRNA variant of embodiment 2, wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
10. The engineered tRNA variant of embodiment 2, wherein the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
11. The engineered tRNA variant of embodiment 2, wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 90; optionally, wherein the sequence is not SEQ ID NO: 90.
12. An engineered tRNA variant comprising SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 191.
13. An engineered tRNA variant comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 260, SEQ ID NO: 266, SEQ ID NO: 267, or SEQ ID NO: 268.
14. A polynucleic acid encoding the engineered tRNA variant of any one of the foregoing embodiments.
15. A polynucleic acid encoding a tRNA and a nucleic acid sequence encoding a tRNA and a regulatory region, wherein the regulatory region has at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%, sequence identity to SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region.
16. The polynucleic acid of embodiment 15, wherein the regulatory region comprises or consists of SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region.
17. The polynucleic acid of embodiment 15 or 16, wherein the regulatory region is 5’ of the tRNA; optionally, wherein the regulatory region is a putative regulatory region.
18. The polynucleic acid of any one of embodiments 15-17, wherein the nucleic acid sequence encoding the tRNA is selected from SEQ ID NOs 3-48, 96-115, 136-155, 196, 197, 199-222, 227-229, 176-179, 180-183, 272-295, 344-353, and 354-365.
19. An expression vector comprising the polynucleic acid of any one of embodiments 14-18.
20. The expression vector of embodiment 19, further comprising a promoter.
21. The expression vector of embodiment 20, wherein the promoter is a polymerase III promoter.
22. The expression vector of embodiment 21, wherein the polymerase III promoter is a polymerase III type 3 promoter.
23. The expression vector of embodiment 22, wherein the polymerase III type 3 promoter is U6.
24. The expression vector of embodiment 23, wherein the U6 is human U6.
25. The expression vector of any one of embodiments 19-24, further comprising a polynucleic acid encoding a reporter protein. 26. The expression vector of embodiment 25, wherein the reporter protein is a fluorescent protein.
27. The expression vector of any one of embodiments 19-26, wherein the expression vector is a lentiviral expression vector.
28. A cell comprising the polynucleotide of any one of embodiments 14-18.
29. A cell comprising the expression vector of any one of embodiments 19-27.
30. A cell expressing the engineered tRNA variant of any one of embodiments 1-13.
31. The cell of any one of embodiments 28-30, wherein the cell expresses a broken reporter protein.
32. The cell of embodiment 31, wherein the broken reporter protein is a broken fluorescent protein.
33. The cell of embodiment 32, wherein the broken fluorescent protein is broken GFP.
34. The cell of any one of embodiments 28-33, wherein the cell expresses an engineered tRNA or an engineered tRNA variant with improved PTC readthrough efficiency as compared to a cell expressing a reference tRNA.
35. The cell of embodiment 34, wherein the reference tRNA is selected from SEQ ID NO: 79 and SEQ ID NO: 54.
36. A method for identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency, the method comprising: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding a tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA; introducing the expression vectors into cells stably expressing a reporter protein having a PTC; incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells into bins based on expression levels of the reporter protein; identifying a sequence of a tRNA variant and/or a regulatory region of a cell from one of the bins; and, based on the sequence, identifying engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency.
37. The method of embodiment 36, wherein the expression vector(s) further comprises a reporter protein.
38. The method of embodiment 37, wherein the reporter protein is a fluorescent protein.
39. The method of embodiment 38, wherein the fluorescent protein is mCherry.
40. The method of any one of the preceding embodiments, wherein the reporter protein is a fluorescent protein having a PTC.
41. The method of embodiment 40, wherein the reporter protein is a GFP protein having a PTC.
42. The method of any one of the preceding embodiments, wherein introducing the expression vectors into cells expressing the reporter protein comprises transfecting the cells with the expression vectors at a multiplicity of infection (MOI) suitable to achieve single copy transduction per cell.
43. The method of any one of the preceding embodiments, wherein sorting the cells comprises fluorescence-activated cell sorting (FACS).
44. The method of any one of the preceding embodiments, wherein identifying the sequence of the tRNA variant and/or regulatory region comprises single cell sequencing of the tRNA variant and/or regulatory region of the cell.

Claims

WHAT IS CLAIMED IS:
1. An engineered tRNA variant comprising one or more mutations at position(s) 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62, according to canonical numbering.
2. The engineered tRNA variant of claim 1, wherein the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 79.
3. The engineered tRNA variant of claim 2, wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79.
4. The engineered tRNA variant of claim 3, wherein the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79.
5. The engineered tRNA variant of claim 4, wherein the engineered tRNA variant has at least 90% sequence identity to SEQ ID NO: 79; optionally, wherein the sequence is not SEQ ID NO: 50 or SEQ ID NO: 79.
6. An engineered tRNA variant comprising SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, or SEQ ID NO: 187.
7. An engineered tRNA variant comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 254, SEQ ID NO: 255, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 261, SEQ ID NO: 262, SEQ ID NO: 263, SEQ ID NO: 264, SEQ ID NO: 268, SEQ ID NO: 269, SEQ ID NO: 270, SEQ ID NO: 271, SEQ ID NO: 296, SEQ ID NO: 297, SEQ ID NO: 298, SEQ ID NO: 299, SEQ ID NO: 300, SEQ ID NO: 301, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 304, SEQ ID NO: 305, SEQ ID NO: 306, SEQ ID NO: 307, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 315, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 319, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 370, SEQ ID NO: 371, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 385, SEQ ID NO: 386, or SEQ ID NO: 387.
8. The engineered tRNA variant of claim 1, wherein the mutations are relative to positions 9, 12, 13, 15, 16, 44, 45, 46, 47, 48, 52, 57, 59, 60, and/or 62 of SEQ ID NO: 54.
9. The engineered tRNA variant of claim 2, wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
10. The engineered tRNA variant of claim 2, wherein the engineered tRNA variant has at least 80% sequence identity to SEQ ID NO: 54; optionally, wherein the sequence is not SEQ ID NO: 54.
11. The engineered tRNA variant of claim 2, wherein the engineered tRNA variant has at least 70% sequence identity to SEQ ID NO: 92; optionally, wherein the sequence is not SEQ ID NO: 92 or SEQ ID NO: 53.
12. An engineered tRNA variant comprising SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 191.
13. An engineered tRNA variant comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 260, SEQ ID NO: 265, SEQ ID NO: 266, or SEQ ID NO: 267.
14. A polynucleic acid encoding the engineered tRNA variant of any one of the foregoing claims; optionally, wherein the polynucleotide comprises at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 196, 197, 199-233, 176-179, 180-183, 272-295, 344-353, or 354-365.
15. A polynucleic acid comprising a nucleic acid sequence encoding a tRNA, optionally an engineered tRNA, and a regulatory region, wherein the regulatory region has at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%, sequence identity to SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region.
16. The polynucleic acid of claim 15, wherein the regulatory region comprises or consists of SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 331, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, or SEQ ID NO: 343; optionally, wherein the regulatory region is a putative regulatory region.
17. The polynucleic acid of claim 15 or 16, wherein the regulatory region is 5’ of the nucleic acid sequence encoding the tRNA; optionally, wherein the regulatory region is a putative regulatory region.
18. The polynucleic acid of any one of claims 15-17, wherein the nucleic acid sequence encoding the tRNA is selected from SEQ ID NOs 3-48, 96-115, 136-155, 196, 197, 199-233, 176-179, 180-183, 272-295, 344-353, and 354-365.
19. An expression vector comprising the polynucleic acid of any one of claims 14-18.
20. The expression vector of claim 19, further comprising a promoter.
21. The expression vector of claim 20, wherein the promoter is a polymerase III promoter.
22. The expression vector of claim 21, wherein the polymerase III promoter is a polymerase III type 3 promoter.
23. The expression vector of claim 22, wherein the polymerase III type 3 promoter is
U6.
24. The expression vector of claim 23, wherein the U6 is human U6; optionally, wherein the human U6 comprises at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 388.
25. The expression vector of any one of claims 19-24, further comprising a polynucleic acid encoding a reporter protein.
26. The expression vector of claim 25, wherein the reporter protein is a fluorescent protein.
27. The expression vector of any one of claims 19-26, wherein the expression vector is a lentiviral expression vector.
28. A cell comprising the polynucleotide of any one of claims 14-18.
29. A cell comprising the expression vector of any one of claims 19-27.
30. A cell expressing the engineered tRNA variant of any one of claims 1-13.
31. The cell of any one of claims 28-30, wherein the cell expresses a broken reporter protein.
32. The cell of claim 31, wherein the broken reporter protein is a broken fluorescent protein.
33. The cell of claim 32, wherein the broken fluorescent protein is broken GFP.
34. The cell of any one of claims 28-33, wherein the cell expresses an engineered tRNA or an engineered tRNA variant with improved PTC readthrough efficiency as compared to a cell expressing a reference tRNA.
35. The cell of claim 34, wherein the reference tRNA is selected from SEQ ID NO: 79 and SEQ ID NO: 54.
36. A method for identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency, the method comprising: providing a library of lentiviral expression vectors, each comprising a nucleic acid sequence encoding an engineered tRNA variant or a nucleic acid sequence encoding a tRNA and a putative regulatory region 5’ of the sequence encoding the tRNA; introducing the expression vectors into cells stably expressing a reporter protein having a PTC; incubating the cells under conditions suitable for expression of the tRNA(s) and/or tRNA variant(s); sorting the cells into bins based on expression levels of PTC-readthrough of the reporter protein; identifying a sequence of an engineered tRNA variant and/or a regulatory region of a cell from one of the bins; and, based on the sequence, identifying an engineered tRNA variant and/or a regulatory region that provides improved PTC readthrough efficiency.
37. The method of claim 36, wherein the expression vector(s) further comprises a reporter protein.
38. The method of claim 37, wherein the reporter protein is a fluorescent protein.
39. The method of claim 38, wherein the fluorescent protein is mCherry.
40. The method of any one of claims 36-39, wherein the reporter protein is a fluorescent protein having a PTC.
41. The method of claim 40, wherein the reporter protein is a GFP protein having a PTC.
42. The method of any one of claims 36-41, wherein introducing the expression vectors into cells expressing the reporter protein comprises transfecting the cells with the expression vectors at a multiplicity of infection (MOI) suitable to achieve single copy transduction per cell.
43. The method of any one of claims 36-42, wherein sorting the cells comprises fluorescence-activated cell sorting (FACS).
44. The method of any one of claims 36-43, wherein identifying the sequence of the tRNA variant and/or regulatory region comprises single cell sequencing, bulk amplicon sequencing, or next-generation sequencing of the tRNA variant and/or regulatory region of the cell.
45. The method of any one of claims 36-44, wherein one of the bins is a bin having the highest expression level of PTC-readthrough of the reporter protein compared to other bins.
46. The method of any one of claims of any one of claims 36-45, wherein the nucleic acid sequence encoding the engineered tRNA variant further comprises a nucleic acid sequence encoding an hU6 promoter 5’ of the engineered tRNA variant.
47. The cell of any one of claims 28-35, wherein the cell comprises a single copy, two copies, three copies, four copies, five copies, six copies, seven copies, or eight copies of the polynucleotide of any one of claims 14-28, the expression vector of any one of claims 19-27, or the engineered tRNA variant of any one of claims 1-13.
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Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021113218A1 (en) 2019-12-02 2021-06-10 Shape Therapeutics Inc. Targeted transfer rnas for treatment of diseases

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB201600512D0 (en) * 2016-01-12 2016-02-24 Univ York Recombinant protein production
BR112020008725A2 (en) * 2017-11-02 2021-03-30 The Wistar Institute Of Anatomy And Biology COMPOSITION TO GENERATE ONE OR MORE RNAT EDITED BY ANTICODON, AND METHOD FOR TREATING A DISEASE ASSOCIATED WITH A PREMATURE TERMINATION CODE
WO2021087401A1 (en) * 2019-11-01 2021-05-06 Tevard Bio, Inc. Methods and compositions for treating a premature termination codon-mediated disorder
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Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021113218A1 (en) 2019-12-02 2021-06-10 Shape Therapeutics Inc. Targeted transfer rnas for treatment of diseases

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
ALTSCHUL ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403 - 410
LASLETTCANBACK: "ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences", NUCLEIC ACIDS RESEARCH, vol. 32, no. 1, 2004, pages 11 - 16, XP002586217, DOI: 10.1093/NAR/GKH152
SUZUKI: "The Expanding World of tRNA Modifications and their Disease Relevance", NATURE REVIEWS MOLECULAR CELL BIOLOGY, vol. 22, 2021, pages 375 - 92, XP037464728, DOI: 10.1038/s41580-021-00342-0

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