Circular RNA for translation in eukaryotic cells
Methods and constructs for engineering circular RNA are disclosed. In some embodiments, the methods and constructs comprise a vector for making circular RNA, the vector comprising the following elements operably connected to each other and arranged in the following sequence: a.) a 5′ homology arm, b.) a 3′ group I intron fragment containing a 3′ splice site dinucleotide, c.) optionally, a 5′ spacer sequence, d.) a protein coding or noncoding region, e.) optionally, a 3′ spacer sequence, f) a 5′ Group I intron fragment containing a 5′ splice site dinucleotide, and g.) a 3′ homology arm, the vector allowing production of a circular RNA that is translatable or biologically active inside eukaryotic cells. Methods for purifying the circular RNA produced by the vector and the use of nucleoside modifications in circular RNA produced by the vector are also disclosed.
1. A method for making a cell population comprising circular RNA, said method comprising contacting the cells in the population with a composition comprising:
a) circular RNA produced from a vector comprising the following elements:
i) a 5′ homology arm,
ii) a 3′ Group I self-splicing intron fragment containing a 3′ splice site dinucleotide,
iii) a 5′ spacer sequence,
iv) an internal ribosome entry site (IRES),
v) a protein coding region encoding a chimeric antigen receptor (CAR),
vi) a 3′ spacer sequence,
vii) a 5′ Group I self-splicing intron fragment containing a 5′ splice site dinucleotide, and
viii) a 3′ homology arm,
said vector allowing production of a circular RNA that is translatable or biologically active inside eukaryotic cells, and
b) a delivery vehicle for delivering the circular RNA to the cells, said delivery vehicle comprising a nanocarrier selected from the group consisting of a lipid, a polymer and a lipo-polymeric hybrid,
wherein the circular RNA is delivered into the cells in vitro, trans-arterially, subcutaneously, intratumorally, intramedullary, intranodally, intravenously, intrathecally or intraperitoneally.
2. The method of claim 1 , wherein the vector further comprises an RNA polymerase promoter.
3. The method of claim 2 , wherein the RNA polymerase promoter is positioned at the 5′ end of the vector.
4. The method of claim 3 , wherein the RNA polymerase promoter is a T7 virus RNA polymerase promoter, T6 virus RNA polymerase promoter, SP6 virus RNA polymerase promoter, T3 virus RNA polymerase promoter, or T4 virus RNA polymerase promoter.
5. The method of claim 1 , wherein at least one spacer sequence comprises a polyA sequence.
6. The method of claim 1 , wherein at least one spacer sequence comprises a polyA-C sequence.
7. The method of claim 1 , wherein the circular RNA is delivered into the cells intravenously.
8. A method of making a cell population comprising circular RNA, said method comprising contacting the cells in the population with a composition comprising circular RNA produced from a vector, wherein the circular RNA comprises in the following order, a portion of a 3′ Group I self-splicing intron fragment, an Internal Ribosome Entry Site (IRES), a protein encoding region encoding a chimeric antigen receptor (CAR), and a portion of a 5′ Group I self-splicing intron fragment, wherein said vector allows the production of a circular RNA that is translatable or biologically active inside eukaryotic cells, and a delivery vehicle for delivering the circular RNA to the cells, said delivery vehicle comprising a nanocarrier selected from the group consisting of a lipid, a polymer and a lipo-polymeric hybrid, wherein the circular RNA is delivered into the cells in vitro, trans-arterially, subcutaneously, intratumorally, intramedullary, intranodally, intravenously, intrathecally or intraperitoneally.
9. The method of claim 8 , wherein the IRES is selected from an IRES sequence from a virus or a gene selected from the group consisting of Taura syndrome virus, Triatoma virus, Theiler's encephalomyelitis virus, simian Virus 40, Solenopsis invicta virus 1, Rhopalosiphum padi virus, Reticuloendotheliosis virus, fuman poliovirus 1, Plautia stall intestine virus, Kashmir bee virus, Human rhinovirus 2 , Homalodisca coagulata virus- 1, Human Immunodeficiency Virus type 1 , Homalodisca coagulata virus- 1, Himetobi P virus, Hepatitis C virus, Hepatitis A virus, Hepatitis GB virus, foot and mouth disease virus, Human enterovirus 71, Equine rhinitis virus, Ectropis obliqua picoma-like virus, Encephalomyocarditis virus (EMCV), Drosophila C Virus, Crucifer tobamo virus, Cricket paralysis virus, Bovine viral diarrhea virus 1, Black Queen Cell Virus, Aphid lethal paralysis virus, Avian encephalomyelitis virus, Acute bee paralysis virus, Hibiscus chlorotic ringspot virus, Classical swine fever virus, Human FGF2, Human SFTPA1, Human AML1/RUNX1, Drosophila antennapedia, Human AQP4, Human AT1R, Human BAG-1, Human BCL2, Human BiP, Human c-IAP1, Human c- myc, Human eIF4G, Mouse NDST4L, Human LEF1, Mouse HIF1 alpha, Human n.myc, Mouse Gtx, Human p27kip1, Human PDGF2/c-sis, Human p53, Human Pim-1, Mouse Rbm3, Drosophila reaper, Canine Scamper, Drosophila Ubx, Salivirus, Cosavirus, Parechovirus, Human UNR, Mouse UtrA, Human VEGF-A, Human XIAP, Drosophila hairless, S. cerevisiae TFIID, S. cerevisiae YAP1, Human c-src, Human FGF-1, Simian picomavirus, Turnip crinkle virus, Coxsackievirus B3 (CVB3) and Coxsackievirus A (CVB1/2).
10. The method of claim 9 , wherein the IRES is a IRES sequence from Coxsackievirus B3 (CVB3).
11. The method of claim 9 , wherein the IRES is a IRES sequence from Encephalomyocarditis virus (EMCV).
12. The method of claim 8 , wherein the 3′ Group I self-splicing intron fragment and the 5′ Group I self-splicing intron fragment are from a Cyanobaterium Anabaena sp. Pre-tRNA-Leu gene.
13. The method of claim 8 , wherein the 3′ Group I self-splicing intron fragment and 5′ Group I self-splicing intron fragment are from a T4 phage Td gene.
14. The method of claim 8 , wherein generating the circular RNA comprises transcribing the vector to produce a precursor RNA, and forming the circular RNA by ligating the precursor RNA.
15. The method of claim 8 , wherein the circular RNA comprises a 5′ spacer sequence between the portion of the 3′ Group I self-splicing intron fragment and the IRES, and a 3′ spacer sequence between the protein encoding region encoding a chimeric antigen receptor (CAR) and the portion of the 5′ Group I self-splicing intron fragment.
16. The method of claim 15 , wherein the 3′ spacer sequence and the 5′ spacer sequence each have a length of about 10 to about 60 nucleotides.
17. The method of claim 8 , wherein the IRES is an IRES sequence of Salivirus.
18. The method of claim 8 , wherein the circular RNA is delivered into the cells intravenously.
19. A method for making a cell population comprising circular RNA, said method comprising contacting the cells in the population with a composition comprising:
a) circular RNA produced from a vector comprising the following elements operably connected to each other and arranged in the following sequence:
i) a 5′ homology arm,
ii) a 3′ Group I self-splicing intron fragment containing a 3′ splice site dinucleotide,
iii) a 5′ spacer sequence,
iv) an internal ribosome entry site (IRES),
v) a protein coding region,
vi) a 3′ spacer sequence,
vii) a 5′ Group I self-splicing intron fragment containing a 5′ splice site dinucleotide, and
viii) a 3′ homology arm,
said vector allowing production of a circular RNA that is translatable or biologically active inside eukaryotic cells, and
b) a delivery vehicle for delivering the circular RNA to the cells, said delivery vehicle comprising a nanocarrier selected from the group consisting of a lipid, a polymer and a lipo-polymeric hybrid,
wherein the circular RNA is delivered into the cells in vitro, trans-arterially, subcutaneously, intratumorally, intramedullary, intranodally, intravenously, intrathecally or intraperitoneally.
20. The method of claim 19 , wherein the circular RNA comprises in the following order, a portion of a 3′ Group I self-splicing intron fragment, an Internal Ribosome Entry Site (IRES), a protein coding region, and a portion of a 5′ Group I self-splicing intron fragment.
21. The method of claim 19 , wherein the protein coding region encodes a chimeric antigen receptor (CAR).
22. The method of claim 19 , wherein the protein coding region encodes a therapeutic protein, a chimeric antigen receptor, an antibody or a bispecific antibody.
23. The method of claim 19 , wherein the circular RNA is delivered into the cells intravenously.
24. A method for making a cell population comprising circular RNA, said method comprising contacting the cells in the population with a composition comprising:
a) a vector comprising the following elements operably connected to each other and arranged in the following sequence:
i) a 5′ homology arm,
ii) a 3′ Group I self-splicing intron fragment containing a 3′ splice site dinucleotide,
iii) a 5′ spacer sequence,
iv) an internal ribosome entry site (IRES),
v) a protein coding region,
vi) a 3′ spacer sequence,
vii) a 5′ Group I self-splicing intron fragment containing a 5′ splice site dinucleotide, and
viii) a 3′ homology arm,
said vector allowing production of a circular RNA that is translatable or biologically active inside eukaryotic cells, and
b) a delivery vehicle for delivering the vector to the cells, said delivery vehicle comprising a nanocarrier selected from the group consisting of a lipid, a polymer and a lipo-polymeric hybrid,
wherein the circular RNA is delivered into the cells in vitro, trans-arterially, subcutaneously, intratumorally, intramedullary, intranodally, intravenously, intrathecally or intraperitoneally.
25. The method of claim 24 , wherein a circular RNA is produced from the vector within the cell population.
26. The method of claim 24 , wherein the circular RNA is delivered into the cells intravenously.