NZ754228B2 - Modified guide rnas - Google Patents
Modified guide rnasInfo
- Publication number
- NZ754228B2 NZ754228B2 NZ754228A NZ75422817A NZ754228B2 NZ 754228 B2 NZ754228 B2 NZ 754228B2 NZ 754228 A NZ754228 A NZ 754228A NZ 75422817 A NZ75422817 A NZ 75422817A NZ 754228 B2 NZ754228 B2 NZ 754228B2
- Authority
- NZ
- New Zealand
- Prior art keywords
- sgrna
- nucleotides
- terminus
- region
- hairpin
- Prior art date
Links
- 102000040650 (ribonucleotides)n+m Human genes 0.000 title 1
- 108091032973 (ribonucleotides)n+m Proteins 0.000 title 1
- 108020005004 Guide RNA Proteins 0.000 claims abstract 2
- 238000000338 in vitro Methods 0.000 claims abstract 2
- 238000000034 method Methods 0.000 claims abstract 2
- 125000003729 nucleotide group Chemical group 0.000 claims 40
- 239000002773 nucleotide Substances 0.000 claims 38
- 239000000203 mixture Substances 0.000 claims 11
- 238000012986 modification Methods 0.000 claims 11
- 230000004048 modification Effects 0.000 claims 11
- 101710163270 Nuclease Proteins 0.000 claims 5
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 claims 4
- 108091033409 CRISPR Proteins 0.000 claims 3
- 108090000623 proteins and genes Proteins 0.000 claims 3
- 102000004169 proteins and genes Human genes 0.000 claims 3
- 102100039856 Histone H1.1 Human genes 0.000 claims 2
- 101001035402 Homo sapiens Histone H1.1 Proteins 0.000 claims 2
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 claims 2
- 108020004999 messenger RNA Proteins 0.000 claims 2
- 108020004414 DNA Proteins 0.000 claims 1
- 108010008532 Deoxyribonuclease I Proteins 0.000 claims 1
- 102000007260 Deoxyribonuclease I Human genes 0.000 claims 1
- 102100023917 Histone H1.10 Human genes 0.000 claims 1
- 102100039855 Histone H1.2 Human genes 0.000 claims 1
- 102100027368 Histone H1.3 Human genes 0.000 claims 1
- 102100027369 Histone H1.4 Human genes 0.000 claims 1
- 102100022653 Histone H1.5 Human genes 0.000 claims 1
- 102100033558 Histone H1.8 Human genes 0.000 claims 1
- 102100023920 Histone H1t Human genes 0.000 claims 1
- 101000905024 Homo sapiens Histone H1.10 Proteins 0.000 claims 1
- 101001035375 Homo sapiens Histone H1.2 Proteins 0.000 claims 1
- 101001009450 Homo sapiens Histone H1.3 Proteins 0.000 claims 1
- 101001009443 Homo sapiens Histone H1.4 Proteins 0.000 claims 1
- 101000899879 Homo sapiens Histone H1.5 Proteins 0.000 claims 1
- 101000872218 Homo sapiens Histone H1.8 Proteins 0.000 claims 1
- 101000905044 Homo sapiens Histone H1t Proteins 0.000 claims 1
- 101000897979 Homo sapiens Putative spermatid-specific linker histone H1-like protein Proteins 0.000 claims 1
- 101000843236 Homo sapiens Testis-specific H1 histone Proteins 0.000 claims 1
- 102100021861 Putative spermatid-specific linker histone H1-like protein Human genes 0.000 claims 1
- 241000193996 Streptococcus pyogenes Species 0.000 claims 1
- 102100031010 Testis-specific H1 histone Human genes 0.000 claims 1
- 201000010099 disease Diseases 0.000 claims 1
- 208000035475 disorder Diseases 0.000 claims 1
- 239000003814 drug Substances 0.000 claims 1
- 239000003937 drug carrier Substances 0.000 claims 1
- 150000002632 lipids Chemical class 0.000 claims 1
- 238000004519 manufacturing process Methods 0.000 claims 1
- 239000002105 nanoparticle Substances 0.000 claims 1
- 108020004707 nucleic acids Proteins 0.000 claims 1
- 102000039446 nucleic acids Human genes 0.000 claims 1
- 150000007523 nucleic acids Chemical class 0.000 claims 1
- 239000008194 pharmaceutical composition Substances 0.000 claims 1
- 230000009977 dual effect Effects 0.000 abstract 1
- 230000000694 effects Effects 0.000 abstract 1
- 238000010362 genome editing Methods 0.000 abstract 1
- 238000001727 in vivo Methods 0.000 abstract 1
Classifications
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
-
- 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
- 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
- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/10—Type of nucleic acid
- C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/31—Chemical structure of the backbone
- C12N2310/315—Phosphorothioates
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/32—Chemical structure of the sugar
- C12N2310/321—2'-O-R Modification
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/32—Chemical structure of the sugar
- C12N2310/322—2'-R Modification
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/34—Spatial arrangement of the modifications
- C12N2310/344—Position-specific modifications, e.g. on every purine, at the 3'-end
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/34—Spatial arrangement of the modifications
- C12N2310/346—Spatial arrangement of the modifications having a combination of backbone and sugar modifications
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/35—Nature of the modification
- C12N2310/352—Nature of the modification linked to the nucleic acid via a carbon atom
- C12N2310/3521—Methyl
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/35—Nature of the modification
- C12N2310/352—Nature of the modification linked to the nucleic acid via a carbon atom
- C12N2310/3525—MOE, methoxyethoxy
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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
- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/35—Nature of the modification
- C12N2310/353—Nature of the modification linked to the nucleic acid via an atom other than carbon
- C12N2310/3533—Halogen
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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
- 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
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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
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
- C12N9/22—Ribonucleases RNAses, DNAses
Abstract
This disclosure relates to modified single and dual guide RNAs having improved in vitro and in vivo activity in gene editing methods.
Claims (34)
1. A single guide RNA (sgRNA) comprising an upper stem region and a hairpin region, wherein (i) a. each nucleotide in the upper stem region is modified with e; and b. the hairpin region comprises a hairpin 1 region and a hairpin 2 region and each nucleotide in the hairpin 2 region is ed with 2’-O-Me; and (ii) a 5’ end modification comprising at least two phosphorothioate (PS) linkages within the first seven nucleotides at the 5’ end of the 5’ terminus.
2. The sgRNA of claim 1, wherein the sgRNA comprises one or more modifications in the hairpin 1 region.
3. The sgRNA of claim 1 or claim 2, n each of the tides in the hairpin 1 region are modified with 2’-O-Me.
4. The sgRNA of any one of claims 1-3, n the sgRNA comprises a modified nucleotide between the hairpin 1 and hairpin 2 regions.
5. The sgRNA of any one of claims 1-4, further comprising a lower stem region comprising a modification.
6. The sgRNA of any one of claims 1-5, further comprising a 3’ terminus region comprising a modification.
7. The sgRNA of claim 6, further comprising a 3’ end modification in the 3’ terminus.
8. The sgRNA of claim 7, wherein at least two of the last four nucleotides at the 3’ end of the 3’ terminus are modified, optionally with e, 2’-F, or 2’-O-moe.
9. The sgRNA of claim 8, further comprising orothioate (PS) bonds between one or more of the last four nucleotides at the 3’ end of the 3’ terminus.
10. The sgRNA of any one of claims 1-9, further comprising a bulge region comprising a modification and/or a nexus region sing a modification.
11. The sgRNA of any one of claims 1-10, wherein at least the first three nucleotides at the 5’ end of the 5’ terminus, and the last three nucleotides at the 3’ end of the 3’ terminus are modified.
12. The sgRNA of any one of claims 1-11, wherein the first four nucleotides at the 5’ end of the 5’ terminus, and the last four nucleotides at the 3’ end of the 3’ terminus are linked with orothioate (PS) bonds.
13. The sgRNA of claim 12, wherein the end modifications comprise 2’-O-Me or 2’-F.
14. The sgRNA of any one of claims 1-13, wherein the first four nucleotides at the 5’ end of the 5’ terminus and the last four nucleotides at the 3’ end of the 3’ terminus are linked with a PS bond, and wherein the first three tides at the 5’ end of the 5’ terminus and the last three or four nucleotides at the 3’ end of the 3’ terminus comprise 2’-O-Me modifications.
15. The sgRNA of any one of claims 1-14, wherein the first four nucleotides at the 5’ us and the last four nucleotides at the 3’ terminus are linked with a PS bond, and wherein the first three nucleotides at the 5’ terminus and the last three nucleotides at the 3’ terminus se 2’-O-Me, 2’-F, and/or 2’-O-moe modifications.
16. The sgRNA of any one of claims 1-15, wherein the first four nucleotides at the 5’ end of the 5’ terminus and the last four nucleotides at the 3’ end of the 3’terminus are linked with a PS bond, and wherein the first three nucleotides at the 5’ end of the 5’ terminus and the last three nucleotides at the 3’ end of the 3’ terminus are modified with 2’-O-Me.
17. The sgRNA of any one of claims 1-15, n the first four nucleotides at the 5’ end of the 5’ us and the last four nucleotides at the 3’ end of the 3’terminus are linked with a PS bond, wherein the first three nucleotides at the 5’ end of the 5’ terminus and the last four nucleotides at the 3’ end of the 3’ terminus are modified with 2’-O-Me.
18. The sgRNA of any one of claims 1-17, wherein the lower stem region comprises tides LS1 to LS12 from the 5’ end to the 3’ end thereof, and LS1, LS6, LS7, LS8, LS11, and/or LS12 are modified with 2’-O-Me and/or wherein the sgRNA ses a bulge region and each nucleotide in the bulge region is modified with 2’-O-Me and/or wherein at least 50% of the nucleotides in the bulge region are modified with 2’-O-Me and/or wherein the sgRNA r comprises a nexus region comprising nucleotides N1 through N18 from the 5’ end to the 3’ end thereof, and N16, N17, and/or N18 in the nexus region are modified with 2’-O-Me and/or wherein N15, N16, N17, and/or N18 in the nexus region are modified.
19. The sgRNA of claim 18, wherein the modifications in the nexus region are selected from e and 2’-F.
20. The sgRNA of claim 1, wherein the sgRNA comprises 2’-O-Me modified nucleotides at: a. the first three nucleotides at the 5’ end of the 5’ terminus; b. each nucleotide in the hairpin 1 region; c. the nucleotide between hairpin 1 and hairpin 2; and d. the last four nucleotides at the 3’ end of the 3’ terminus.
21. The sgRNA of claim 1, wherein the hairpin 1 region comprises H1-1 to H1-12 from the 5’ end to the 3’ end thereof and the hairpin 2 region comprises H2-1 to H2-15 from the 5’ end to the 3’ end thereof, and wherein the sgRNA comprises 2’-O-Me ed nucleotides at: a. the first three nucleotides at the 5’ end of the 5’ terminus; b. each of nucleotides H1-1, H1-2, H1-3, H1-4, H1-5, H1-6, H1-7, H1-8, H1-9, H1-10, H1-11, and H1-12; c. the nucleotide between hairpin 1 and hairpin 2; and d. the last four nucleotides at the 3’ end of the 3’ us; and e. three PS bonds linking the first four nucleotides at the 5' end of the 5' terminus and three PS bonds linking the last four nucleotides at the 3' end of the 3' terminus.
22. The sgRNA of claim 1, n the sgRNA is a sgRNA comprising any of SEQ ID NOs: 240, 265-283, 309-327, and 331.
23. The sgRNA of claim 1, wherein the sgRNA is a sgRNA comprising SEQ ID No: 242 or SEQ ID No: 358.
24. A composition comprising an sgRNA of any one of claims 1-23, further comprising a lipid nanoparticle (LNP).
25. The composition of claim 25, further comprising an mRNA which encodes a nuclease.
26. A composition sing an sgRNA of any one of claims 1-23, further comprising a se or an mRNA which encodes the nuclease.
27. The composition of claim 25 or claim 26, wherein the nuclease is a Cas protein.
28. The composition of any one or claims 25-27, wherein the Cas protein is a Cas9.
29. The composition of claim 28, wherein the Cas9 protein is an S. pyogenes Cas9.
30. The composition of any one of claims 25-29, wherein the nuclease is a nickase.
31. The composition of any one of claims 25-30, n the nuclease is modified.
32. A pharmaceutical formulation comprising the sgRNA of any one of claims 1-24 or the composition of any one of claims 24-31, and further comprising a pharmaceutically acceptable carrier.
33. A method of modifying a target DNA in vitro or ex vivo comprising delivering (1) a Cas n or a nucleic acid encoding a Cas protein, and (2) the sgRNA of any one of claims 1-23 or the composition of any one of claims 24-31.
34. Use of the sgRNA of any one of claims 1-23, the composition of any one of claims 24-31 in the manufacture of a medicament for treating a disease or disorder. 2’2?»in 162.?
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201662431756P | 2016-12-08 | 2016-12-08 | |
| PCT/US2017/065306 WO2018107028A1 (en) | 2016-12-08 | 2017-12-08 | Modified guide rnas |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| NZ754228A NZ754228A (en) | 2023-12-22 |
| NZ754228B2 true NZ754228B2 (en) | 2024-03-26 |
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