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  • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
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  • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
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  • C07K14/08—RNA viruses
  • C07K14/18—Togaviridae; Flaviviridae
  • C07K14/1808—Alphaviruses or Group A arboviruses, e.g. sindbis, VEE, EEE, WEE, semliki forest virus
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  • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
  • A61K2039/53—DNA (RNA) vaccination
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  • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
  • A61K2039/55511—Organic adjuvants
  • A61K2039/55555—Liposomes; Vesicles, e.g. nanoparticles; Spheres, e.g. nanospheres; Polymers
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  • A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
  • A61K2039/575—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 humoral response
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  • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
  • C12N2760/00011—Details
  • C12N2760/16011—Orthomyxoviridae
  • C12N2760/16111—Influenzavirus A, i.e. influenza A virus
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  • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
  • C12N2770/00011—Details
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  • C12N2770/00011—Details
  • C12N2770/20011—Coronaviridae
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  • C12N2830/00—Vector systems having a special element relevant for transcription
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  • C12N2840/00—Vectors comprising a special translation-regulating system
  • C12N2840/20—Vectors comprising a special translation-regulating system translation of more than one cistron
  • C12N2840/203—Vectors comprising a special translation-regulating system translation of more than one cistron having an IRES
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
  • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

• the present disclosure relates generally to inducing immune responses against infectious agents and more specifically to RNA molecules and liponanoparticles as vaccines.
• SARS-CoV-2 severe acute respiratory syndrome-coronavirus-2
• SARS-CoV-2 is a novel coronavirus that was first identified in December 2019 in Wuhan, China and that has caused more than 184 million confirmed infections and nearly 4 million deaths worldwide as of July 2021.
• Control measures to curb the rapid worldwide spread of SARS-CoV-2, such as national lockdowns, closure of workplaces and schools, and reduction of international travel have been damaging to global economies and social wellbeing.
• RNAs e.g., RNAs derived from viral replicons, and messenger RNAs (mRNAs) are useful for expression of proteins, such as heterologous proteins, for a variety of purposes, such as expression of therapeutic proteins and expression of antigens for vaccines.
• mRNAs messenger RNAs
• a desirable property of replicons is the ability for sustained expression of the protein.
• RNA molecules that are useful for inducing immune responses. Both self-replicating RNA molecules and messenger RNA (mRNA) molecules are provided.
• mRNA messenger RNA
• RNA molecules comprising: (a) a first polynucleotide encoding one or more viral replication proteins, wherein one or more miRNA binding sites in the first polynucleotide have been modified as compared to a reference polynucleotide; and (b) a second polynucleotide comprising a first transgene encoding a first antigenic protein or a fragment thereof.
• RNA molecules comprising: (i) a first polynucleotide comprising a sequence having at least 80% identity to a sequence of SEQ ID NO:6; and (ii) a second polynucleotide comprising a first transgene encoding a first antigenic protein or a fragment thereof.
• modification of the one or more miRNA binding sites reduces or eliminates miRNA binding.
• two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, or 15 miRNA binding sites in the first polynucleotide have been modified.
• the one or more miRNA binding sites are selected from regions that bind a miRNA having a sequence of SEQ ID NOs:58, 59, 72, 80, 81, 83, 101, 102, 103, 112, 113, 114, 128, 131, 142, 156, 157, 171, 175, and any combination thereof.
• the one or more viral replication proteins of RNA molecules provided herein are alphavirus proteins or rubivirus proteins.
• the alphavirus proteins are from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (K
• first polynucleotides of RNA molecules provided herein encode a polyprotein comprising an alphavirus nsPl protein, an alphavirus nsP2 protein, an alphavirus nsP3 protein, an alphavirus nsP4 protein, or any combination thereof.
• first polynucleotides encode a polyprotein comprising an alphavirus nsPl protein, an alphavirus nsP2 protein, an alphavirus nsP3 protein, or any combination thereof, and an alphavirus nsP4 protein.
• first polynucleotides comprise a sequence having at least 80% identity to a sequence of SEQ ID NO:6.
• first polynucleotides comprise a sequence having at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO:6.
• first polynucleotides encode a polyprotein comprising a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO: 187.
• RNA molecules provided herein include a 5’ untranslated region (UTR).
• the 5’ UTR comprises a viral 5’ UTR, a non-viral 5’ UTR, or a combination of viral and non-viral 5’ UTR sequences.
• the 5’ UTR comprises an alphavirus 5’ UTR.
• the alphavirus 5’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan
• RNA molecules provided herein include a 3’ untranslated region (UTR).
• the 3’ UTR comprises a viral 3’ UTR, a non-viral 3’ UTR, or a combination of viral and non-viral 3’ UTR sequences.
• the 3’ UTR comprises an alphavirus 3’ UTR.
• the alphavirus 3’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan
• the 3’ UTR comprises a sequence of SEQ ID NO:9. In some aspects, the 3’ UTR further comprises a poly-A sequence.
• the first antigenic protein of RNA molecules provided herein is a viral protein, a bacterial protein, a fungal protein, a protozoan protein, or a parasite protein.
• the viral protein is a coronavirus protein, an orthomyxovirus protein, a paramyxovirus protein, a picornavirus protein, a flavivirus protein, a filovirus protein, a rhabdovirus protein, a togavirus protein, an arterivirus protein, a bunyavirus protein, an arenavirus protein, a reovirus protein, a bornavirus protein, a retrovirus protein, an adenovirus protein, a herpesvirus protein, a polyomavirus protein, a papillomavirus protein, a poxvirus protein, or a hepadnavirus protein.
• the first antigenic protein is a SARS-CoV- 2 protein, an influenza virus protein, a respiratory syncytial virus (RSV) protein, a human immunodeficiency virus (HIV) protein, a hepatitis C virus (HCV) protein, a cytomegalovirus (CMV) protein, a Lassa Fever Virus (LFV) protein, an Ebola Virus (EBOV) protein, a Mycobacterium protein, a Bacillus protein, a Yersinia protein, a Streptococcus protein, a Pseudomonas protein, a Shigella protein, a Campylobacter protein, a Salmonella protein, a Plasmodium protein, or a Toxoplasma protein.
• SARS-CoV- 2 protein an influenza virus protein, a respiratory syncytial virus (RSV) protein, a human immunodeficiency virus (HIV) protein, a hepatitis C virus (HCV) protein
• the first antigenic protein is a SARS-CoV-2 spike glycoprotein.
• the SARS-CoV-2 spike glycoprotein comprises an amino acid sequence having at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17.
• the second polynucleotide of RNA molecules provided herein comprises a sequence having at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, or SEQ ID NO: 13.
• the first transgene of RNA molecules provided herein is expressed from a first subgenomic promoter.
• the second polynucleotide of RNA molecules provided herein includes at least two transgenes.
• a second transgene of the second polynucleotide encodes a second antigenic protein or a fragment thereof or an immunomodulatory protein.
• the second polynucleotide further comprises a sequence encoding a 2A peptide, an internal ribosomal entry site (IRES), a second subgenomic promoter, or a combination thereof, located between transgenes.
• the immunomodulatory protein is a cytokine, a chemokine, or an interleukin.
• first and second transgenes of second polynucleotides encode viral proteins, bacterial proteins, fungal proteins, protozoan proteins, parasite proteins, immunomodulatory proteins, or any combination thereof.
• RNA molecules provided herein further include an intergenic region located between the first polynucleotide and the second polynucleotide. In some aspects, the intergenic region comprises a sequence having at least 85% identity to a sequence of SEQ ID NO:7. [0018] In some aspects, RNA molecules provided herein are self-replicating RNA molecules.
• RNA molecules provided herein include a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.
• RNA molecules provided herein are self-replicating RNA molecules.
• RNA molecules provided herein include a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:40, or SEQ ID NO:48.
• RNA molecules provided herein further include a 5’ cap.
• the 5’ cap has a Cap 1 structure, a Cap 1 ( m6 A) structure, a Cap 2 structure, or a Cap 0 structure.
• DNA molecules encoding any of the RNA molecules provided herein include a promoter.
• the promoter is located 5’ of the 5 ’UTR.
• the promoter is a T7 promoter, a T3 promoter, or an SP6 promoter.
• compositions comprising any RNA molecule provided herein and a lipid.
• the lipid comprises an ionizable cationic lipid.
• the ionizable cationic lipid has a structure of thereof.
• compositions comprising any RNA molecule provided herein and a lipid formulation.
• the lipid formulation comprises an ionizable cationic lipid.
• the ionizable cationic lipid has a structure of
• the lipid formulation is selected from a lipoplex, a liposome, a lipid nanoparticle, a polymer-based carrier, an exosome, a lamellar body, a micelle, and an emulsion.
• the lipid formulation is a liposome selected from a cationic liposome, a nanoliposome, a proteoliposome, a unilamellar liposome, a multilamellar liposome, a ceramide-containing nanoliposome, and a multivesicular liposome.
• the lipid formulation is a lipid nanoparticle.
• the lipid nanoparticle has a size of less than about 200 nm.
• the lipid nanoparticle has a size of less than about 150 nm. In some aspects, the lipid nanoparticle has a size of less than about 100 nm. In some aspects, the lipid nanoparticle has a size of about 55 nm to about 90 nm. In some aspects, the lipid formulation comprises one or more cationic lipids.
• the one or more cationic lipids is selected from 5-carboxyspermylglycinedioctadecylamide (DOGS), 2,3- dioleyloxy-N-[2(spermine-carboxamido)ethyl]-N,N-dimethyl-l-propanaminium (DOSPA), l,2-Dioleoyl-3-Dimethylammonium-Propane (DODAP), l,2-Dioleoyl-3-
• DOGS 5-carboxyspermylglycinedioctadecylamide
• DOSPA 2,3- dioleyloxy-N-[2(spermine-carboxamido)ethyl]-N,N-dimethyl-l-propanaminium
• DODAP 2-Dioleoyl-3-Dimethylammonium-Propane
• DOTAP Trimethylammonium-Propane
• DSDMA disearyloxy-N,N-dimethyl-3-aminopropane
• DODMA dioleyloxy-N,N-dimethyl-3-aminopropane
• DenDMA 1,2-dilinoleyloxy- N,N-dimethyl-3-aminopropane
• DLenDMA l,2-dilinolenyloxy-N,N-dimethyl-3- aminopropane
• DODAC N-dioleyl-N,N-dimethylammonium chloride
• DDAB N,N- distearyl-N,N-dimethylammonium bromide
• DMRIE 3-dimethylamino-2-(cholest-5-en-3- beta-oxybutyl
• the lipid formulation comprises an ionizable cationic lipid.
• the ionizable cationic lipid has a structure of Formula I: or a pharmaceutically acceptable salt or solvate thereof, wherein R 5 and R 6 are each independently selected from the group consisting of a linear or branched C 1 -C 31 alkyl, C 2 -C 31 alkenyl or C 2 -C 31 alkynyl and cholesteryl; L 5 and L 6 are each independently selected from the group consisting of a linear C 1 -C 20 alkyl and C 2 -C 20 alkenyl; X 5 is -C(0)0-, whereby -C(0)0- R 6 is formed or -OC(O)- whereby -0C(0)-R 6 is formed; X 6 is -C(0)0- whereby -C(0)0-R 5 is formed or -OC(O)- whereby -0C(0)-R 5 is formed; X 7 is S or O; L 7 is absent or lower
• the ionizable cationic lipid is ATX-126:
• the lipid formulation of compositions provided herein encapsulates the nucleic acid molecule. In some aspects, the lipid formulation is complexed to the nucleic acid molecule.
• the lipid formulation further comprises a helper lipid.
• the helper lipid is a phospholipid.
• the helper lipid is selected from dioleoylphosphatidyl ethanolamine (DOPE), dimyristoylphosphatidyl choline (DMPC), distearoylphosphatidyl choline (DSPC), dimyristoylphosphatidyl glycerol (DMPG), dipalmitoyl phosphatidylcholine (DPPC), and phosphatidylcholine (PC).
• DOPE dioleoylphosphatidyl ethanolamine
• DMPC dimyristoylphosphatidyl choline
• DSPC distearoylphosphatidyl choline
• DMPG dimyristoylphosphatidyl glycerol
• DPPC dipalmitoyl phosphatidylcholine
• PC phosphatidylcholine
• the helper lipid is distearoy
• the lipid formulation of compositions provided herein further comprises cholesterol.
• the lipid formulation further comprises a polyethylene glycol (PEG)-lipid conjugate.
• PEG-lipid conjugate is PEG-DMG.
• PEG-DMG is PEG2000-DMG.
• the lipid portion of the lipid formulation comprises about 40 mol% to about 60 mol% of the ionizable cationic lipid, about 4 mol% to about 16 mol% DSPC, about 30 mol% to about 47 mol% cholesterol, and about 0.5 mol% to about 3 mol% PEG2000-DMG. In some aspects, the lipid portion of the lipid formulation comprises about 42 mol% to about 58 mol% of the ionizable cationic lipid, about 6 mol% to about 14 mol% DSPC, about 32 mol% to about 44 mol% cholesterol, and about 1 mol% to about 2 mol% PEG2000-DMG.
• the lipid portion of the lipid formulation comprises about 45 mol% to about 55 mol% of the ionizable cationic lipid, about 8 mol% to about 12 mol% DSPC, about 35 mol% to about 42 mol% cholesterol, and about 1.25 mol% to about 1.75 mol% PEG2000-DMG.
• the composition has a total lipidmucleic acid molecule weight ratio of about 50:1 to about 10:1. In some aspects, the composition has a total lipidmucleic acid molecule weight ratio of about 44: 1 to about 24: 1. In some aspects, the composition has a total lipid: nucleic acid molecule weight ratio of about 40:1 to about 28:1. In some aspects, the composition has a total lipid: nucleic acid molecule weight ratio of about 38:1 to about 30:1. In some aspects, the composition has a total lipid: nucleic acid molecule weight ratio of about 37:1 to about 33:1.
• the composition comprises a HEPES or TRIS buffer at a pH of about 7.0 to about 8.5.
• the HEPES or TRIS buffer is at a concentration of about 7 mg/mL to about 15 mg/mL.
• the composition further comprises about 2.0 mg/mL to about 4.0 mg/mL of NaCl.
• the composition further comprises one or more cryoprotectants.
• the one or more cryoprotectants are selected from sucrose, glycerol, or a combination of sucrose and glycerol.
• the composition comprises a combination of sucrose at a concentration of about 70 mg/mL to about 110 mg/mL and glycerol at a concentration of about 50 mg/mL to about 70 mg/mL.
• the composition is a lyophilized composition.
• the lyophilized composition comprises one or more lyoprotectants.
• the lyophilized composition comprises a poloxamer, potassium sorbate, sucrose, or any combination thereof.
• the poloxamer is poloxamer 188.
• the lyophilized composition comprises about 0.01 to about 1.0 % w/w of the RNA molecule. In some aspects, the lyophilized composition comprises about 1.0 to about 5.0 % w/w lipids. In some aspects, the lyophilized composition comprises about 0.5 to about 2.5 % w/w of TRIS buffer. In some aspects, the lyophilized composition comprises about 0.75 to about 2.75 % w/w of NaCl. In some aspects, the lyophilized composition comprises about 85 to about 95 % w/w of a sugar. In some aspects, the sugar is sucrose. In some aspects, the lyophilized composition comprises about 0.01 to about 1.0 % w/w of a poloxamer. In some aspects, the poloxamer is poloxamer 188. In some aspects, the lyophilized composition comprises about 1.0 to about 5.0 % w/w of potassium sorbate.
• compositions provided herein include an RNA molecule comprising (A) a sequence of SEQ ID NO: 1; (B) a sequence of SEQ ID NO:2; (C) a sequence of SEQ ID NO:3; or (D) a sequence of SEQ ID NO:4.
• compositions provided herein include an RNA molecule comprising a sequence of SEQ ID NO:29.
• compositions provided herein include an RNA molecule comprising a sequence of SEQ ID NO:32.
• compositions provided herein include an RNA molecule comprising a sequence of SEQ ID NO:48.
• compositions provided herein include an RNA molecule comprising a sequence of SEQ ID NO:40.
• lipid nanoparticle compositions comprising a. a lipid formulation comprising i. about 45 mol% to about 55 mol% of an ionizable cationic lipid having the structure of ATX- 126: ii. about 8 mol% to about 12 mol% DSPC; iii. about 35 mol% to about 42 mol% cholesterol; and iv. about 1.25 mol% to about 1.75 mol% PEG2000-DMG; and b.
• RNA molecule having at least 80% identity to a sequence of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; wherein the lipid formulation encapsulates the RNA molecule and the lipid nanoparticle has a size of about 60 to about 90 nm.
• the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:29.
• the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:32.
• the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:40. In some aspects, the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:48. In some aspects, the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:29. In some aspects, the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:32.
• compositions provided herein are administered intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, by aerosol, or by a pulmonary route. In some aspects, compositions provided herein are administered intramuscularly.
• compositions provided herein are methods of administering a composition provided herein to a subject in need thereof, wherein the composition is lyophilized and is reconstituted prior to administration.
• compositions provided herein comprising administering a composition provided herein to a subject in need thereof.
• the composition is administered one time.
• the composition is administered two times.
• kits for administering a booster dose to a vaccinated subject comprising administering a composition provided herein to a subject who was previously vaccinated against coronavirus.
• a composition provided herein is administered at a dosage of about 0.01 ⁇ g to about 1,000 ⁇ g of nucleic acid in the methods provided herein. In some aspects, a composition provided herein is administered at a dosage of about 1, 2, 5, 7.5, or 10 ⁇ g of nucleic acid.
• RNA molecules are administered intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, by aerosol, or by a pulmonary route.
• compositions are administered intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, by aerosol, or by a pulmonary route.
• RNA molecules for use in inducing an immune response to the first antigenic protein or fragment thereof.
• RNA molecule provided herein in the manufacture of a medicament for inducing an immune response to the first antigenic protein or fragment thereof.
• the present disclosure provides an RNA molecule for expressing an antigen comprising an open reading frame having at least 80% identity to a sequence of SEQ ID NO:33 or SEQ ID NO:30, wherein T is substituted with U.
• RNA molecule further comprises a 5’ UTR having a sequence selected from SEQ ID NO:35, SEQ ID NOs: 189-218, or SEQ ID NOs:233-279.
• RNA molecule further comprises a 3’ UTR having a sequence selected from SEQ ID NO:37, SEQ ID NOs:219-225, or SEQ ID NOs:280-317.
• the RNA molecule further comprises a 5’ cap.
• the 5’ cap has a Cap 1 structure, a Cap 1 (m6A) structure, a Cap 2 structure, or a Cap 0 structure.
• RNA molecule further comprises a poly- A tail.
• the present disclosure provides an RNA molecule for expressing an antigen comprising an open reading frame having at least 80% identity to a sequence of SEQ ID NO:33, a 5’ UTR comprising a sequence of SEQ ID NO:35, and a 3’ UTR comprising a sequence of SEQ ID NO:37; or an open reading frame having at least 80% identity to a sequence of SEQ ID NO:30, a 5’ UTR comprising a sequence of SEQ ID NO:35, and a 3’ UTR comprising a sequence of SEQ ID NO:37, wherein T is substituted with U.
• the RNA molecule further comprises a 5’ cap.
• the 5’ cap has a Cap 1 structure, a Cap 1 (m6A) structure, a Cap 2 structure, or a Cap 0 structure.
• RNA molecule further comprises a poly- A tail.
• the present disclosure provides a DNA molecule encoding any one of the RNA molecules described herein.
• the DNA molecule comprises a promoter.
• the promoter is a T7 promoter, a T3 promoter, or an SP6 promoter.
• the present disclosure provides a composition comprising any of the RNA molecules described herein, and a lipid formulation.
• the lipid formulation is selected from a lipoplex, a liposome, a lipid nanoparticle, a polymer-based carrier, an exosome, a lamellar body, a micelle, and an emulsion.
• the lipid formulation is a liposome selected from a cationic liposome, a nanoliposome, a proteoliposome, a unilamellar liposome, a multilamellar liposome, a ceramide-containing nanoliposome, and a multivesicular liposome.
• the lipid formulation is a lipid nanoparticle.
• the lipid formulation comprises one or more cationic lipids.
• the one or more cationic lipids is selected from 5- carboxyspermylglycinedioctadecylamide (DOGS), 2,3-dioleyloxy-N-[2(spermine- carboxamido)ethyl]-N,N-dimethyl-l-propanaminium (DOSPA), l,2-Dioleoyl-3-
• DODAP Dimethylammonium-Propane
• DOTAP Trimethylammonium-Propane
• DADMA dimethylammonium-Propane
• DODMA dimethylammonium-Propane
• DODMA dimethylammonium-Propane
• DODMA dimethylammonium-Propane
• DODMA dimethyl-3-aminopropane
• DODMA dimethyl-3-aminopropane
• DODMA dimethyl-3-aminopropane
• DLinDMA l,2-dilinoleyloxy-N,N-dimethyl-3-aminopropane
• DLenDMA N-dioleyl- N,N-dimethylammonium chloride
• DODAC N,N-distearyl-N,N-dimethylammonium bromide
• DDAB N-(l,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyeth
• the lipid formulation comprises an ionizable cationic lipid.
• the ionizable cationic lipid has a structure of Formula I: or a pharmaceutically acceptable salt or solvate thereof, wherein R5 and R6 are each independently selected from the group consisting of a linear or branched C1-C31 alkyl, C2- C31 alkenyl or C2-C31 alkynyl and cholesteryl; L5 and L6 are each independently selected from the group consisting of a linear C1-C20 alkyl and C2-C20 alkenyl; X5 is -C(0)0-, whereby -C(0)0-R6 is formed or -OC(O)- whereby -OC(0)-R6 is formed; X6 is -C(0)0- whereby -C(0)0-R5 is formed or -OC(O)- whereby -OC(0)-R5 is formed; X7 is S or O; L7 is absent or lower alkyl; R4 is
• the ionizable cationic lipid is selected from
• the lipid formulation comprises a helper lipid.
• the helper lipid is a phospholipid.
• helper lipid is selected from dioleoylphosphatidyl ethanolamine (DOPE), dimyristoylphosphatidyl choline (DMPC), distearoylphosphatidyl choline (DSPC), dimyristoylphosphatidyl glycerol (DMPG), dipalmitoyl phosphatidylcholine (DPPC), and phosphatidylcholine (PC).
• DOPE dioleoylphosphatidyl ethanolamine
• DMPC dimyristoylphosphatidyl choline
• DSPC distearoylphosphatidyl choline
• DMPG dimyristoylphosphatidyl glycerol
• DPPC dipalmitoyl phosphatidylcholine
• PC phosphatidylcholine
• the lipid formulation comprises cholesterol.
• the lipid formulation comprises a polyethylene glycol (PEG)-lipid conjugate.
• PEG polyethylene glycol
• the present disclosure provides a method of inducing an immune response in a subject comprising administering to the subject an effective amount of any of the RNA molecules or compositions described herein.
• the method comprises administering the RNA molecule or the composition intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, or by a pulmonary route.
• the present disclosure provides a method of administering administering a booster dose to a vaccinated subject, comprising administering any of the RNA molecules or compositions described herein to a subject who was previously vaccinated against coronavirus.
• the method comprises administering the RNA molecule or the composition intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, or by a pulmonary route.
• RNA molecules or compositions described herein are used for inducing an immune response to the antigen.
• RNA molecules or compositions described herein are used in the manufacture of a medicament for inducing an immune response to the antigen.
• FIG. 1A shows a schematic of an exemplary self-replicating RNA, including nsPl- nsP4 replicase and coronavirus spike transgene regions.
• FIG. IB shows exemplary miRNA binding sites based on predictions by miRanda (Enright, A.J., John, B., Gaul, U. et al. MicroRNA targets in Drosophila. Genome Biol 5, R1 (2003). doi.org/10.1186/gb-2003-5-l-rl).
• the Venezuelan equine encephalitis virus (VEEV) non- structural protein coding region is shown, with 15 predicted binding sites shown by grey rectangles.
• FIG. 2A shows a Western blot of SARS-CoV-2 spike protein expressed from the indicated construct. Full-length spike protein and the SI and S2 domains are indicated by arrows.
• FIG. 2B shows quantitation of SARS-CoV-2 spike protein expressed from the indicated constructs.
• FIG. 3A shows a Western blot of SARS-CoV-2 South African variant spike protein expressed from the indicated construct. The arrow indicates the full-length spike protein.
• FIG. 3B shows a Western blot of SARS-CoV-2 D614G variant spike protein expressed from the indicated construct. The arrow indicates the full-length spike protein.
• FIG. 3C shows a Western blot of SARS-CoV-2 D614G variant spike protein expressed from the indicated construct. The arrow indicates the full-length spike protein.
• FIG. 3D shows quantitation of SARS-CoV-2 spike protein expression from the indicated constructs.
• FIG. 4A shows quantitation of SARS-CoV-2 South African variant spike protein expression from the indicated construct as compared to reference.
• FIG. 4B shows quantitation of SARS-CoV-2 D614G variant spike protein expression from the indicated construct as compared to reference.
• FIG. 4C shows quantitation of SARS-CoV-2 D614G variant spike protein expression from the indicated construct as compared to reference.
• FIG. 5A shows total Immunoglobulin G (IgG) against the indicated SARS-CoV-2 spike proteins following immunization of mice with self-replicating RNA encoding a SARS- CoV-2 wild-type spike protein (Wuhan).
• FIG. 5B shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of mice with self-replicating RNA encoding a SARS-CoV-2 wild-type spike protein (Wuhan).
• FIG. 5C shows total IgG against the indicated SARS-CoV-2 spike protein variants following immunization of mice with self-replicating RNA encoding a SARS-CoV-2 D614G spike protein variant.
• FIG. 5D shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of mice with self-replicating RNA encoding a SARS-CoV-2 D614G spike protein variant.
• FIG. 5E shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of mice with self-replicating RNA encoding a SARS-CoV-2 South African spike protein variant.
• FIG. 5F shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of mice with self-replicating RNA encoding a SARS-CoV-2 South African spike protein variant.
• FIG. 6A shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of mice with 2 ⁇ g of an mRNA RNA encoding a SARS-CoV-2 D614G spike protein variant.
• FIG. 6B shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of mice with 15 ⁇ g of an mRNA RNA encoding a SARS-CoV-2 D614G spike protein variant.
• FIG. 6C shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of mice with 2 ⁇ g of an mRNA RNA encoding a SARS-CoV- 2 D614G spike protein variant.
• FIG. 6D shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of mice with 15 ⁇ g of an mRNA RNA encoding a SARS- CoV-2 D614G spike protein variant.
• FIG. 7A shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with self-replicating RNA encoding a SARS- CoV-2 wild-type spike protein (Wuhan).
• FIG. 7B shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with self-replicating RNA encoding a SARS-CoV-2 wild-type spike protein (Wuhan).
• FIG. 7C shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with self-replicating RNA encoding a SARS- CoV-2 D614G spike protein variant.
• NHS non-human primates
• FIG. 7D shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with self-replicating RNA encoding a SARS-CoV-2 D614G spike protein variant.
• NHS non-human primates
• FIG. 7E shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with self-replicating RNA encoding a SARS- CoV-2 South African spike protein variant.
• NHS non-human primates
• FIG. 7F shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with self-replicating RNA encoding a SARS-CoV-2 South African spike protein variant.
• FIG. 7G shows total IgG against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with an mRNA RNA encoding a SARS-CoV-2 D614G spike protein variant.
• FIG. 7H shows neutralizing antibodies against the indicated SARS-CoV-2 spike proteins following immunization of non-human primates (NHPs) with an mRNA RNA encoding a SARS-CoV-2 D614G spike protein variant.
• FIG. 8 shows HAI titers obtained for self-replicating RNA and mRNA constructs encoding the hemagglutinin of influenza virus A/California/07/2009 (H1N1).
• FIGs. 9A-9D show results of Luminex Assay for anti-SARS-Cov-2 Spike Glycoprotein IgG in two pre-clinical studies.
• BALB/c mice were vaccinated with increasing RNA doses of self-replicating RNA (SEQ ID NO: 18) formulated as lyophilized lipid nanoparticles (LYO-LNP) and liquid (frozen) lipid nanoparticles (Liquid-LNP).
• SEQ ID NO: 18 self-replicating RNA
• LYO-LNP lyophilized lipid nanoparticles
• Liquid-LNP Liquid-LNP
• FIGs. 10A-10B show the Area Under the Curve (AUC) Analysis for anti-SARS- Cov-2 Spike Glycoprotein IgG (First and Second Study combined data).
• First Study Day 19 and 31 results were combined with Second Study Day 20 and 30 results, respectively, and an Area Under the Curve (AUC) analysis was performed.
• Sidak Sidak’s multiple comparison post-test compared LYO-LNP to Liquid-LNP and resulted in no statistical differences.
• RNAs e.g ., self-repli eating RNAs and messenger RNAs (mRNAs), and nucleic acids encoding the same for expression of transgenes such as antigenic proteins, for example.
• methods of administration e.g., to a host, such as a mammalian subject
• the heterologous protein-coding sequence is expressed and, e.g., can elicit an immune response to the heterologous protein-coding sequence in the recipient or provide a therapeutic effect, including induction of an immune response, where the heterologous protein-coding sequence is a therapeutic or an antigenic protein.
• RNAs e.g, self-replicating RNAs and messenger RNAs (mRNAs), provided herein are useful as vaccines that can be rapidly generated and that can be effective at low and/or single doses.
• the present disclosure further relates to methods of inducing an immune response using RNAs provided herein.
• an immune response can be elicited against coronavirus.
• Immunogens include, but are not limited to, those derived from a SARS coronavirus, avian infectious bronchitis (IBV), Mouse hepatitis virus (MHV), and Porcine transmissible gastroenteritis virus (TGEV).
• the coronavirus immunogen may be a spike polypeptide.
• Self-replicating RNAs are described, for example, in U.S. 2018/0036398, the contents of which are incorporated by reference in their entirety.
• fragment when referring to a protein or nucleic acid, for example, means any shorter sequence than the full-length protein or nucleic acid. Accordingly, any sequence of a nucleic acid or protein other than the full-length nucleic acid or protein sequence can be a fragment.
• a protein fragment includes an epitope. In other aspects, a protein fragment is an epitope.
• nucleic acid refers to any deoxyribonucleic acid (DNA) molecule, ribonucleic acid (RNA) molecule, or nucleic acid analogues.
• a DNA or RNA molecule can be double-stranded or single-stranded and can be of any size.
• Exemplary nucleic acids include, but are not limited to, chromosomal DNA, plasmid DNA, cDNA, cell-free DNA (cfDNA), mitochondrial DNA, chloroplast DNA, viral DNA, mRNA, tRNA, rRNA, long noncoding RNA, siRNA, micro RNA (miRNA or miR), hnRNA, and viral RNA.
• nucleic analogues include peptide nucleic acid, morpholino- and locked nucleic acid, glycol nucleic acid, and threose nucleic acid.
• nucleic acid molecule is meant to include fragments of nucleic acid molecules as well as any full-length or non- fragmented nucleic acid molecule, for example.
• nucleic acid and nucleic acid molecule can be used interchangeably, unless context clearly indicates otherwise.
• polynucleotide refers to a nucleic acid sequence that includes at least two nucleotide monomers.
• the term “polynucleotide” can refer to DNA, RNA, or nucleic acid analogues.
• a “polynucleotide” can be double-stranded or single-stranded and can be of any size.
• a polynucleotide can be a separate nucleic acid molecule or be a part of a nucleic acid molecule. Accordingly, the term “polynucleotide” can refer to a nucleic acid molecule or to a region of a nucleic acid molecule.
• protein refers to any polymeric chain of amino acids.
• peptide and “polypeptide” can be used interchangeably with the term protein, unless context clearly indicates otherwise, and can also refer to a polymeric chain of amino acids.
• protein encompasses native or artificial proteins, protein fragments and polypeptide analogs of a protein sequence.
• a protein may be monomeric or polymeric.
• protein encompasses fragments and variants (including fragments of variants) thereof, unless otherwise contradicted by context.
• sequence identity or “sequence homology,” which can be used interchangeably, refer to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively.
• techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and/or determining the amino acid sequence encoded thereby or the amino acid sequence of a polypeptide, and comparing these sequences to a second nucleotide or amino acid sequence.
• percent (%) sequence identity or “percent (%) identity,” also including “percent homology,” refers to the percentage of amino acid residues or nucleotides in a sequence that are identical with the amino acid residues or nucleotides in a reference sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
• two or more sequences can be compared by determining their “percent identity,” also referred to as “percent homology.”
• the percent identity to a reference sequence e.g., nucleic acid or amino acid sequences
• the percent identity to a reference sequence may be calculated as the number of exact matches between two optimally aligned sequences divided by the length of the reference sequence and multiplied by 100.
• Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul, Proc.
• the BLAST program defines identity as the number of identical aligned symbols (i.e., nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences. The program may be used to determine percent identity over the entire length of the sequences being compared.
• Default parameters are provided to optimize searches with short query sequences, for example, with the blastp program.
• the program also allows use of an SEG filter to mask-off segments of the query sequences as determined by the SEG program of Wootton and Federhen, Computers and Chemistry 17: 149-163 (1993). Ranges of desired degrees of sequence identity are approximately 80% to 100% and integer values in between. Percent identities between a reference sequence and a claimed sequence can be at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%. In general, an exact match indicates 100% identity over the length of the reference sequence.
• Additional programs and methods for comparing sequences and/or assessing sequence identity include the Needleman-Wunsch algorithm (see, e.g., the EMBOSS Needle aligner available at ebi.ac.uk/Tools/psa/emboss needle/, optionally with default settings), the Smith-Waterman algorithm (see, e.g., the EMBOSS Water aligner available at ebi.ac.uk/Tools/psa/emboss water/, optionally with default settings), the similarity search method of Pearson and Lipman, 1988, Proc. Natl. Acad. Sci.
• Needleman-Wunsch algorithm see, e.g., the EMBOSS Needle aligner available at ebi.ac.uk/Tools/psa/emboss needle/, optionally with default settings
• the Smith-Waterman algorithm see, e.g., the EMBOSS Water aligner available at ebi.ac.uk/Tools/psa/e
• reference to percent sequence identity refers to sequence identity as measured using BLAST (Basic Local Alignment Search Tool).
• ClustalW is used for multiple sequence alignment. Optimal alignment may be assessed using any suitable parameters of a chosen algorithm, including default parameters.
• homologous sequences refers to sequences that share sequence similarity and/or structural similarity (Pearson, 2013, An Introduction to Sequence similarity (“Homology”) Searching, Current Protoc Bioinformatics, 42:3.1.1-3.1.8). Accordingly, homologous sequences share common evolutionary ancestry or are derived from a common sequence. Homologous sequences can also share structural or sequence similarity to an intermediate sequence. Homologous sequences can have similar functions, i.e., have functional similarity. Homology can be inferred based on nucleic acid and/or amino acid sequence, with protein similarity searches generally having greater sensitivity than nucleic acid sequence searches.
• homologous sequences that include similar amino acids, i.e., amino acids with similar physiochemical properties, rather than identical amino acids over at least a region of sequence.
• homologous sequences i.e., amino acids with similar physiochemical properties
• homologous nucleic acid i.e., amino acids with similar physiochemical properties
• the term “drug” or “medicament,” means a pharmaceutical formulation or composition as described herein.
• the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise.
• references to “the method” includes one or more methods, and/or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.
• the term “expression” refers to the process by which a nucleic acid sequence or a polynucleotide is transcribed from a DNA template (such as into mRNA or other RNA transcript) and/or the process by which a transcribed mRNA or other RNA is subsequently translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be collectively referred to as “gene product.”
• RNA self-replicating RNA
• self-transcribing and self- replicating RNA self-amplifying RNA (saRNA),” and “replicon” may be used interchangeably, unless context clearly indicates otherwise.
• replicon or “viral replicon” refers to a self-replicating subgenomic RNA derived from a viral genome that includes viral genes encoding non- structural proteins important for viral replication and that lacks viral genes encoding structural proteins.
• a self-replicating RNA can encode further subgenomic RNAs that are not able to self-replicate.
• a self-replicating RNA can also be referred to as a “STARRTM” RNA.
• operably linked refers to juxtaposition of genetic elements, e.g., a promoter, an enhancer, a polyadenylation sequence, etc., wherein the elements are in a relationship permitting them to operate in the expected manner.
• a regulatory element which can comprise promoter and/or enhancer sequences, is operatively linked to a coding region if the regulatory element helps initiate transcription of the coding sequence. There may be intervening residues between the regulatory element and coding region so long as this functional relationship is maintained.
• RNA molecules comprising: (a) a first polynucleotide encoding one or more viral replication proteins, wherein one or more miRNA binding sites in the first polynucleotide have been modified as compared to a reference polynucleotide; and (b) a second polynucleotide comprising a first transgene encoding an antigenic protein or a fragment thereof.
• RNA molecules comprising: (i) a first polynucleotide comprising a sequence having at least 80% identity to a sequence of SEQ ID NO:6; and (ii) a second polynucleotide comprising a first transgene encoding a first antigenic protein or a fragment thereof.
• RNA molecules for expressing an antigen comprising an open reading frame having at least 80% identity to a sequence of SEQ ID NO:33 or SEQ ID NO:30, wherein T is substituted with U.
• RNA molecules for expressing an antigen comprising an open reading frame having at least 80% identity to a sequence of SEQ ID NO:33, a 5’ UTR comprising a sequence of SEQ ID NO:35, and a 3’ UTR comprising a sequence of SEQ ID NO: 37; or an open reading frame having at least 80% identity to a sequence of SEQ ID NO: 30, a 5’ UTR comprising a sequence of SEQ ID NO:35, and a 3’ UTR comprising a sequence of SEQ ID NO:37, wherein T is substituted with U.
• RNA molecule can encode a single polypeptide immunogen or multiple polypeptides. Multiple immunogens can be presented as a single polypeptide immunogen (fusion polypeptide) or as separate polypeptides. If immunogens are expressed as separate polypeptides from a replicon then one or more of these may be provided with an upstream IRES or an additional viral promoter element. Alternatively, multiple immunogens may be expressed from a polyprotein that encodes individual immunogens fused to a short autocatalytic protease (e.g. foot-and-mouth disease virus 2A protein), or as inteins.
• a short autocatalytic protease e.g. foot-and-mouth disease virus 2A protein
• first polynucleotides of RNA molecules provided herein encoding one or more viral replication proteins include codon-optimized sequences.
• codon-optimized means a polynucleotide, nucleic acid sequence, or coding sequence has been redesigned as compared to a wild-type or reference polynucleotide, nucleic acid sequence, or coding sequence by choosing different codons without altering the amino acid sequence of the encoded protein. Accordingly, codon-optimization generally refers to replacement of codons with synonymous codons to optimize expression of a protein while keeping the amino acid sequence of the translated protein the same.
• Codon optimization of a sequence can increase protein expression levels (Gustafsson et al., Codon bias and heterologous protein expression. 2004, Trends Biotechnol 22: 346-53) of the encoded proteins, for example, and provide other advantages. Variables such as codon usage preference as measured by codon adaptation index (CAI), for example, the presence or frequency of U and other nucleotides, mRNA secondary structures, cis-regulatory sequences, GC content, and other variables may correlate with protein expression levels (Villalobos et al., Gene Designer: a synthetic biology tool for constructing artificial DNA segments. 2006, BMC Bioinformatics 7:285). First polynucleotides can be codon-optimized before modifying miRNA binding sites.
• CAI codon adaptation index
• miRNA binding sites can be modified to replace one or more codons with synonymous codons.
• Any method of codon optimization can be used to codon optimize polynucleotides and nucleic acid molecules provided herein, and any variable can be altered by codon optimization. Accordingly, any combination of codon optimization methods can be used. Exemplary methods include the high codon adaptation index (CAI) method, the Low U method, and others.
• CAI high codon adaptation index
• the CAI method chooses a most frequently used synonymous codon for an entire protein coding sequence. As an example, the most frequently used codon for each amino acid can be deduced from 74,218 protein-coding genes from a human genome.
• the Low U method targets U-containing codons that can be replaced with a synonymous codon with fewer U moieties, generally without changing other codons. If there is more than one choice for replacement, the more frequently used codon can be selected. Any polynucleotide, nucleic acid sequence, or codon sequence provided herein can be codon-optimized.
• the nucleotide sequence of any region of the RNA or DNA templates described herein may be codon optimized.
• the primary cDNA template may include reducing the occurrence or frequency of appearance of certain nucleotides in the template strand.
• the occurrence of a nucleotide in a template may be reduced to a level below 25% of said nucleotides in the template.
• the occurrence of a nucleotide in a template may be reduced to a level below 20% of said nucleotides in the template.
• the occurrence of a nucleotide in a template may be reduced to a level below 16% of said nucleotides in the template.
• the occurrence of a nucleotide in a template may be reduced to a level below 15%, and preferably may be reduced to a level below 12% of said nucleotides in the template.
• the nucleotide reduced is uridine.
• the present disclosure provides nucleic acids with altered uracil content wherein at least one codon in the wild-type sequence has been replaced with an alternative codon to generate a uracil-altered sequence.
• Altered uracil sequences can have at least one of the following properties:
• an increase or decrease in global uracil content i.e., the percentage of uracil of the total nucleotide content in the nucleic acid of a section of the nucleic acid, e.g., the open reading frame
• an increase or decrease in local uracil content i.e., changes in uracil content are limited to specific subsequences
• a change in uracil clustering e.g., number of clusters, location of clusters, or distance between clusters
• the percentage of uracil nucleobases in the nucleic acid sequence is reduced with respect to the percentage of uracil nucleobases in the wild-type nucleic acid sequence.
• 30% of nucleobases may be uracil in the wild-type sequence but the nucleobases that are uracil are preferably lower than 15%, preferably lower than 12% and preferably lower than 10% of the nucleobases in the nucleic acid sequences of the disclosure.
• the percentage uracil content can be determined by dividing the number of uracil in a sequence by the total number of nucleotides and multiplying by 100.
• the percentage of uracil nucleobases in a subsequence of the nucleic acid sequence is reduced with respect to the percentage of uracil nucleobases in the corresponding subsequence of the wild-type sequence.
• the wild-type sequence may have a 5 '-end region (e.g., 30 codons) with a local uracil content of 30%, and the uracil content in that same region could be reduced to preferably 15% or lower, preferably 12% or lower and preferably 10% or lower in the nucleic acid sequences of the disclosure.
• These subsequences can also be part of the wild-type sequences of the heterologous 5’ and 3’ UTR sequences of the present disclosure.
• codons in the nucleic acid sequence of the disclosure reduce or modify, for example, the number, size, location, or distribution of uracil clusters that could have deleterious effects on protein translation.
• lower uracil content is desirable in certain aspects, the uracil content, and in particular the local uracil content, of some subsequences of the wild-type sequence can be greater than the wild-type sequence and still maintain beneficial features (e.g., increased expression).
• the uracil-modified sequence induces a lower Toll-Like Receptor (TLR) response when compared to the wild-type sequence.
• TLR Toll-Like Receptor
• ds Double-stranded
• ss Single-stranded
• RNA oligonucleotides for example RNA with phosphorothioate internucleotide linkages, are ligands of human TLR8.
• DNA containing unmethylated CpG motifs characteristic of bacterial and viral DNA, activate TLR9.
• TLR response is defined as the recognition of single- stranded RNA by a TLR7 receptor, and preferably encompasses the degradation of the RNA and/or physiological responses caused by the recognition of the single-stranded RNA by the receptor.
• Methods to determine and quantify the binding of an RNA to a TLR7 are known in the art.
• methods to determine whether an RNA has triggered a TLR7-mediated physiological response are well known in the art.
• a TLR response can be mediated by TLR3, TLR8, or TLR9 instead of TLR7. Suppression of TLR7-mediated response can be accomplished via nucleoside modification.
• Human rRNA for example, has ten times more pseudouracil ('R) and 25 times more 2'-0-methylated nucleosides than bacterial rRNA.
• Bacterial RNA contains no nucleoside modifications, whereas mammalian RNAs have modified nucleosides such as 5-methylcytidine (m5C), N6- methyladenosine (m6A), inosine and many 2'-0-methylated nucleosides in addition to N7- methylguanosine (m7G).
• the uracil content of polynucleotides disclosed herein is less than about 50%, 49%, 48%, 47%, 46%, 45%, 44%, 43%, 42%, 41%, 40%, 39%, 38%, 37%, 36%, 35%, 34%, 33%, 32%, 31%, 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1% of the total nucleobases in the sequence in the reference sequence.
• the uracil content of polynucleotides disclosed herein is between about 5% and about 25%. In some embodiments, the uracil content of polynucleotides disclosed herein is between about 15% and about 25%.
• the nucleotide that is increased or decreased is a nucleotide other than or in addition to uracil.
• Sequences with altered nucleotide content can have (i) an increase or decrease in local C content (i.e., changes in cytosine content are limited to specific subsequences); (ii) an increase or decrease in local G content (i.e., changes in guanosine content are limited to specific subsequences); or (iii) a combination thereof.
• first polynucleotides of nucleic acid molecules provided herein comprise a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO:6.
• first polynucleotides of nucleic acid molecules provided herein comprise a sequence of SEQ ID NO:6.
• first polynucleotides and second polynucleotides of nucleic acid molecules provided herein are included in the same (i.e., a single) or in separate nucleic acid molecules.
• first polynucleotides and second polynucleotides of nucleic acid molecules provided herein are included in a single nucleic acid molecule.
• the first polynucleotide is located 5’ of the second polynucleotide.
• first polynucleotides and second polynucleotides of nucleic acid molecules provided herein are included in separate nucleic acid molecules.
• first polynucleotides and second polynucleotides are included in two separate nucleic acid molecules.
• first polynucleotides and second polynucleotides are included in the same (i.e., a single) nucleic acid molecule.
• First polynucleotides and second polynucleotides of nucleic acid molecules provided herein can be contiguous, i.e., adjacent to each other without nucleotides in between.
• an intergenic region is located between the first polynucleotide and the second polynucleotide.
• the terms “intergenic region” and intergenic sequence” can be used interchangeably, unless context clearly indicates otherwise.
• An intergenic region located between the first polynucleotide and the second polynucleotide can be of any length and can have any nucleotide sequence.
• the intergenic region between the first polynucleotide and the second polynucleotide can include about one nucleotide, about two nucleotides, about three nucleotides, about four nucleotides, about five nucleotides, about six nucleotides, about seven nucleotides, about eight nucleotides, about nine nucleotides, about ten nucleotides, about 11 nucleotides, about 12 nucleotides, about 13 nucleotides, about 14 nucleotides, about 15 nucleotides, about 16 nucleotides, about 17 nucleotides, about 18 nucleotides, about 19 nucleotides, about 20 nucleotides, about 21 nucleotides, about 22 nucleotides, about 23 nucleotides,
• the intergenic region between first and second polynucleotides includes about 10-100 nucleotides, about 10-200 nucleotides, about 10-300 nucleotides, about 10-400 nucleotides, or about 10-500 nucleotides.
• the intergenic region between first and second polynucleotides includes about 1-10 nucleotides, about 1-20 nucleotides, about 1-30 nucleotides, about 1-40 nucleotides, or about 1- 50 nucleotides.
• the region includes about 44 nucleotides.
• the intergenic region between first and second polynucleotides includes a viral sequence.
• the intergenic region between first and second polynucleotides can include a sequence from any virus, such as alphaviruses and rubiviruses, for example.
• the intergenic region between the first polynucleotide and the second polynucleotide comprises an alphavirus sequence, such as a sequence from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV
• the intergenic region between first and second polynucleotides comprises a sequence from Venezuelan Equine Encephalitis Virus (VEEV).
• VEEV Venezuelan Equine Encephalitis Virus
• the intergenic region between first and second polynucleotides comprises a sequence having at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO:7.
• the intergenic region between first and second polynucleotides comprises a sequence of SEQ ID NO:7.
• the intergenic region between first and second polynucleotides is a second intergenic region comprising a sequence having at least 85% identity to a sequence of SEQ ID NO:7.
• a self-replicating RNA of the disclosure can comprise one or more chemically modified nucleotides.
• nucleic acid monomers include non-natural, modified, and chemically-modified nucleotides, including any such nucleotides known in the art.
• Nucleotides can be artificially modified at either the base portion or the sugar portion.
• most polynucleotides comprise nucleotides that are “unmodified” or “natural” nucleotides, which include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
• RNA polynucleotides comprising chemically modified nucleotides have been shown to improve RNA expression, expression rates, half-life and/or expressed protein concentrations. RNA polynucleotides comprising chemically modified nucleotides have also been useful in optimizing protein localization thereby avoiding deleterious bio-responses such as immune responses and/or degradation pathways.
• modified or chemically-modified nucleotides include 5- hydroxycytidines, 5-alkylcytidines, 5-hydroxyalkylcytidines, 5-carboxycytidines, 5- formylcytidines, 5-alkoxycytidines, 5-alkynylcytidines, 5-halocytidines, 2-thiocytidines, N4- alkylcytidines, N4-aminocytidines, N4-acetylcytidines, and N4,N4-dialkylcytidines.
• modified or chemically-modified nucleotides include 5- hydroxycytidine, 5-methylcytidine, 5-hydroxymethylcytidine, 5-carboxycytidine, 5- formylcytidine, 5-methoxycytidine, 5-propynylcytidine, 5-bromocytidine, 5-iodocytidine, 2- thiocytidine; N4-methylcytidine, N4-aminocytidine, N4-acetylcytidine, and N4,N4- dimethylcytidine.
• modified or chemically-modified nucleotides include 5- hydroxyuridines, 5-alkyluridines, 5-hydroxyalkyluridines, 5-carboxyuridines, 5- carboxyalkylesteruridines, 5-formyluridines, 5-alkoxyuridines, 5-alkynyluridines, 5- halouridines, 2-thiouridines, and 6-alkyluridines.
• modified or chemically-modified nucleotides include 5- hydroxyuridine, 5-methyluridine, 5-hydroxymethyluridine, 5-carboxyuridine, 5- carboxymethylesteruridine, 5-formyluridine, 5-methoxyuridine (also referred to herein as “5MeOU”), 5-propynyluridine, 5-bromouridine, 5-fluorouridine, 5-iodouridine, 2-thiouridine, and 6-methyluridine.
• modified or chemically-modified nucleotides include 5- methoxycarbonylmethyl-2-thiouridine, 5-methylaminomethyl-2-thiouridine, 5- carbamoylmethyluridine, 5-carbamoylmethyl-2’-0-methyluridine, 1 -methyl-3 -(3 -amino-3 - carboxypropy)pseudouridine, 5-methylaminomethyl-2-selenouridine, 5- carboxymethyluridine, 5-methyldihydrouridine, 5-taurinomethyluridine, 5-taurinomethyl-2- thiouridine, 5-(isopentenylaminomethyl)uridine, 2 , -0-methylpseudouridine, 2-thio-2’0- methyluridine, and 3,2’-0-dimethyluridine.
• modified or chemically-modified nucleotides include N6- methyladenosine, 2-aminoadenosine, 3-methyladenosine, 8-azaadenosine, 7-deazaadenosine, 8-oxoadenosine, 8-bromoadenosine, 2-methylthio-N6-methyladenosine, N6- isopentenyladenosine, 2-methylthio-N6-isopentenyladenosine, N6-(cis- hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine, N6- glycinylcarbamoyladenosine, N6-threonylcarbamoyl-adenosine, N6-methyl-N6- threonylcarbamoyl-adenosine, 2-methylthio-N6-
• modified or chemically-modified nucleotides include Nl- alkylguanosines, N2-alkylguanosines, thienoguanosines, 7-deazaguanosines, 8- oxoguanosines, 8-bromoguanosines, 06-alkylguanosines, xanthosines, inosines, and Nl- alkylinosines.
• modified or chemically-modified nucleotides include Nl- methylguanosine, N2-methylguanosine, thienoguanosine, 7-deazaguanosine, 8-oxoguanosine, 8-bromoguanosine, 06-methylguanosine, xanthosine, inosine, and Nl-methylinosine.
• Examples of modified or chemically-modified nucleotides include pseudouridines.
• Examples of pseudouridines include Nl-alkylpseudouridines, Nl-cycloalkylpseudouridines, Nl-hydroxypseudouri dines, Nl-hydroxyalkylpseudouri dines, Nl-phenylpseudouri dines, Nl- phenylalkylpseudouridines, Nl-aminoalkylpseudouridines, N3-alkylpseudouri dines, N6- alkylpseudouridines, N6-alkoxypseudouridines, N6-hydroxypseudouridines, N6- hydroxyalkylpseudouridines, N6-morpholinopseudouridines, N6-phenylpseudouridines,
• pseudouridines examples include Nl-alkyl-N6- alkylpseudouridines, Nl-alkyl-N6-alkoxypseudouridines, Nl-alkyl-N6- hydroxypseudouridines, Nl-alkyl-N6-hydroxyalkylpseudouridines, Nl-alkyl-N6- morpholinopseudouridines, Nl-alkyl-N6-phenylpseudouridines, and Nl-alkyl-N6- halopseudouridines.
• alkyl, cycloalkyl, and phenyl substituents may be unsubstituted, or further substituted with alkyl, halo, haloalkyl, amino, or nitro substituents.
• pseudouridines include Nl-methylpseudouridine (also referred to herein as “N1MPU”), Nl-ethylpseudouridine, Nl-propylpseudouridine, Nicy cl opropylpseudouri dine, Nl-phenylpseudouridine, Nl-aminomethylpseudouridine, N3- methylpseudouridine, Nl-hydroxypseudouridine, and Nl-hydroxym ethylpseudouri dine.
• nucleic acid monomers include modified and chemically-modified nucleotides, including any such nucleo
• modified and chemically-modified nucleotide monomers include any such nucleotides known in the art, for example, 2'-0-methyl ribonucleotides, 2'-0-methyl purine nucleotides, 2'-deoxy-2'-fluoro ribonucleotides, 2'-deoxy-2'-fluoro pyrimidine nucleotides, 2'-deoxy ribonucleotides, 2'-deoxy purine nucleotides, universal base nucleotides, 5-C-methyl-nucleotides, and inverted deoxyabasic monomer residues.
• modified and chemically-modified nucleotide monomers include 3'- end stabilized nucleotides, 3'-glyceryl nucleotides, 3'-inverted abasic nucleotides, and 3'- inverted thymidine.
• modified and chemically-modified nucleotide monomers include locked nucleic acid nucleotides (LNA), 2'-0,4'-C-methylene-(D-ribofuranosyl) nucleotides, 2'- methoxyethoxy (MOE) nucleotides, 2'-methyl-thio-ethyl, 2'-deoxy-2'-fluoro nucleotides, and 2'-0-methyl nucleotides.
• the modified monomer is a locked nucleic acid nucleotide (LNA).
• modified and chemically-modified nucleotide monomers include 2',4 - constrained 2'-0-methoxyethyl (cMOE) and 2 '-O-Ethyl (cEt) modified DNAs.
• modified and chemically-modified nucleotide monomers include 2- amino nucleotides, 2'-0-amino nucleotides, 2'-C-allyl nucleotides, and 2'-0-allyl nucleotides.
• modified and chemically-modified nucleotide monomers include N6- methyladenosine nucleotides.
• modified and chemically-modified nucleotide monomers include nucleotide monomers with modified bases 5-(3-amino)propyluridine, 5-(2- mercapto)ethyluridine, 5-bromouridine; 8-bromoguanosine, or 7-deazaadenosine.
• modified and chemically-modified nucleotide monomers include T- O-aminopropyl substituted nucleotides.
• modified and chemically-modified nucleotide monomers include replacing the 2'-OH group of a nucleotide with a 2'-R, a 2'-OR, a 2'-halogen, a 2'-SR, or a 2'- amino, where R can be H, alkyl, alkenyl, or alkynyl.
• Preferred nucleotide modifications include Nl-methylpseudouridine and 5- methoxyuridine.
• RNA molecules comprising a first polynucleotide encoding one or more viral replication proteins.
• replication protein or “viral replication protein” refers to any protein or any protein subunit of a protein complex that functions in replication of a viral genome.
• viral replication proteins are non- structural proteins.
• Viral replication proteins encoded by nucleic acid molecules provided herein can function in the replication of any viral genome.
• the viral genome can be a single- stranded positive-sense RNA genome, a single-stranded negative-sense RNA genome, a double-stranded RNA genome, a single-stranded positive-sense DNA genome, a single-stranded negative-sense DNA genome, or a double-stranded DNA genome.
• Viral genomes can include a single nucleic acid molecule or more than one nucleic acid molecule.
• Nucleic acid molecules provided herein can encode one or more viral replication proteins from any virus or virus family, including animal viruses and plant viruses, for example. Viral replication proteins encoded by first polynucleotides included in nucleic acid molecules provided herein can be expressed from self-replicating RNA.
• first polynucleotides of RNA molecules provided herein include modifications or mutations of one or more microRNA (miRNA; miR) binding sites.
• miRNA microRNA
• modification or mutation of miRNA binding sites reduces or eliminates miRNA binding.
• miRNA binding is reduced by 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
• miRNA binding is reduced by 100%, z ' .e., there is no miRNA binding.
• one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, or 15 miRNA binding sites are modified or mutated.
• miRNAs are small single-stranded non-coding RNA molecules that function in RNA silencing and post-transcriptional regulation of gene expression. For example, binding of miRNA to a miRNA binding site in a transcript or messenger RNA (mRNA) can inhibit translation. miRNAs can be found in many eukaryotic cells, including in mammals and plants. Some viruses also produce miRNAs. Generally, miRNAs are produced from larger pri-miRNA molecules that form hairpin loop structures with double-stranded regions. Pri-miRNAs are processed to pre-miRNAs in the nucleus and exported to the cytoplasm.
• mRNA messenger RNA
• Pre-miRNA hairpins are cleaved in the cytoplasm by the RNase III enzyme Dicer, with one miRNA strand being incorporated into the RNA-induced silencing complex (RISC) and interacting with an mRNA target.
• RISC RNA-induced silencing complex
• miRNAs can recognize a target mRNA via a seed region at the 5’ end of the miRNA that can include as few as 6-8 nucleotides of the miRNA. Binding of miRNA to a target mRNA can result in cleavage of the mRNA in the case of perfect or near-perfect pairing or inhibition of translation without mRNA cleavage.
• Putative miRNA binding sites can be identified using algorithms, such as miRanda (Enright, A.J., John, B., Gaul, U. et al. MicroRNA targets in Drosophila. Genome Biol 5, R1 (2003). doi.org/10.1186/gb-2003-5-l- rl).
• modifications or mutations of miRNA binding sites include point mutations. More than one nucleotide can be changed in identified or putative miRNA binding sites, including one, two, three, four, five, six, seven, eight, nine, ten, or more nucleotides.
• point mutations include synonymous nucleotide changes, i.e., changes that do not alter an encoded amino acid. Binding sites for any miRNA provided herein can be modified or mutated.
• miRNA binding sites that are modified or mutated in first polynucleotides of RNA molecules provided herein are selected from regions that bind a miRNA having a sequence of SEQ ID NOs:58, 59, 72, 80, 81, 83, 101, 102, 103, 112, 113, 114, 128, 131, 142, 156, 157, 171, 175, and any combination thereof.
• binding of any miRNA or any combination of miRNAs is reduced by 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 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between.
• miRNA binding is reduced by 100%, z ' .e., there is no miRNA binding.
• reduction of miRNA binding increases protein expression. Protein expression can be increased by 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 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, at least 100%, at least 150%, at least 200%
• protein expression is increased by about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, about 99.9%, about 100%, about 150%, about 200%, about 250%, about 300%, about 350%, about 400%, about 450%, about 500%, about 550%, about 600%, about 650%, about 700%, about 750%, about 800%, about 850%, about 900%, about 950%, about 1000%, or more, and any number or range in between.
• Protein expression can also be increased about 1-fold, about 2- fold, about 3-fold, about 4-fold, about 5-fold, about 6-fold, about 7-fold, about 8-fold, about 9- fold, about 10-fold, about 20-fold, about 30-fold, about 40-fold, about 50-fold, about 60-fold, about 70-fold, about 80-fold, about 90-fold, about 100-fold, about 150-fold, about 200-fold, about 250-fold, about 300-fold, about 350-fold, about 400-fold, about 450-fold, about 500- fold, about 600-fold, about 700-fold, about 800-fold, about 900-fold, about 1000-fold, or more, and any number or range in between.
• protein expression is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5- fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold, at least about 150-fold, at least about 200-fold, at least about 250-fold, at least about 300-fold, at least about 350-fold, at least about 400-fold, at least about 450-fold, at least about 500-fold, at least about 600-fold, at least about 700-fold, at least about 800-fold, at least about 900-fold, at least about 1000-fold, or more, and any number or range in between.
• First polynucleotide sequences of RNA molecules provided herein can encode one or more togavirus replication proteins.
• the one or more viral replication proteins encoded by first polynucleotides of RNA molecules provided herein are alphavirus proteins.
• the one or more viral replication proteins encoded by first polynucleotides of RNA molecules provided herein are rubivirus proteins.
• First polynucleotide sequences of RNA molecules provided herein can encode any alphavirus replication protein and any rubivirus replication protein.
• Exemplary replication proteins from alphaviruses include proteins from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan Virus
• Viral replication proteins encoded by first polynucleotides of RNA molecules provided herein can be expressed as one or more polyproteins or as separate or single proteins.
• polyproteins are precursor proteins that are cleaved to generate individual or separate proteins.
• proteins derived from a precursor polyprotein can be expressed from a single open reading frame (ORF).
• ORF refers to a nucleotide sequence that begins with a start codon, generally ATG, and that ends with a stop codon, such as TAA, TAG, or TGA, for example. It will be appreciated that T is present in DNA, while U is present in RNA.
• a start codon of ATG in DNA corresponds to AUG in RNA
• the stop codons TAA, TAG, and TGA in DNA correspond to UAA, UAG, and UGA in RNA.
• T is present in DNA
• U is present in RNA
• T present in DNA is substituted with U for an RNA molecule
• U present in RNA is substituted with T for a DNA molecule.
• the protease cleaving a polyprotein can be a viral protease or a cellular protease.
• the first polynucleotide of RNA molecules provided herein encodes a polyprotein comprising an alphavirus nsPl protein, an alphavirus nsP2 protein, an alphavirus nsP3 protein, an alphavirus nsP4 protein, or any combination thereof.
• the first polynucleotide of RNA molecules provided herein encodes a polyprotein comprising an alphavirus nsPl protein, an alphavirus nsP2 protein, an alphavirus nsP3 protein, or any combination thereof, and an alphavirus nsP4 protein.
• the polyprotein is a VEEV polyprotein.
• the alphavirus nsPl, nsP2, nsP3, and nsP4 proteins are VEEV proteins.
• first polynucleotides of RNA molecules provided herein lack a stop codon between sequences encoding an nsP3 protein and an nsP4 protein. Accordingly, in some aspects, first polynucleotides of RNA molecules provided herein encode a P1234 polyprotein comprising nsPl, nsP2, nsP3, and nsP4. First polynucleotides of RNA molecules provided herein can also include a stop codon between sequences encoding an nsP3 and an nsP4 protein.
• first polynucleotides of nucleic acid molecules provided herein encode a PI 23 polyprotein comprising nsPl, nsP2, and nsP3 and a PI 234 polyprotein comprising nsPl, nsP2, nsP3, and nsP4 as a result of stop codon readthrough, for example.
• first polynucleotides of RNA molecules provided herein encode a polyprotein having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO: 187.
• first polynucleotides of nucleic acid molecules provided herein encode a polyprotein having a sequence of SEQ ID NO: 187.
• nsP2 and nsP3 proteins include mutations. Exemplary mutations include G1309R and S1583G mutations of VEEV proteins.
• the nsPl, nsP2, and nsP4 proteins are VEEV proteins, and the nsP3 protein is a chikungunya virus (CHIKV) nsP3 protein.
• the first polynucleotide comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identity to a sequence of SEQ ID NO:6.
• the first polynucleotide comprises a sequence of SEQ ID NO:6.
• the first polynucleotide comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identity to a sequence of SEQ ID NO:42.
• the first polynucleotide comprises a sequence of SEQ ID NO:42.
• Nucleic acid molecules provided herein can further comprise untranslated regions (UTRs).
• Untranslated regions including 5’ UTRs and 3’ UTRs, for example, can affect RNA stability and/or efficiency of RNA translation, such as translation of cellular and viral mRNAs, for example.
• 5’ UTRs and 3’ UTRs can also affect stability and translation of viral genomic RNAs and self-replicating RNAs, including virally derived self-replicating RNAs or replicons.
• Exemplary viral genomic RNAs whose stability and/or efficiency of translation can be affected by 5’ UTRs and 3’ UTRs include the genome nucleic acid of positive-sense RNA viruses. Both genome nucleic acid of positive-sense RNA viruses and self-replicating RNAs, including virally derived self-replicating RNAs or replicons, can be translated upon infection or introduction into a cell.
• nucleic acid molecules provided herein further include a 5’ untranslated region (5’ UTR). Any 5’ UTR sequence can be included in nucleic acid molecules provided herein.
• nucleic acid molecules provided herein include a viral 5’ UTR.
• nucleic acid molecules provided herein include a non-viral 5’ UTR. Any non-viral 5’ UTR can be included in nucleic acid molecules provided herein, such as 5’ UTRs of transcripts expressed in any cell or organ, including muscle, skin, subcutaneous tissue, liver, spleen, lymph nodes, antigen-presenting cells, and others.
• nucleic acid molecules provided herein include a 5’ UTR comprising viral and non-viral sequences. Accordingly, a 5’ UTR included in nucleic acid molecules provided herein can comprise a combination of viral and non-viral 5’ UTR sequences. In some aspects, the 5’ UTR included in nucleic acid molecules provided herein is located upstream of or 5’ of the first polynucleotide that encodes one or more viral replication proteins.
• the 5’ UTR is located 5’ of or upstream of the first polynucleotide of nucleic acid molecules provided herein that encodes one or more viral replication proteins, and the first polynucleotide is located 5’ of or upstream of the second polynucleotide of nucleic acid molecules provided herein.
• the 5’ UTR of nucleic acid molecules provided herein comprises an alphavirus 5’ UTR.
• a 5’ UTR from any alphavirus can be included in nucleic acid molecules provided herein, including 5’ UTR sequences from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis
• the 5’ UTR comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO:5 or a sequence of SEQ ID NO:41, for example.
• the 5’ UTR comprises a sequence of SEQ ID NO:5 or SEQ ID NO:41.
• the 5’ UTR comprises a sequence selected from the 5’ UTRs of human IL-6, alanine aminotransferase 1, human apolipoprotein E, human fibrinogen alpha chain, human transthyretin, human haptoglobin, human alpha- 1 -anti chymotrypsin, human antithrombin, human alpha- 1 -antitrypsin, human albumin, human beta globin, human complement C3, human complement C5, SynK (thylakoid potassium channel protein derived from the cyanobacteria, Synechocystis sp.), mouse beta globin, mouse albumin, and a tobacco etch virus, or fragments of any of the foregoing.
• SynK thylakoid potassium channel protein derived from the cyanobacteria, Synechocystis sp.
• mouse beta globin mouse albumin
• a tobacco etch virus or fragments of any of the foregoing.
• the 5’ UTR is derived from a tobacco etch virus (TEV).
• TEV tobacco etch virus
• the 5’ UTR includes a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to sequence of SEQ ID NO:35 or SEQ ID NO:49.
• the 5’ UTR includes a sequence of SEQ OD NO:35 or SEQ ID NO:49.
• an mRNA or any other RNA described herein can comprise any 5’ UTR sequence provided herein.
• an RNA described herein can comprise a 5’ UTR sequence that is derived from a gene expressed by Arabidopsis thaliana.
• the 5’ UTR sequence of a gene expressed by Arabidopsis thaliana is AT1G58420.
• Examples of 5 UTRs and 3’ UTRs are described in PCT/US2018/035419, the contents of which are herein incorporated by reference.
• Exemplary 5’ UTR sequences include sequences of SEQ ID NOs: 189-218, as shown in Table 1.
• nucleic acid molecules provided herein further include a 3’ untranslated region (3’ UTR). Any 3’ UTR sequence can be included in nucleic acid molecules provided herein.
• nucleic acid molecules provided herein include a viral 3’ UTR.
• nucleic acid molecules provided herein include a non-viral 3’ UTR. Any non-viral 3’ UTR can be included in nucleic acid molecules provided herein, such as 3’ UTRs of transcripts expressed in any cell or organ, including muscle, skin, subcutaneous tissue, liver, spleen, lymph nodes, antigen-presenting cells, and others.
• nucleic acid molecules provided herein include a 3’ UTR comprising viral and non-viral sequences. Accordingly, a 3’ UTR included in nucleic acid molecules provided herein can comprise a combination of viral and non-viral 3’ UTR sequences. In one aspect, the 3’ UTR is located 3’ of or downstream of the second polynucleotide of nucleic acid molecules provided herein that comprises a first transgene encoding a first antigenic protein or a fragment thereof.
• the 3’ UTR is located 3’ of or downstream of the second polynucleotide of nucleic acid molecules provided herein that comprises a first transgene encoding a first antigenic protein or a fragment thereof, and the second polynucleotide is located 3’ of or downstream of the first polynucleotide of nucleic acid molecules provided herein.
• the 3’ UTR of nucleic acid molecules provided herein comprises an alphavirus 3’ UTR.
• a 3’ UTR from any alphavirus can be included in nucleic acid molecules provided herein, including 3’ UTR sequences from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WH
• the 3’ UTR comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO:9 or a sequence of SEQ ID NO:45, for example.
• the 3’ UTR further comprises a poly-A sequence.
• the 3’ UTR comprises a sequence of SEQ ID NO:9 or SEQ ID NO:45. In yet a further aspect, the 3’ UTR comprises a sequence of SEQ ID NO:8 or a sequence of SEQ ID NO:44, for example.
• the 3 ’ UTR comprises a sequence selected from the 3 ’ UTRs of alanine aminotransferase 1, human apolipoprotein E, human fibrinogen alpha chain, human haptoglobin, human antithrombin, human alpha globin, human beta globin, human complement C3, human growth factor, human hepcidin, MALAT-1, mouse beta globin, mouse albumin, and Xenopus beta globin, or fragments of any of the foregoing.
• the 3’ UTR is derived from Xenopus beta globin. Any 3’ UTR provided herein can include a poly- A tail, as detailed further below.
• the 3 ’ UTR includes a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO:50, or SEQ ID NO:51.
• the 3’ UTR includes a sequence of SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:50, or SEQ ID NO:51.
• a 3 ’ UTR provided herein can be included in any RNA molecule provided herein, including self-replicating RNA and mRNA molecules.
• Exemplary 3’ UTR sequences include SEQ ID NOs:219-225, as shown in Table 3.
• RNA molecules provided herein may comprise a sequence immediately downstream of a coding region (i.e., ORF) that creates a triple stop codon.
• a triple stop codon is a sequence of three consecutive stop codons. The triple stop codon can ensure total insulation of an expression cassette and may be incorporated to enhance the efficiency of translation.
• RNA molecules of the disclosure may comprise a triple combination of any of the sequences UAG, UGA, or UAA immediately downstream of an ORF described herein. The triple combination can be three of the same codons, three different codons, or any other permutation of the three stop codons.
• an RNA molecule described herein such as a self-replicating RNA or an mRNA, comprises a translation enhancer sequence. These translation enhancer sequences enhance the translation efficiency of a self- replicating RNA or mRNA of the disclosure and thereby provide increased production of the protein encoded by the RNA.
• the translation enhancer region may be located in the 5’ or 3’ UTR of a self-replicating RNA or an mRNA sequence.
• Examples of translation enhancer regions include naturally-occurring enhancer regions from the TEV 5’ UTR and the Xenopus beta-globin 3’ UTR.
• Exemplary 5’ UTR enhancer sequences include but are not limited to those derived from mRNAs encoding human heat shock proteins (HSP) including HSP70-P2, HSP70-M1 HSP72-M2, HSP17.9 and HSP70-P1.
• HSP human heat shock proteins
• Exemplary translation enhancer sequences used in accordance with the embodiments of the present disclosure are represented by SEQ ID NOs:226-230, as shown in Table 5.
• a self-replicating RNA or mRNA of the disclosure comprises a Kozak sequence.
• a Kozak sequence is a short consensus sequence centered around the translational initiation site of eukaryotic mRNAs that allows for efficient initiation of translation of the self-replicating RNA or mRNA. See, for example, Kozak, Marilyn (1988) Mol. and Cell Biol, 8:2737-2744; Kozak, Marilyn (1991) J. Biol. Chem, 266: 19867-19870; Kozak, Marilyn (1990) Proc Natl. Acad. Sci. USA, 87:8301-8305; and Kozak, Marilyn (1989) J.
• a self-replicating RNA or mRNA described herein comprises a Kozak sequence having the sequence GCCACC (SEQ ID NO: 231).
• a self-replicating RNA or mRNA described herein can comprise a partial Kozak sequence “p” having the nucleotide sequence GCCA (SEQ ID NO: 232).
• Transgenes included in nucleic acid molecules provided herein can encode an antigenic protein or a fragment thereof.
• second polynucleotides of RNA molecules provided herein comprise a first transgene.
• a first transgene included in second polynucleotides of nucleic acid molecules provided herein can encode a first antigenic protein or a fragment thereof.
• a transgene included in second polynucleotides of RNA molecules provided herein can comprise a sequence encoding the full amino acid sequence of an antigenic protein or a sequence encoding any suitable portion or fragment of the full amino acid sequence of an antigenic protein.
• a transgene included in second polynucleotides of RNA molecules provided herein can also include a homolog of any antigenic protein provided herein.
• Any antigenic protein can be encoded by transgenes included in nucleic acid molecules provided herein.
• the first antigenic protein is a viral protein, a bacterial protein, a fungal protein, a protozoan protein, or a parasite protein.
• Transgenes included in RNA molecules provided herein can be expressed from a subgenomic RNA derived from a self-replicating RNA or from an mRNA.
• the antigenic protein when administered to a mammalian subject, raises an immune response to a pathogen, optionally wherein the pathogen is viral, bacterial, fungal, protozoan, or any other type of pathogen.
• the antigenic protein is expressed on the outer surface of the pathogen; while in further aspects, the antigen may be a non-surface antigen, e.g., useful as a T-cell epitope.
• the immune response may comprise an antibody response (usually including IgG) and/or a cell mediated immune response.
• the polypeptide immunogen will typically elicit an immune response that recognizes the corresponding pathogen polypeptide, but in some embodiments, the polypeptide may act as a mimotope to elicit an immune response that recognizes a saccharide.
• the immunogen can be a surface polypeptide, e.g., an adhesin, a hemagglutinin, an envelope glycoprotein, a spike glycoprotein, etc.
• RNA molecules provided herein Any viral, bacterial, fungal, protozoan, parasite, or other protein can be encoded by transgenes included in RNA molecules provided herein.
• a protein from any infectious agent can be encoded by transgenes included in RNA molecules provided herein.
• infectious agent refers to any agent capable of infecting an organism, including humans and animals, and causing disease or deterioration in health.
• infectious agent and infectious pathogen may be used interchangeably, unless context clearly indicates otherwise.
• the viral protein encoded by transgenes included in RNA molecules provided herein is a coronavirus protein, an orthomyxovirus protein, a paramyxovirus protein, a picornavirus protein, a flavivirus protein, a filovirus protein, a rhabdovirus protein, a togavirus protein, an arterivirus protein, a bunyavirus protein, an arenavirus protein, a reovirus protein, a bomavirus protein, a retrovirus protein, an adenovirus protein, a herpesvirus protein, a polyomavirus protein, a papillomavirus protein, a poxvirus protein, or a hepadnavirus protein.
• the antigenic protein is a SARS-CoV-2 protein, an influenza virus protein, a respiratory syncytial virus (RSV) protein, a human immunodeficiency virus (HIV) protein, a hepatitis C virus (HCV) protein, a cytomegalovirus (CMV) protein, a Lassa Fever Virus (LFV) protein, an Ebola Virus (EBOV) protein, a Mycobacterium protein, a Bacillus protein, a Yersinia protein, a Streptococcus protein, a Pseudomonas protein, a Shigella protein, a Campylobacter protein, a Salmonella protein, a Plasmodium protein, or a Toxoplasma protein.
• SARS-CoV-2 protein an influenza virus protein, a respiratory syncytial virus (RSV) protein, a human immunodeficiency virus (HIV) protein, a hepatitis C virus (HCV) protein, a
• the antigenic protein is from a prokaryotic organism, including gram positive bacteria, gram negative bacteria, or other bacteria, such as Bacillus ( e.g. , Bacillus anthracis), Mycobacterium (e.g., Mycobacterium tuberculosis, Mycobacterium Leprae), Shigella (e.g., Shigella sonnei, Shigella dysenteriae, Shigella flexneri), Helicobacter (e.g., Helicobacter pylori ), Salmonella (e.g., Salmonella enterica, Salmonella typhi, Salmonella typhi murium), Neisseria (e.g., Neisseria gonorrhoeae, Neisseria meningitidis), Moraxella (e.g., Moraxella calarrhaHs), Haemophilus (e.g., Haemophilus influenzae), Klebsiella (e.g., Kleb), Bacillus (e.
• the antigenic protein is from a eukaryotic organism, including protists and fungi, such as Plasmodium (e.g., Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malar iae, Plasmodium diarrhea), Candida (e.g., Candida albicans), Aspergillus (e.g., Aspergillus fumigatus), Cryptococcus (e.g., Cryptococcus neoformans), Histoplasma (e.g., Histoplasma capsulatum), Pneumocystis (e.g., Pneumocystis jirovecii), and Coccidiodes (e.g., Coccidiodes immitis).
• Plasmodium e.g., Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malar iae, Plasmod
• the viral protein encoded by transgenes included in RNA molecules provided herein is a coronavirus protein.
• the antigenic protein is a SARS-CoV-2 protein.
• the antigenic protein is a SARS-CoV-2 spike glycoprotein or a fragment thereof.
• the SARS-CoV-2 spike glycoprotein is a wild-type SARS- CoV-2 spike glycoprotein.
• the SARS-CoV-2 spike glycoprotein is prefusion stabilized. Prefusion stabilized SARS-CoV-2 glycoproteins can include K986P, V987P, or both K986P and V987P mutations.
• the SARS-Cov-2 spike glycoprotein is a variant spike glycoprotein.
• variant SARS-CoV-2 spike glycoprotein refers to any spike glycoprotein other than that of the SARS-CoV-2 Wuhan isolate(s) that emerged in Wuhan, China in 2019 (Wu, F., Zhao, S., Yu, B. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265-269 (2020). doi.org/10.1038/s41586-020-2008-3).
• wild-type SARS-CoV-2 spike glycoprotein and “SARS-CoV-2 spike glycoprotein, Wuhan,” for example, can be used interchangeably, unless context clearly indicates otherwise.
• Exemplary variant SARS-CoV-2 spike glycoproteins include, without limitation, the Alpha (B.l.1.7; UK), Beta (B.1.351; South Africa), Gamma (P.l; Brazil), Delta (B.1.617.2; India), and Lambda (C.37; Peru) variants. Additional variants, including further variants of concern, can be found at, e.g., COVID-19 Weekly Epidemiological Update, Edition 44, 15 June 2021 (who.int/publications/m/item/weekly-epidemiological-update-on-covid-19 — 15- june-2021).
• any SARS-CoV-2 spike glycoprotein variant or a fragment thereof and any SARS-CoV-2 spike glycoprotein mutant protein or a fragment thereof can be encoded by second polynucleotides of RNA molecules provided herein.
• the second polynucleotide of RNA molecules provided herein can encode a SARS-CoV-2 spike protein comprising one or more mutations as compared to a wild-type SARS-CoV-2 spike glycoprotein sequence. Mutations can include substitutions, deletions, insertions, and others. Mutations can be present at any position or at any combination of positions of a SARS-CoV-2 spike glycoprotein.
• substitutions can be present at any one or more positions of a SARS-CoV-2 spike glycoprotein.
• substitutions can include a change of a wild-type amino acid at any position or at any combination of positions to any other amino acid or combination of any other amino acids.
• Exemplary mutations include mutations at positions 614, 936, 320, 477, 986, 987, 988, or any combination thereof.
• a SARS-CoV-2 spike glycoprotein or a fragment thereof encoded by transgenes of second polynucleotides included in nucleic acid molecules provided herein includes a D614G mutation, a D936Y mutation, a D936H mutation, a V320G mutation, an S477N mutation, an S477I mutation, an S477T mutation, a K986P mutation, a V987P mutation, or any combination thereof.
• Variant spike glycoproteins can also include proteins referred to as “VFLIP” spike glycoproteins, also designated “5P FL2 DS3” (Olmedillas et ah, Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity, bioRxiv 2021.05.06.441046; doi.org/10.1101/2021.05.06.441046).
• variant spike glycoproteins can include 5 proline substitutions.
• proline substitutions include V986P and V987P, and proline substitutions at positions 817, 892, 899, and 942 (Hsieh et ak, 2020, Structure-Based Design of PrefusionStabilized SARS-CoV-2 Spikes. Science 369 (6510): 1501-5).
• Any combination of proline substitutions can be included in variant spike glycoproteins provided herein.
• variant spike glycoproteins include proline substitutions at positions 987, 817, 892, 899, and 942.
• Variant spike glycoproteins can also include a S1/S2 linker.
• exemplary linkers include GP, GGGS (SEQ ID NO:318), GPGP (SEQ ID NO:319), and GGGSGGGS (SEQ ID NO:320).
• the linker is GGGSGGGS (SEQ ID NO:320).
• variant spike glycoproteins include proline substitutions at positions 987, 817, 892, 899, and 942 and further include a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320) and/or a disulfide bond Y707C-T883C (Olmedillas et ak, Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity, bioRxiv 2021.05.06.441046; doi.org/10.1101/2021.05.06.441046).
• Variant spike glycoproteins can also include a D614G substitution.
• variant spike glycoproteins include proline substitutions at positions 987, 817, 892, 899, and 942, a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320), and a disulfide bond Y707C-T883C.
• variant spike glycoproteins include proline substitutions at positions 987, 817, 892, 899, and 942, a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320), a disulfide bond Y707C-T883C, and a D614G substitution.
• Transgenes encoding any variant spike glycoprotein described herein can be included in RNA molecules provided herein, such as self- replicating RNA and mRNA molecules.
• one or more transgenes encoding a variant spike glycoprotein that includes proline substitutions at positions 987, 817, 892, 899, and 942, a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320), and a disulfide bond Y707C-T883C is included in self-replicating RNA molecules provided herein.
• one or more transgenes encoding a variant spike glycoprotein that includes proline substitutions at positions 987, 817, 892, 899, and 942, a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320), and a disulfide bond Y707C-T883C is included in mRNA molecules provided herein.
• one or more transgenes encoding a variant spike glycoprotein that includes proline substitutions at positions 987, 817, 892, 899, and 942, a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320), a disulfide bond Y707C-T883C, and a D614G substitution is included in self-replicating RNA molecules provided herein.
• one or more transgenes encoding a variant spike glycoprotein that includes proline substitutions at positions 987, 817, 892, 899, and 942, a GGGSGGGS S1/S2 linker sequence (SEQ ID NO:320), a disulfide bond Y707C-T883C, and a D614G substitution is included in mRNA molecules provided herein.
• the variant SARS-CoV-2 spike glycoprotein encoded by second polynucleotides of RNA molecules provided herein has an amino acid sequence of SEQ ID NO: SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO:31, or SEQ ID NO:34.
• the second polynucleotide of RNA molecules provided herein encodes a SARS-VoV-2 spike glycoprotein sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to a sequence of SEQ ID NO: SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO:31, or SEQ ID NO:34.
• the second polynucleotide of RNA molecules provided herein comprises a sequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 30, or SEQ ID NO:33.
• first transgenes included in second polynucleotides of RNA molecules provided herein comprise a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, or 100% identity to a sequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO:30, or SEQ ID NO:33.
• the antigenic protein encoded by first transgenes of second polynucleotides included in nucleic acid molecules provided herein is an influenza virus protein or a fragment thereof.
• the second polynucleotide includes one or more transgenes encoding one or more influenza virus proteins or fragments thereof.
• Exemplary influenza virus proteins that can be encoded by transgenes of second polynucleotides included in nucleic acid molecules provided herein include proteins from any human or animal virus, including influenza A virus, influenza B virus, influenza C virus, influenza D virus, or any combination thereof.
• influenza proteins include hemagglutinin (HA), neuraminidase (NA), M2, Ml, NP, NS1, NS2, PA, PB1, PB2, and PB1- F2.
• Hemagglutinin proteins from any influenza virus subtype such as HI -HI 8 and any emerging hemagglutinin
• neuraminidase proteins from any influenza virus subtype such as Nl-Nl 1 and any emerging neuraminidase, can be antigenic proteins encoded by transgenes included in second polynucleotides of nucleic acid molecules provided herein.
• any suitable fragment of influenza virus proteins can be encoded by transgenes included in second polynucleotides of nucleic acid molecules provided herein, including, for example, one or more helper T lymphocyte (HTL) epitope, one or more cytotoxic T lymphocyte (CTL) epitope, or any combination thereof.
• first transgenes of second polynucleotides included in RNA molecules provided herein comprise a sequence of SEQ ID NO:46 or SEQ ID NO:52.
• first transgenes included in second polynucleotides of RNA molecules provided herein comprise a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, or 100% identity to a sequence of SEQ ID NO:46 or SEQ ID NO:52.
• first transgenes of second polynucleotides included in RNA molecules provided herein encode a protein having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, or 100% identity to a sequence of SEQ ID NO:47 or SEQ ID NO:53.
• transgenes included in second polynucleotides of nucleic acid molecules provided herein encode a reporter or a marker, including selectable markers.
• Reporters and markers can include fluorescent proteins, such as green fluorescent protein (GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP), luciferase enzymes, such as firefly and Renilla luciferases, and antibiotic selection markers, for example.
• the second polynucleotide of nucleic acid molecules provided herein comprises at least two transgenes. Any number of transgenes can be included in second polynucleotides of nucleic acid molecules provided herein, such as one, two, three, four, five, six, seven, eight, nine, ten, or more transgenes. In one aspect, the second polynucleotide of nucleic acid molecules provided herein includes a second transgene encoding a second antigenic protein or a fragment thereof or an immunomodulatory protein.
• the second polynucleotide further comprises an internal ribosomal entry site (IRES), a sequence encoding a 2A peptide, or a combination thereof, located between transgenes.
• IRS internal ribosomal entry site
• 2A peptide refers to a small (generally 18-22 amino acids) sequence that allows for efficient, stoichiometric production of discrete protein products within a single reading frame through a ribosomal skipping event within the 2A peptide sequence.
• the term “internal ribosomal entry site” or “IRES” refers to a nucleotide sequence that allows for the initiation of protein translation of a messenger RNA (mRNA) sequence in the absence of an AUG start codon or without using an AUG start codon.
• An IRES can be found anywhere in an mRNA sequence, such as at or near the beginning, at or near the middle, or at or near the end of the mRNA sequence, for example.
• the second polynucleotide further comprises a subgenomic promoter located between transgenes.
• the subgenomic promoter located between transgenes can be a further subgenomic promoter, such as a second, third, fourth, etc. subgenomic promoter located between second and third, third and fourth, fourth and fifth, etc. transgenes, for example.
• transgenes included in second polynucleotides of nucleic acid molecules provided herein can be expressed via any combination of 2A peptide and IRES sequences.
• a second transgene located 3’ of a first transgene can be expressed via a 2A peptide sequence or via an IRES sequence.
• a second transgene located 3’ of a first transgene and a third transgene located 3’ of the second transgene can be expressed via 2A peptide sequences located between the first and second transgenes and the second and third transgenes, via an IRES sequence located between the first and second transgenes and the second and third transgenes, via a 2A peptide sequence located between the first and second transgenes and an IRES located between the second and third transgenes, or via an IRES sequence located between the first and second transgenes and a 2A peptide sequence located between the second and third transgenes.
• transgenes included in second polynucleotides of nucleic acid molecules provided herein Similar configurations and combinations of 2A peptide and IRES sequences located between transgenes are contemplated for any number of transgenes included in second polynucleotides of nucleic acid molecules provided herein. In addition to expression via 2A peptide and IRES sequences, two or more transgenes included in nucleic acid molecules provided herein can also be expressed from separate subgenomic RNAs.
• a second, third, fourth, fifth, sixth, seventh, eighth, ninth, tenth, etc., transgene included in second polynucleotides of nucleic acid molecules provided herein can encode an immunomodulatory protein or a functional fragment or functional variant thereof. Any immunomodulatory protein or a functional fragment or functional variant thereof can be encoded by a transgene included in second polynucleotides.
• the terms “functional variant” or “functional fragment” refer to a molecule, including a nucleic acid or protein, for example, that comprises a nucleotide and/or amino acid sequence that is altered by one or more nucleotides and/or amino acids compared to the nucleotide and/or amino acid sequences of the parent or reference molecule.
• a functional variant is still able to function in a manner that is similar to the parent molecule.
• the modifications in the amino acid and/or nucleotide sequence of the parent molecule do not significantly affect or alter the functional characteristics of the molecule encoded by the nucleotide sequence or containing the amino acid sequence.
• the functional variant may have conservative sequence modifications including nucleotide and amino acid substitutions, additions and deletions. These modifications can be introduced by standard techniques known in the art, such as site-directed mutagenesis and random PCR- mediated mutagenesis.
• Functional variants can also include, but are not limited to, derivatives that are substantially similar in primary structural sequence, but which contain, e.g., in vitro or in vivo modifications, chemical and/or biochemical, that are not found in the parent molecule.
• Such modifications include, inter alia, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI-anchor formation, hydroxyl ati on, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer- RNA-mediated addition of amino acids to proteins such as arginylation, ubiquit
• a second transgene included in second polynucleotides of nucleic acid molecules provided herein encodes a cytokine, a chemokine, or an interleukin.
• cytokines include interferons, TNF-a, TGF-b, G-CSF, and GM-CSF.
• chemokines include CCL3, CCL26, and CXCL7.
• interleukins include IL-I, IL-2, IL-3, IL-4, IL- 5, IL-6, IL-7, IL-8, IL-10, IL-12, IL-15, IL-18, IL-21, and IL-23. Any transgene or combination of transgenes encoding any cytokine, chemokine, interleukin, or combinations thereof, can be included in second polynucleotides of nucleic acid molecules provided herein.
• first and second transgenes included in second polynucleotides of nucleic acid molecules provided herein encode viral proteins, bacterial proteins, fungal proteins, protozoan proteins, parasite proteins, immunomodulatory proteins, or any combination thereof.
• first, second, third, fourth, fifth, sixth, seventh, eighth, ninth, tenth, or more transgenes included in second polynucleotides of nucleic acid molecules provided herein encode viral proteins, bacterial proteins, fungal proteins, protozoan proteins, parasite proteins, immunomodulatory proteins, or any combination thereof.
• the second transgene encodes a second coronavirus protein. In other aspects, the second transgene encodes a second influenza virus protein. In still other aspects, the first and second transgenes encode a coronavirus protein and an influenza virus protein, respectively. In further aspects, the first and second transgenes encode an influenza virus protein and a coronavirus protein, respectively.
• Nucleic acid molecules provided herein can be DNA molecules or RNA molecules. It will be appreciated that T present in DNA is substituted with U in RNA, and vice versa.
• nucleic acid molecules provided herein are RNA molecules, wherein the first polynucleotide is located 5’ of the second polynucleotide.
• RNA molecules provided herein further include an intergenic region.
• the intergenic region can have at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, or 100% identity to a sequence of SEQ ID NO:7 or to a sequence of SEQ ID NO:43.
• RNA molecules provided herein can be self-replicating RNAs.
• RNA molecules provided herein include a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, or 100% identity to a sequence of SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:40.
• RNA molecules provided herein can also be mRNAs.
• RNA molecules provided herein include a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to a sequence of SEQ ID NO:29, SEQ ID NO:32, or SEQ ID NO:48. It will be appreciated that T of sequences provided herein will be substituted with U in an RNA molecule.
• RNA molecules provided herein can be generated by in vitro transcription (IVT) of DNA molecules provided herein.
• RNA molecules provided herein are self- replicating RNA molecules.
• RNA molecules provided herein are mRNA molecules.
• RNA molecules provided herein further comprise a 5’ cap. Any 5’ cap can be included in RNA molecules provided herein, including 5’ caps having a Cap 1 structure, a Cap 1 (m6A) structure, a Cap 2 structure, or a Cap 0 structure.
• a population or plurality of RNA molecules provided herein can have the same 5’ cap or can have different 5’ caps.
• a population or plurality of RNA molecules can have 5’ caps having a Cap 1 structure, a Cap 1 (m6A) structure, a Cap 2 structure, a Cap 0 structure, or any combination thereof.
• RNA molecules provided herein include a 5’ cap having Cap 1 structure.
• RNA molecules provided herein are self-replicating RNA molecules comprising a 5’ cap having a Cap 1 structure.
• RNA molecules provided herein comprise a cap having a Cap 1 structure, wherein a m7G is linked via a 5’ -5’ triphosphate to the 5’ end of the 5’ UTR.
• RNA molecules provided herein comprise a cap having a Cap 1 structure, wherein a m7G is linked via a 5’-5’ triphosphate to the 5’ end of the 5’ UTR comprising a sequence of SEQ ID NO:5 or SEQ ID NO:41.
• capping can be used, including, but not limited to using a Vaccinia Capping enzyme (New England Biolabs, Ipswich, Mass.) and co-transcriptional capping or capping at or shortly after initiation of in vitro transcription (IVT), by for example, including a capping agent as part of an in vitro transcription (IVT) reaction.
• a Vaccinia Capping enzyme New England Biolabs, Ipswich, Mass.
• IVT co-transcriptional capping or capping at or shortly after initiation of in vitro transcription
• IVT in vitro transcription
• RNA molecules such mRNAs and self-replicating RNAs that can function as mRNAs, that carry the Cap structure are active in Cap dependent translation; “decapitation” of mRNA results in an almost complete loss of their template activity for protein synthesis (Nature, 255:33-37, (1975); J. Biol. Chem., vol. 253:5228-5231, (1978); and Proc. Natl. Acad. Sci. USA, 72:1189-1193, (1975)).
• Another element of eukaryotic mRNA is the presence of 2'-0-methyl nucleoside residues at transcript position 1 (Cap 1), and in some cases, at transcript positions 1 and 2 (Cap 2).
• the 2'-0-methylation of mRNA provides higher efficacy of mRNA translation in vivo (Proc. Natl. Acad. Sci. USA, 77:3952-3956 (1980)) and further improves nuclease stability of the 5'-capped mRNA.
• the mRNA with Cap 1 (and Cap 2) is a distinctive mark that allows cells to recognize the bona fide mRNA 5' end, and in some instances, to discriminate against transcripts emanating from infectious genetic elements (Nucleic Acid Research 43: 482-492 (2015)).
• 5' cap structures and methods for preparing mRNAs comprising the same are given in WO2015/051169A2, WO/2015/061491, US 2018/0273576, and US Patent Nos. 8,093,367, 8,304,529, and U.S. 10,487,105.
• the 5’ cap is m7GpppAmpG, which is known in the art.
• the 5’ cap is m7GpppG or m7GpppGm, which are known in the art. Structural formulas for embodiments of 5’ cap structures are provided below.
• a self-replicating RNA or mRNA of the disclosure comprises a 5’ cap having the structure of Formula (Cap I).
• B 1 is a natural or modified nucleobase
• R 1 and R 2 are each independently selected from a halogen, OH, and OC3 ⁇ 4
• each L is independently selected from the group consisting of phosphate, phophorothioate, and boranophosphate wherein each L is linked by diester bonds
• n is 0 or 1.
• mRNA represents an mRNA of the present disclosure linked at its 5’ end.
• B 1 is G, m 7 G, or A.
• n is 0.
• n is 1.
• B 1 is A or m 6 A and R 1 is OC3 ⁇ 4; wherein G is guanine, m 7 G is 7- methylguanine, A is adenine, and m 6 A is N 6 -methyladenine.
• a self-replicating RNA or mRNA of the disclosure comprises a 5’ cap having the structure of Formula (Cap II).
• B 1 and B 2 are each independently a natural or modified nucleobase
• R 1 , R 2 , andR 3 are each independently selected from a halogen, OH, and OCH 3
• each L is independently selected from the group consisting of phosphate, phophorothioate, and boranophosphate wherein each L is linked by diester bonds
• mRNA represents an mRNA of the present disclosure linked at its 5’ end
• n is 0 or 1.
• B 1 is G, m 7 G, or A.
• n is 0.
• n is 1.
• B 1 is A or m 6 A and R 1 is OCH 3 ; wherein G is guanine, m 7 G is 7-methyl guanine, A is adenine, and m 6 A is N 6 -methyladenine.
• a self-replicating RNA or mRNA of the disclosure comprises a 5’ cap having the structure of Formula (Cap III).
• Bl, B2, and B3 are each independently a natural or modified nucleobase; Rl, R2, R3, and R4 are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or l.
• at least one of Rl, R2, R3, and R4 is OH.
• Bl is G, m7G, or A.
• B 1 is A or m6A and Rl is OCH3; wherein G is guanine, m7G is 7-methyl guanine, A is adenine, and m6A is N6-methyladenine. In some embodiments, n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7GpppG 5’ cap analog having the structure of Formula (Cap IV).
• R 1 , R 2 , and R 3 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; n is 0 or 1.
• at least one of R 1 , R 2 , and R 3 is OH.
• the 5’ cap is m 7 GpppG wherein R 1 , R 2 , andR 3 are each OH, n is i, and each L is a phosphate. In some embodiments, n is 1. In some embodiments, the 5’ cap is m7GpppGm, wherein R 1 and R 2 are each OH, R 3 is OCH 3 , each L is a phosphate, and n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7G 5’ cap analog having the structure of Formula (Cap V).
• R 1 , R 2 , and R 3 are each independently selected from a halogen, OH, and OCH 3 ; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1.
• at least one of R 1 , R 2 , and R 3 is OH.
• n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7GpN, 5’ cap analog, wherein N is a natural or modified nucleotide, the 5’ cap analog having the structure of Formula (Cap VI).
• B 3 is a natural or modified nucleobase
• R 1 , R 2 , R 3 , andR 4 are each independently selected from a halogen, OH, and OCH3
• each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds
• mRNA represents an mRNA of the present disclosure linked at its 5’ end
• n is 0 or 3.
• at least one of R 1 , R 2 , R 3 , and R 4 is OH.
• B 1 is G, m 7 G, or A.
• B 1 is A or m 6 A and R 1 is OCH3; wherein G is guanine, m 7 G is 7-methyl guanine, A is adenine, and m 6 A is N 6 -methyladenine. In some embodiments, n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7GpG 5’ cap analog having the structure of Formula (Cap VII).
• R 1 , R 2 , R 3 , andR 4 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1.
• at least one of R 1 , R 2 , R 3 , andR 4 is OH.
• a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7Gpm7G 5’ cap analog having the structure of Formula (Cap VIII).
• R 1 , R 2 , R 3 , andR 4 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; n is 0 or 1.
• at least one of R 1 , R 2 , R 3 , andR 4 is OH.
• n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7GpppA 5’ cap analog having the structure of Formula (Cap IX).
• R 1 , R 2 , and R 3 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1.
• at least one of R 1 , R 2 , and R 3 is OH.
• n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7GpppApN 5’ cap analog, wherein N is a natural or modified nucleotide, and the 5’ cap has the structure of Formula (Cap X).
• B 3 is a natural or modified nucleobase
• R 1 , R 2 , R 3 , and R 4 are each independently selected from a halogen, OH, and OCH 3
• each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds
• mRNA represents an mRNA of the present disclosure linked at its 5’ end
• n is 0 or 1.
• at least one of R 1 , R 2 , R 3 , andR 4 is OH.
• B 3 is G, m 7 G, A or m 6 A; wherein G is guanine, m 7 G is 7-methyl guanine, A is adenine, and m 6 A is N 6 -methyladenine. In some embodiments, n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7GpppAmpG 5’ cap analog having the structure of Formula (Cap XI).
• R 1 , R 2 , and R 4 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1.
• at least one of R 1 , R 2 , and R 4 is OH.
• the compound of Formula Cap XI is m 7 GpppAmpG, wherein R 1 , R 2 , andR 4 are each OH, n is 1, and each L is a phosphate linkage. In some embodiments, n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7GpppApm7G 5’ cap analog having the structure of Formula (Cap XII).
• R 1 , R 2 , R 3 , andR 4 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 orl. In some embodiments, at least one of R 1 , R 2 , R 3 , andR 4 is OH. In some embodiments, n is 1.
• a self-replicating RNA or mRNA of the disclosure comprises a m7GpppApm7G 5’ cap analog having the structure of Formula (Cap XIII).
• R 1 , R 2 , andR 4 are each independently selected from a halogen, OH, and OCH 3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds;
• mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1.
• at least one of R 1 , R 2 , andR 4 is OH.
• n is 1.
• Poly- Adenine (Poly- A) Tail Poly- Adenine (Poly- A) Tail
• Polyadenylation is the addition of a poly(A) tail, a chain of adenine nucleotides usually about 100-120 monomers in length, to a mRNA or an RNA that can function as an mRNA.
• polyadenylation is part of the process that produces mature mRNA for translation and begins as the transcription of a gene terminates.
• the 3 '-most segment of a newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the 3' end.
• the poly(A) tail is important for the nuclear export, translation, and stability of mRNA.
• the tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded.
• mRNAs with short poly(A) tails are stored for later activation by re-polyadenylation in the cytosol.
• an RNA molecule of the disclosure comprises a 3’ tail region, which can serve to protect the RNA from exonuclease degradation.
• the tail region may be a 3 ’poly(A) and/or 3’poly(C) region.
• the tail region is a 3’ poly(A) tail.
• Any self-replicating RNA and any mRNA, and any 3’ UTR of any self-replicating RNA or mRNA provided herein can include a poly(A) tail.
• a “3 ’ poly(A) tail” is a polymer of sequential adenine nucleotides that can range in size from, for example: 10 to 250 sequential adenine nucleotides; 60-125 sequential adenine nucleotides, 90-125 sequential adenine nucleotides, 95-125 sequential adenine nucleotides, 95-121 sequential adenine nucleotides, 100 to 121 sequential adenine nucleotides, 110-121 sequential adenine nucleotides; 112-121 sequential adenine nucleotides; 114-121 adenine sequential nucleotides; or 115 to 121 sequential adenine nucleotides.
• a 3’ poly(a) tail as described herein includes about 10, about 20, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, about 220, about 230, 240, 250, 260, 270, 280, 290, 300, and any number or range in between, sequential adenine nucleotides.
• a 3’ poly(A) tail as described herein comprises 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, or 125 sequential adenine nucleotides.
• 3’ Poly(A) tails can be added using a variety of methods known in the art, e.g., using poly(A) polymerase to add tails to synthetic or in vitro transcribed RNA.
• Other methods include the use of a transcription vector to encode poly(A) tails or the use of a ligase (e.g., via splint ligation using a T4 RNA ligase and/or T4 DNA ligase), wherein poly(A) may be ligated to the 3' end of a sense RNA.
• a combination of any of the above methods is utilized.
• DNA molecules encoding the RNA molecules disclosed herein are DNA molecules encoding the RNA molecules disclosed herein.
• DNA molecules provided herein further comprise a promoter.
• promoter refers to a regulatory sequence that initiates transcription.
• a promoter can be operably linked to first and second polynucleotides of DNA molecules provided herein, with first and second polynucleotides of DNA molecules corresponding to encoded first and second polynucleotides of RNA molecules provided herein.
• promoters included in DNA molecules provided herein include promoters for in vitro transcription (IVT).
• any suitable promoter for in vitro transcription can be included in DNA molecules provided herein, such as a T7 promoter, a T3 promoter, an SP6 promoter, and others.
• DNA molecules provided herein comprise a T7 promoter.
• the promoter is located 5’ of the 5’ UTR included in DNA molecules provided herein.
• the promoter is a T7 promoter located 5’ of the 5’ UTR included in DNA molecules provided herein.
• the promoter overlaps with the 5’ UTR.
• a promoter and a 5’ UTR can overlap by about one nucleotide, about two nucleotides, about three nucleotides, about four nucleotides, about five nucleotides, about six nucleotides, about seven nucleotides, about eight nucleotides, about nine nucleotides, about ten nucleotides, about 11 nucleotides, about 12 nucleotides, about 13 nucleotides, about 14 nucleotides, about 15 nucleotides, about 16 nucleotides, about 17 nucleotides, about 18 nucleotides, about 19 nucleotides, about 20 nucleotides, about 21 nucleotides, about 22 nucleotides, about 23 nucleotides, about 24 nucleotides, about 25 nucleotides, about 26 nucleotides, about 27 nucleotides, about 28 nucleotides, about 29 nucleotides, about 30 nucleotides,
• DNA molecules provided herein include a promoter for in vivo transcription.
• the promoter for in vivo transcription is an RNA polymerase II (RNA pol II) promoter.
• RNA pol II RNA polymerase II
• Any RNA pol II promoter can be included in DNA molecules provided herein, including constitutive promoters, inducible promoters, and tissue-specific promoters.
• Exemplary constitutive promoters include a cytomegalovirus (CMV) promoter, an EFla promoter, an SV40 promoter, a PGK1 promoter, a Ubc promoter, a human beta actin promoter, a CAG promoter, and others.
• CMV cytomegalovirus
• RNA pol II promoter is a muscle-specific promoter, skin-specific promoter, subcutaneous tissue-specific promoter, liver-specific promoter, spleen-specific promoter, lymph node-specific promoter, or a promoter with any other tissue specificity.
• DNA molecules provided herein can also include an enhancer. Any enhancer that increases transcription can be included in DNA molecules provided herein. Design and Synthesis of RNA and DNA Molecules
• RNA molecules provided herein can include any combination of the RNA sequences provided herein, including, for example, any 5’ UTR sequences, any sequences encoding a polyprotein that includes nsPl, nsP2, nsP3, and nsP4, any sequences encoding any transgene, and any 3’ UTR sequences provided herein.
• RNA molecules provided herein are self-replicating RNA molecules. Self-replicating RNA molecules can include sequences encoding a polyprotein that includes nsPl, nsP2, nsP3, and nsP4, for example.
• RNA molecules provided herein are mRNA molecules.
• RNA molecules do not include sequences encoding a polyprotein for replication of the RNA.
• RNA molecules provided herein include modified nucleotides. For example, 0% to 100%, 1% to 100%, 25% to 100%, 50% to 100% and 75% to 100% of the uracil nucleotides of the RNA molecules can be modified. In some aspects, 1% to 100% of the uracil nucleotides are Nl-methylpseudouridine or 5-methoxyuridine. In some embodiments, 100% of the uracil nucleotides are Nl-methylpseudouridine. In some embodiments, 100% of the uracil nucleotides are 5-methoxyuridine.
• RNA molecule such as a self-replicating RNA or mRNA, of the disclosure may be obtained by any suitable means. Methods for the manufacture of RNA molecules are known in the art and would be readily apparent to a person of ordinary skill. An RNA molecule of the disclosure may be prepared according to any available technique including, but not limited to chemical synthesis, in vitro transcription (IVT) or enzymatic or chemical cleavage of a longer precursor, etc.
• IVTT in vitro transcription
• enzymatic or chemical cleavage of a longer precursor etc.
• an RNA molecule such as a self-replicating RNA or mRNA, of the disclosure is produced from a primary complementary DNA (cDNA) construct.
• the cDNA constructs can be produced on an RNA template by the action of a reverse transcriptase (e.g., RNA-dependent DNA-polymerase).
• a reverse transcriptase e.g., RNA-dependent DNA-polymerase.
• the process of design and synthesis of the primary cDNA constructs described herein generally includes the steps of gene construction, RNA production (either with or without modifications) and purification.
• a target polynucleotide sequence encoding an RNA molecule of the disclosure is first selected for incorporation into a vector which will be amplified to produce a cDNA template.
• the target polynucleotide sequence and/or any flanking sequences may be codon optimized.
• the cDNA template is then used to produce an RNA molecule of the disclosure through in vitro transcription (IVT). After production, the RNA molecule of the disclosure may undergo purification and clean-up processes. The steps of which are provided in more detail below. [00235]
• the step of gene construction may include, but is not limited to gene synthesis, vector amplification, plasmid purification, plasmid linearization and clean-up, and cDNA template synthesis and clean-up. Once a protein of interest is selected for production, a primary construct is designed.
• a first region of linked nucleosides encoding the polypeptide of interest may be constructed using an open reading frame (ORF) of a selected nucleic acid (DNA or RNA) transcript.
• the ORF may comprise the wild type ORF, an isoform, variant or a fragment thereof.
• an “open reading frame” or “ORF” is meant to refer to a nucleic acid sequence (DNA or RNA) which is can encode a polypeptide of interest. ORFs often begin with the start codon, ATG and end with a nonsense or termination codon or signal.
• the cDNA templates may be transcribed to produce an RNA molecule of the disclosure using an in vitro transcription (IVT) system.
• the system typically comprises a transcription buffer, nucleotide triphosphates (NTPs), an RNase inhibitor and a polymerase.
• NTPs may be selected from, but are not limited to, those described herein including natural and unnatural (modified) NTPs.
• the polymerase may be selected from, but is not limited to, T7 RNA polymerase, T3 RNA polymerase and mutant polymerases such as, but not limited to, polymerases able to incorporate modified nucleic acids.
• the primary cDNA template or transcribed RNA sequence may also undergo capping and/or tailing reactions.
• a capping reaction may be performed by methods known in the art to add a 5 ' cap to the 5 ' end of the primary construct. Methods for capping include, but are not limited to, using a Vaccinia Capping enzyme (New England Biolabs, Ipswich, Mass.) or capping at initiation of in vitro transcription, by for example, including a capping agent as part of the IVT reaction. (Nuc. Acids Symp. (2009) 53 : 129).
• a poly(A) tailing reaction may be performed by methods known in the art, such as, but not limited to, 2' O-methyltransferase and by methods as described herein. If the primary construct generated from cDNA does not include a poly-T, it may be beneficial to perform the poly(A)-tailing reaction before the primary construct is cleaned.
• Codon optimized cDNA constructs encoding the non- structural proteins and the transgene for a self-replicating RNA are particularly suitable for generating self-replicating RNA sequences described herein.
• such cDNA constructs may be used as the basis to transcribe, in vitro, a polyribonucleotide encoding a protein of interest as part of a self- replicating RNA.
• Codon optimized cDNA constructs can also be used to generate mRNAs provided herein.
• the present disclosure also provides expression vectors comprising a nucleotide sequence encoding a self-replicating RNA or mRNA that is preferably operably linked to at least one regulatory sequence. Regulatory sequences are art-recognized and are selected to direct expression of the encoded polypeptide.
• regulatory sequence includes promoters, enhancers, and other expression control elements.
• the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed.
• the present disclosure also provides polynucleotides (e.g. DNA, RNA, cDNA, mRNA, etc.) directed to a self-replicating RNA or mRNA of the disclosure that may be operably linked to one or more regulatory nucleotide sequences in an expression construct, such as a vector or plasmid.
• an expression construct such as a vector or plasmid.
• such constructs are DNA constructs.
• Regulatory nucleotide sequences will generally be appropriate for a host cell used for expression. Numerous types of appropriate expression vectors and suitable regulatory sequences are known in the art for a variety of host cells.
• said one or more regulatory nucleotide sequences may include, but are not limited to, promoter sequences, leader or signal sequences, ribosomal binding sites, transcriptional start and termination sequences, translational start and termination sequences, and enhancer or activator sequences.
• constitutive or inducible promoters as known in the art are contemplated by the embodiments of the present disclosure.
• the promoters may be either naturally occurring promoters, or hybrid promoters that combine elements of more than one promoter.
• An expression construct may be present in a cell on an episome, such as a plasmid, or the expression construct may be inserted in a chromosome.
• the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selectable marker genes are well known in the art and will vary with the host cell used.
• the present disclosure also provides a host cell transfected with a self-replicating RNA, mRNA, or DNA described herein.
• the self-replicating RNA, mRNA, or DNA can encode any protein of interest, for example an antigen, including the spike glycoprotein of the SARS-CoV-2 virus or any other viral glycoprotein, such as the influenza virus hemagglutinin and neuraminidase.
• the host cell may be any prokaryotic or eukaryotic cell.
• a polypeptide encoded by a self-replicating RNA or mRNA may be expressed in bacterial cells such as A. coli , insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art.
• a host cell transfected with an expression vector comprising a self-replicating RNA or mRNA of the disclosure can be cultured under appropriate conditions to allow expression of the self-replicating RNA or mRNA and translation of the polypeptide to occur. Once expressed, a self-replicating RNA generally undergoes self-amplification and translation.
• the polypeptide may be secreted and isolated from a mixture of cells and medium containing the polypeptides. Alternatively, the polypeptides may be retained in the cytoplasm or in a membrane fraction and the cells harvested, lysed and the protein isolated.
• a cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art.
• the expressed proteins described herein can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion- exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffmity purification with antibodies specific for particular epitopes of the polypeptide.
• compositions comprising any of the RNA or DNA molecules provided herein.
• Compositions provided herein can include a lipid. Any lipid can be included in compositions provided herein. In one aspect, the lipid is an ionizable cationic lipid. Any ionizable cationic lipid can be included in compositions comprising nucleic acid molecules provided herein.
• compositions and polynucleotides of the present disclosure may be used to immunize or vaccinate a subject against a viral infection.
• the compositions and polynucleotides of the present disclosure may be used to vaccinate or immunize a subject against SARS-CoV-2, the virus causing COVID-19.
• compositions comprising any of the RNA and DNA molecules provided herein and a lipid formulation.
• Any lipid can be included in lipid formulations of pharmaceutical compositions provided herein.
• lipid formulations of pharmaceutical compositions provided herein include an ionizable cationic lipid.
• Exemplary ionizable cationic lipids of compositions and pharmaceutical compositions provided herein include the following: ATX-013 ATX-014
• the ionizable cationic lipid of compositions provided herein has a structure of
• the ionizable cationic lipid of compositions provided herein has a structure of
• the ionizable cationic lipid included in lipid formulations of pharmaceutical compositions provided herein has a structure of
• the ionizable cationic lipid included in lipid formulations of pharmaceutical compositions provided herein has a structure of
• nucleic acid material e.g., mRNA
• RES reticuloendothelial system
• RNAs or DNAs are anionic hydrophilic polymers that are not favorable for uptake by cells, which are also anionic at the surface. The success of nucleic acid- based therapies thus depends largely on the development of vehicles or vectors that can efficiently and effectively deliver genetic material to target cells and obtain sufficient levels of expression in vivo with minimal toxicity.
• nucleic acid delivery vectors upon internalization into a target cell, nucleic acid delivery vectors are challenged by intracellular barriers, including endosome entrapment, lysosomal degradation, nucleic acid unpacking from vectors, translocation across the nuclear membrane (for DNA), release at the cytoplasm (for RNA), and so on.
• Successful nucleic acid-based therapy thus depends upon the ability of the vector to deliver the nucleic acids to the target sites inside of the cells in order to obtain sufficient levels of a desired activity such as expression of a gene.
• lipid-based formulations have been increasingly recognized as one of the most promising delivery systems for RNA and other nucleic acid compounds due to their biocompatibility and their ease of large-scale production.
• AAV viral delivery vector
• lipid-based formulations have been increasingly recognized as one of the most promising delivery systems for RNA and other nucleic acid compounds due to their biocompatibility and their ease of large-scale production.
• One of the most significant advances in lipid-based nucleic acid therapies happened in August 2018 when Patisiran (ALN-TTR02) was the first siRNA therapeutic approved by the Food and Drug Administration (FDA) and by the European Commission (EC).
• FDA Food and Drug Administration
• EC European Commission
• ALN-TTR02 is an siRNA formulation based upon the so- called Stable Nucleic Acid Lipid Particle (SNALP) transfecting technology.
• SNALP Stable Nucleic Acid Lipid Particle
• lipid-formulated delivery vehicles for nucleic acid therapeutics include, according to various embodiments, polymer based carriers, such as polyethyleneimine (PEI), lipid nanoparticles and liposomes, nanoliposomes, ceramide- containing nanoliposomes, multivesicular liposomes, proteoliposomes, both natural and synthetically-derived exosomes, natural, synthetic and semi-synthetic lamellar bodies, nanoparticulates, micelles, and emulsions.
• PEI polyethyleneimine
• lipid nanoparticles and liposomes such as polyethyleneimine (PEI)
• nanoliposomes such as lipid nanoliposomes, ceramide- containing nanoliposomes, multivesicular liposomes, proteoliposomes, both natural and synthetically-derived exosomes, natural, synthetic and semi-synthetic lamellar bodies, nanoparticulates, micelles, and emulsions.
• lipid formulations can vary in their structure
• lipid formulations have varied as to their intended meaning throughout the scientific literature, and this inconsistent use has caused confusion as to the exact meaning of several terms for lipid formulations.
• liposomes, cationic liposomes, and lipid nanoparticles are specifically described in detail and defined herein for the purposes of the present disclosure.
• Bilayer membranes of liposomes are typically formed by amphiphilic molecules, such as lipids of synthetic or natural origin that comprise spatially separated hydrophilic and hydrophobic domains (Lasic, Trends Biotechnol., 16: 307-321, 1998).
• Bilayer membranes of the liposomes can also be formed by amphiphilic polymers and surfactants (e.g., polymerosomes, niosomes, etc.). They generally present as spherical vesicles and can range in size from 20 nm to a few microns.
• Liposomal formulations can be prepared as a colloidal dispersion or they can be lyophilized to reduce stability risks and to improve the shelf-life for liposome-based drugs. Methods of preparing liposomal compositions are known in the art and would be within the skill of an ordinary artisan.
• Liposomes that have only one bilayer are referred to as being unilamellar, and those having more than one bilayer are referred to as multilamellar.
• the most common types of liposomes are small unilamellar vesicles (SUV), large unilamellar vesicle (LUV), and multilamellar vesicles (MLV).
• lysosomes, micelles, and reversed micelles are composed of monolayers of lipids.
• a liposome is thought of as having a single interior compartment, however some formulations can be multivesicular liposomes (MVL), which consist of numerous discontinuous internal aqueous compartments separated by several nonconcentric lipid bilayers.
• MDL multivesicular liposomes
• Liposomes have long been perceived as drug delivery vehicles because of their superior biocompatibility, given that liposomes are basically analogs of biological membranes, and can be prepared from both natural and synthetic phospholipids (Int J Nanomedicine. 2014; 9:1833-1843).
• a liposome has an aqueous solution core surrounded by a hydrophobic membrane, hydrophilic solutes dissolved in the core cannot readily pass through the bilayer, and hydrophobic compounds will associate with the bilayer.
• a liposome can be loaded with hydrophobic and/or hydrophilic molecules.
• a liposome is used to carry a nucleic acid such as RNA, the nucleic acid will be contained within the liposomal compartment in an aqueous phase.
• Liposomes can be composed of cationic, anionic, and/or neutral lipids.
• cationic liposomes are liposomes that are made in whole or part from positively charged lipids, or more specifically a lipid that comprises both a cationic group and a lipophilic portion.
• the positively charged moieties of cationic lipids used in cationic liposomes provide several advantages and some unique structural features.
• the lipophilic portion of the cationic lipid is hydrophobic and thus will direct itself away from the aqueous interior of the liposome and associate with other nonpolar and hydrophobic species.
• cationic moiety will associate with aqueous media and more importantly with polar molecules and species with which it can complex in the aqueous interior of the cationic liposome.
• cationic liposomes are increasingly being researched for use in gene therapy due to their favorability towards negatively charged nucleic acids via electrostatic interactions, resulting in complexes that offer biocompatibility, low toxicity, and the possibility of the large- scale production required for in vivo clinical applications.
• Cationic lipids suitable for use in cationic liposomes are listed herein below.
• lipid nanoparticles In contrast to liposomes and cationic liposomes, lipid nanoparticles (LNP) have a structure that includes a single monolayer or bilayer of lipids that encapsulates a compound in a solid phase. Thus, unlike liposomes, lipid nanoparticles do not have an aqueous phase or other liquid phase in its interior, but rather the lipids from the bilayer or monolayer shell are directly complexed to the internal compound thereby encapsulating it in a solid core. Lipid nanoparticles are typically spherical vesicles having a relatively uniform dispersion of shape and size.
• lipid nanoparticle can have a diameter in the range of from 10 nm to 1000 nm. However, more commonly they are considered to be smaller than 120 nm or even 100 nm.
• the lipid shell is formulated to include an ionizable cationic lipid which can complex to and associate with the negatively charged backbone of the nucleic acid core.
• Ionizable cationic lipids with apparent pKa values below about 7 have the benefit of providing a cationic lipid for complexing with the nucleic acid’s negatively charged backbone and loading into the lipid nanoparticle at pH values below the pKa of the ionizable lipid where it is positively charged. Then, at physiological pH values, the lipid nanoparticle can adopt a relatively neutral exterior allowing for a significant increase in the circulation half-lives of the particles following i.v. administration.
• lipid nanoparticles offer many advantages over other lipid-based nucleic acid delivery systems including high nucleic acid encapsulation efficiency, potent transfection, improved penetration into tissues to deliver therapeutics, and low levels of cytotoxicity and immunogenicity.
• cationic lipids Prior to the development of lipid nanoparticle delivery systems for nucleic acids, cationic lipids were widely studied as synthetic materials for delivery of nucleic acid medicines. In these early efforts, after mixing together at physiological pH, nucleic acids were condensed by cationic lipids to form lipid-nucleic acid complexes known as lipoplexes.
• lipoplexes proved to be unstable and characterized by broad size distributions ranging from the submicron scale to a few microns. Lipoplexes, such as the Lipofectamine® reagent, have found considerable utility for in vitro transfection. However, these first- generation lipoplexes have not proven useful in vivo.
• nucleic acid molecules provided herein and lipids or lipid formulations provided herein form a lipid nanoparticle (LNP).
• LNP lipid nanoparticle
• nucleic acid molecules provided herein are incorporated into a lipid formulation (i.e., a lipid-based delivery vehicle).
• a lipid-based delivery vehicle typically serves to transport a desired RNA to a target cell or tissue.
• the lipid-based delivery vehicle can be any suitable lipid-based delivery vehicle known in the art.
• the lipid-based delivery vehicle is a liposome, a cationic liposome, or a lipid nanoparticle containing a self- replicating RNA or mRNA of the disclosure.
• the lipid-based delivery vehicle comprises a nanoparticle or a bilayer of lipid molecules and a self-replicating RNA or mRNA of the disclosure.
• the lipid bilayer further comprises a neutral lipid or a polymer.
• the lipid formulation comprises a liquid medium. In some aspects, the formulation further encapsulates a nucleic acid. In some aspects, the lipid formulation further comprises a nucleic acid and a neutral lipid or a polymer. In some aspects, the lipid formulation encapsulates the nucleic acid. [00268] The description provides lipid formulations comprising one or more RNA molecules encapsulated within the lipid formulation. In some aspects, the lipid formulation comprises liposomes. In some aspects, the lipid formulation comprises cationic liposomes. In some aspects, the lipid formulation comprises lipid nanoparticles.
• the self-replicating RNA or mRNA is fully encapsulated within the lipid portion of the lipid formulation such that the RNA in the lipid formulation is resistant in aqueous solution to nuclease degradation.
• the lipid formulations described herein are substantially non-toxic to animals such as humans and other mammals.
• the lipid formulations of the disclosure also typically have a total lipid:RNA ratio (mass/mass ratio) of from about 1:1 to about 100:1, from about 1:1 to about 50:1, from about 2:1 to about 45:1, from about 3:1 to about 40:1, from about 5:1 to about 45:1, or from about 10: 1 to about 40: 1, or from about 15: 1 to about 40: 1, or from about 20: 1 to about 40: 1; or from about 25:1 to about 45:1; or from about 30:1 to about 45:1; or from about 32:1 to about 42:1; or from about 34: 1 to about 42: 1.
• the total lipid:RNA ratio (mass/mass ratio) is from about 30:1 to about 45:1.
• the ratio may be any value or subvalue within the recited ranges, including endpoints.
• the lipid formulations of the present disclosure typically have a mean diameter of from about 30 nm to about 150 nm, from about 40 nm to about 150 nm, from about 50 nm to about 150 nm, from about 60 nm to about 130 nm, from about 70 nm to about 110 nm, from about 70 nm to about 100 nm, from about 80 nm to about 100 nm, from about 90 nm to about 100 nm, from about 70 to about 90 nm, from about 80 nm to about 90 nm, from about 70 nm to about 80 nm, or about 30 nm, about 35 nm, about 40 nm, about 45 nm, about 50 nm, about 55 nm, about 60 nm, about 65 nm, about 70 nm, about 75 nm, about 80 nm, about 85 nm, about 90 nm, about 95 nm, about 100 nm, about 105
• the diameter may be any value or subvalue within the recited ranges, including endpoints.
• nucleic acids when present in the lipid nanoparticles of the present disclosure, generally are resistant in aqueous solution to degradation with a nuclease.
• the lipid nanoparticle has a size of less than about 500 nm, less than about 400 nm, less than about 300 nm, less than about 200 nm, less than about 100 nm, or less than about 50 nm. In specific embodiments, the lipid nanoparticle has a size of about 55 nm to about 90 nm.
• the lipid formulations comprise a self-replicating RNA or mRNA, a cationic lipid (e.g., one or more cationic lipids or salts thereof described herein), a phospholipid, and a conjugated lipid that inhibits aggregation of the particles (e.g., one or more PEG-lipid conjugates).
• the lipid formulations can also include cholesterol.
• the cationic lipid is an ionizable cationic lipid.
• the RNA may be fully encapsulated within the lipid portion of the formulation, thereby protecting the nucleic acid from nuclease degradation.
• a lipid formulation comprising an RNA is fully encapsulated within the lipid portion of the lipid formulation, thereby protecting the nucleic acid from nuclease degradation.
• the RNA in the lipid formulation is not substantially degraded after exposure of the particle to a nuclease at 37°C for at least 20, 30, 45, or 60 minutes.
• the RNA in the lipid formulation is not substantially degraded after incubation of the formulation in serum at 37°C for at least 30, 45, or 60 minutes or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36 hours.
• the RNA is complexed with the lipid portion of the formulation.
• the nucleic acid-lipid compositions are substantially non-toxic to animals such as humans and other mammals.
• the present disclosure provides a nucleic acid-lipid composition comprising a plurality of nucleic acid-liposomes, nucleic acid-cationic liposomes, or nucleic acid-lipid nanoparticles.
• the nucleic acid-lipid composition comprises a plurality of RNA-liposomes.
• the nucleic acid-lipid composition comprises a plurality of RNA-cationic liposomes.
• the nucleic acid-lipid composition comprises a plurality of RNA-lipid nanoparticles.
• the lipid formulations comprise RNA that is fully encapsulated within the lipid portion of the formulation, such that from about 30% to about 100%, from about 40% to about 100%, from about 50% to about 100%, from about 60% to about 100%, from about 70% to about 100%, from about 80% to about 100%, from about 90% to about 100%, from about 30% to about 95%, from about 40% to about 95%, from about 50% to about
• RNA encapsulated therein has the RNA encapsulated therein.
• the amount may be any value or subvalue within the recited ranges, including endpoints.
• the RNA included in any RNA-lipid composition or RNA-lipid formulation provided herein can be a self-replicating RNA or an mRNA.
• the proportions of the components can be varied, and the delivery efficiency of a particular formulation can be measured using assays known in the art.
• nucleic acid molecules provided herein are lipid formulated.
• the lipid formulation is preferably selected from, but not limited to, liposomes, cationic liposomes, and lipid nanoparticles.
• a lipid formulation is a cationic liposome or a lipid nanoparticle (LNP) comprising:
• an aggregation reducing agent such as polyethylene glycol (PEG) lipid or PEG- modified lipid
• lipid optionally a non-cationic lipid (such as a neutral lipid), and
• the cationic lipid is an ionizable cationic lipid.
• Any ionizable cationic lipid can be included in lipid formulations, including exemplary cationic lipids provided herein.
• compositions that include lipids and/or lipid formulations provided herein include an RNA molecule comprising (A) a sequence of SEQ ID NO: 1; (B) a sequence of SEQ ID NO:2; (C) a sequence of SEQ ID NO:3; or (D) a sequence of SEQ ID NO:4.
• compositions provided herein include an RNA molecule comprising a sequence of SEQ ID NO:40.
• compositions provided herein include an RNA molecule comprising a sequence of SEQ ID NO: 29, SEQ ID NO: 32, or SEQ ID NO:48.
• compositions provided herein include lipid nanoparticles (LNPs).
• compositions provided herein include lyophilized LNPs.
• lipid nanoparticle compositions comprising a. a lipid formulation comprising i. about 45 mol% to about 55 mol% of an ionizable cationic lipid having the structure of ATX- 126:
• RNA molecule having at least 80% identity to a sequence of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; wherein the lipid formulation encapsulates the RNA molecule and the lipid nanoparticle has a size of about 60 to about 90 nm.
• the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:40.
• the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO: 29, SEQ ID NO: 32, or SEQ ID NO:48. In some aspects, lipid nanoparticle compositions provided herein are lyophilized. In some aspects, the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:29. In some aspects, the RNA molecule included in lipid nanoparticle compositions provided herein has at least 80% identity to a sequence of SEQ ID NO:32.
• the lipid nanoparticle formulation comprises (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid.
• the cationic lipid is an ionizable cationic lipid.
• the lipid nanoparticle formulation comprises (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid, in a molar ratio of about 40-70% ionizable cationic lipid: about 2-15% helper lipid: about 20-45% sterol; about 0.5-5% PEG-lipid.
• the cationic lipid is an ionizable cationic lipid.
• the lipid nanoparticle formulation consists of (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid.
• the cationic lipid is an ionizable cationic lipid.
• the lipid nanoparticle formulation consists of (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid, in a molar ratio of about 40-70% ionizable cationic lipid: about 2-15% helper lipid: about 20-45% sterol; about 0.5-5% PEG-lipid.
• the cationic lipid is an ionizable cationic lipid.
• the cationic lipid may be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N- dimethylammonium bromide (DDAB), 1,2-dioleoyltrimethylammoniumpropane chloride (DOTAP) (also known as N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride and l,2-Dioleyloxy-3-trimethylaminopropane chloride salt), N-(l-(2,3-dioleyloxy)propyl)- N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), l,2-DiLinoleyloxy-N,N-dimethylaminopropane
• DODAC N,N-dioleyl-
• cationic lipids include, but are not limited to, N,N-distearyl-N,N-dimethylammonium bromide (DDAB), 3P-(N- (N',N'-dimethylaminoethane)- carbarn oyl)cholesterol (DC-Choi), N-(l-(2,3- dioleyloxy)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethylammonium trifluoracetate (DOSPA), dioctadecylamidoglycyl carboxyspermine (DOGS), l,2-dileoyl-sn-3- phosphoethanolamine (DOPE), l,2-dioleoyl-3-dimethylammonium propane (DODAP), N-(l,2- dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammonium bromide (DMRIE
• cationic lipids can be used, such as, e.g., LIPOFECTIN (including DOTMA and DOPE, available from GIBCO/BRL), and Lipofectamine (comprising DOSPA and DOPE, available from GIBCO/BRL).
• LIPOFECTIN including DOTMA and DOPE, available from GIBCO/BRL
• Lipofectamine comprising DOSPA and DOPE, available from GIBCO/BRL
• Suitable cationic lipids are disclosed in International Publication Nos. WO 09/086558, WO 09/127060, WO 10/048536, WO 10/054406, WO 10/088537, WO 10/129709, and WO 2011/153493; U.S. Patent Publication Nos. 2011/0256175, 2012/0128760, and 2012/0027803; U.S. Patent Nos. 8,158,601; and Love et ah, PNAS, 107(5), 1864-69, 2010, the contents of which are herein incorporated by reference.
• RNA-lipid formulations of the present disclosure can comprise a helper lipid, which can be referred to as a neutral helper lipid, non-cationic lipid, non-cationic helper lipid, anionic lipid, anionic helper lipid, or a neutral lipid. It has been found that lipid formulations, particularly cationic liposomes and lipid nanoparticles have increased cellular uptake if helper lipids are present in the formulation. (Curr. Drug Metab. 2014; 15(9):882-92).
• neutral and zwitterionic lipids such as 1,2-dioleoylsn-glycero- 3 -phosphatidylcholine (DOPC), Di-Oleoyl-Phosphatidyl-Ethanoalamine (DOPE) and 1,2- DiStearoyl-sn-glycero-3-PhosphoCholine (DSPC), being more fusogenic (i.e., facilitating fusion) than cationic lipids, can affect the polymorphic features of lipid-nucleic acid complexes, promoting the transition from a lamellar to a hexagonal phase, and thus inducing fusion and a disruption of the cellular membrane.
• DOPC 1,2-dioleoylsn-glycero- 3 -phosphatidylcholine
• DOPE Di-Oleoyl-Phosphatidyl-Ethanoalamine
• DSPC 1,2- DiStearoyl-sn-glycero-3
• Non-limiting examples of non-cationic lipids suitable for lipid formulations of the present disclosure include phospholipids such as lecithin, phosphatidylethanolamine, lysolecithin, lysophosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, egg sphingomyelin (ESM), cephalin, cardiolipin, phosphatidic acid, cerebrosides, dicetylphosphate, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatid
• acyl groups in these lipids are preferably acyl groups derived from fatty acids having C10-C24 carbon chains, e.g., lauroyl, myristoyl, palmitoyl, stearoyl, or oleoyl.
• non-cationic lipids include sterols such as cholesterol and derivatives thereof.
• cholesterol increases the spacing of the charges of the lipid layer interfacing with the nucleic acid making the charge distribution match that of the nucleic acid more closely.
• Non-limiting examples of cholesterol derivatives include polar analogues such as 5a-cholestanol, 5a- coprostanol, cholesteryl-(2'-hydroxy)-ethyl ether, cholesteryl-(4'- hydroxy)-butyl ether, and 6- ketocholestanol; non-polar analogues such as 5a-cholestane, cholestenone, 5a-cholestanone, 5a-cholestanone, and cholesteryl decanoate; and mixtures thereof.
• the cholesterol derivative is a polar analogue such as cholesteryl-(4'-hydroxy)-butyl ether.
• the helper lipid present in the lipid formulation comprises or consists of a mixture of one or more phospholipids and cholesterol or a derivative thereof.
• the neutral lipid present in the lipid formulation comprises or consists of one or more phospholipids, e.g., a cholesterol-free lipid formulation.
• the neutral lipid present in the lipid formulation comprises or consists of cholesterol or a derivative thereof, e.g., a phospholipid-free lipid formulation.
• helper lipids include nonphosphorous containing lipids such as, e.g., stearylamine, dodecylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stearate, isopropyl myristate, amphoteric acrylic polymers, triethanolamine-lauryl sulfate, alkyl-aryl sulfate polyethyloxylated fatty acid amides, dioctadecyldimethyl ammonium bromide, ceramide, and sphingomyelin.
• nonphosphorous containing lipids such as, e.g., stearylamine, dodecylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stearate, isopropyl myristate,
• Suitable cationic lipids include those having alternative fatty acid groups and other dialkylamino groups, including those, in which the alkyl substituents are different (e.g., N-ethyl- N-methylamino-, and N-propyl-N-ethylamino-). These lipids are part of a subcategory of cationic lipids referred to as amino lipids.
• the cationic lipid is an amino lipid.
• amino lipids having less saturated acyl chains are more easily sized, particularly when the complexes must be sized below about 0.3 microns, for purposes of filter sterilization.
• Amino lipids containing unsaturated fatty acids with carbon chain lengths in the range of C14 to C22 may be used.
• Other scaffolds can also be used to separate the amino group and the fatty acid or fatty alkyl portion of the amino lipid.
• the lipid formulation comprises the cationic lipid with Formula I according to the patent application PCT/EP2017/064066.
• PCT/EP2017/064066 the disclosure of PCT/EP2017/064066 is also incorporated herein by reference.
• amino or cationic lipids of the present disclosure are ionizable and have at least one protonatable or deprotonatable group, such that the lipid is positively charged at a pH at or below physiological pH (e.g., pH 7.4), and neutral at a second pH, preferably at or above physiological pH.
• physiological pH e.g., pH 7.4
• second pH preferably at or above physiological pH.
• Lipids that have more than one protonatable or deprotonatable group, or which are zwitterionic, are not excluded from use in the disclosure.
• the protonatable lipids have a pKa of the protonatable group in the range of about 4 to about 11.
• the ionizable cationic lipid has a pKa of about 5 to about 7.
• the pKa of an ionizable cationic lipid is about 6 to about 7.
• the lipid formulation comprises an ionizable cationic lipid of Formula I: or a pharmaceutically acceptable salt or solvate thereof, wherein R5 and R6 are each independently selected from the group consisting of a linear or branched C1-C31 alkyl, C2- C31 alkenyl or C2-C31 alkynyl and cholesteryl; L5 and L6 are each independently selected from the group consisting of a linear C1-C20 alkyl and C2-C20 alkenyl; X5 is -C(0)0-, whereby -C(0)0-R6 is formed or -OC(O)- whereby -0C(0)-R6 is formed; X6 is -C(0)0- whereby -C(0)0-R5 is formed or -OC(O)- whereby -0C(0)-R5 is formed; X7 is S or O; L7 is absent or lower alkyl; R4 is a linear or branched C1-C6 alkyl
• X7 is S.
• X5 is -C(0)0-, whereby -C(0)0-R6 is formed and X6 is - C(0)0- whereby -C(0)0-R5 is formed.
• R7 and R8 are each independently selected from the group consisting of methyl, ethyl and isopropyl.
• L5 and L6 are each independently a Cl -CIO alkyl. In some embodiments, L5 is C1-C3 alkyl, and L6 is C1-C5 alkyl. In some embodiments, L6 is C1-C2 alkyl. In some embodiments, L5 and L6 are each a linear C7 alkyl. In some embodiments, L5 and L6 are each a linear C9 alkyl.
• R5 and R6 are each independently an alkenyl. In some embodiments, R6 is alkenyl. In some embodiments, R6 is C2-C9 alkenyl. In some embodiments, the alkenyl comprises a single double bond. In some embodiments, R5 and R6 are each alkyl. In some embodiments, R5 is a branched alkyl. In some embodiments, R5 and R6 are each independently selected from the group consisting of a C9 alkyl, C9 alkenyl and C9 alkynyl. In some embodiments, R5 and R6 are each independently selected from the group consisting of a Cl 1 alkyl, Cl 1 alkenyl and Cl 1 alkynyl.
• R5 and R6 are each independently selected from the group consisting of a C7 alkyl, C7 alkenyl and C7 alkynyl.
• R5 is -CH((CH2)pCH3)2 or -CH((CH2)pCH3)((CH2)p- 1CH3), wherein p is 4-8.
• p is 5 and L5 is a C1-C3 alkyl.
• p is 6 and L5 is a C3 alkyl.
• p is 7.
• p is 8 and L5 is a C1-C3 alkyl.
• R5 consists of - CH((CH2)pCH3 )((CH2)p- 1 CH3 ), wherein p is 7 or 8.
• R4 is ethylene or propylene. In some embodiments, R4 is n- propylene or isobutylene.
• L7 is absent, R4 is ethylene, X7 is S and R7 and R8 are each methyl. In some embodiments, L7 is absent, R4 is n-propylene, X7 is S and R7 and R8 are each methyl. In some embodiments, L7 is absent, R4 is ethylene, X7 is S and R7 and R8 are each ethyl.
• X7 is S
• X5 is -C(0)0-, whereby -C(0)0-R6 is formed
• X6 is -C(0)0- whereby -C(0)0-R5 is formed
• L5 and L6 are each independently a linear C3- C7 alkyl
• L7 is absent
• R5 is -CH((CH2)pCH3)2
• R6 is C7-C12 alkenyl.
• p is 6 and R6 is C9 alkenyl.
• the helper lipid comprises from about 2 mol% to about 20 mol%, from about 3 mol% to about 18 mol%, from about 4 mol% to about 16 mol%, about 5 mol% to about 14 mol%, from about 6 mol% to about 12 mol%, from about 5 mol% to about 10 mol%, from about 5 mol% to about 9 mol%, or about 2 mol%, about 3 mol%, about 4 mol%, about 5 mol%, about 6 mol%, about 7 mol%, about 8 mol%, about 9 mol%, about 10 mol%, about 11 mol%, or about 12 mol% (or any fraction thereof or the range therein) of the total lipid present in the lipid formulation.
• the lipid portion, or the cholesterol or cholesterol derivative in the lipid formulation may comprise up to about 40 mol%, about 45 mol%, about 50 mol%, about 55 mol%, or about 60 mol% of the total lipid present in the lipid formulation.
• the cholesterol or cholesterol derivative comprises about 15 mol% to about 45 mol%, about 20 mol% to about 40 mol%, about 25 mol% to about 35 mol%, or about 28 mol% to about 35 mol%; or about 25 mol%, about 26 mol%, about 27 mol%, about 28 mol%, about 29 mol%, about 30 mol%, about 31 mol%, about 32 mol%, about 33 mol%, about 34 mol%, about 35 mol%, about 36 mol%, or about 37 mol% of the total lipid present in the lipid formulation.
• the lipid portion of the lipid formulation is about 35 mol% to about 42 mol% cholesterol.
• the phospholipid component in the mixture may comprise from about 2 mol% to about 20 mol%, from about 3 mol% to about 18 mol%, from about 4 mol % to about 16 mol %, about 5 mol % to about 14 mol %, from about 6 mol % to about 12 mol%, from about 5 mol% to about 10 mol%, from about 5 mol% to about 9 mol%, or about 2 mol%, about 3 mol%, about 4 mol%, about 5 mol%, about 6 mol%, about 7 mol%, about 8 mol%, about 9 mol%, about 10 mol%, about 11 mol%, or about 12 mol% (or any fraction thereof or the range therein) of the total lipid present in the lipid formulation.
• the lipid portion of the lipid formulation comprises about, but is not necessarily limited to, 40 mol% to about 60 mol% of the ionizable cationic lipid, about 4 mol% to about 16 mol% DSPC, about 30 mol% to about 47 mol% cholesterol, and about 0.5 mol% to about 3 mol% PEG2000-DMG.
• the lipid portion of the lipid formulation may comprise, but is not necessarily limited to, about 42 mol% to about 58 mol% of the ionizable cationic lipid, about 6 mol% to about 14 mol% DSPC, about 32 mol% to about 44 mol% cholesterol, and about 1 mol% to about 2 mol% PEG2000-DMG.
• the lipid portion of the lipid formulation may comprise, but is not necessarily limited to, about 45 mol% to about 55 mol% of the ionizable cationic lipid, about 8 mol% to about 12 mol% DSPC, about 35 mol% to about 42 mol% cholesterol, and about 1.25 mol% to about 1.75 mol% PEG2000-DMG.
• the percentage of helper lipid present in the lipid formulation is a target amount, and the actual amount of helper lipid present in the formulation may vary, for example, by ⁇ 5 mol%.
• a lipid formulation that includes a cationic lipid compound or ionizable cationic lipid compound may be on a molar basis about 30-70% cationic lipid compound, about 25-40 % cholesterol, about 2-15% helper lipid, and about 0.5-5% of a polyethylene glycol (PEG) lipid, wherein the percent is of the total lipid present in the formulation.
• the composition is about 40-65% cationic lipid compound, about 25- 35% cholesterol, about 3-9% helper lipid, and about 0.5-3% of a PEG-lipid, wherein the percent is of the total lipid present in the formulation.
• the formulation may be a lipid particle formulation, for example containing 8-30% nucleic acid compound, 5-30% helper lipid, and 0-20% cholesterol; 4-25% cationic lipid, 4- 25% helper lipid, 2- 25% cholesterol, 10- 35% cholesterol -PEG, and 5% cholesterol-amine; or 2-30% cationic lipid, 2-30% helper lipid, 1-15% cholesterol, 2-35% cholesterol -PEG, and 1- 20% cholesterol-amine; or up to 90% cationic lipid and 2-10% helper lipids, or even 100% cationic lipid.
• the lipid formulations described herein may further comprise a lipid conjugate.
• the conjugated lipid is useful in that it prevents the aggregation of particles.
• Suitable conjugated lipids include, but are not limited to, PEG-lipid conjugates, cationic-polymer-lipid conjugates, and mixtures thereof.
• lipid delivery vehicles can be used for specific targeting by attaching ligands (e.g., antibodies, peptides, and carbohydrates) to its surface or to the terminal end of the attached PEG chains (Front Pharmacol. 2015 Dec 1; 6:286).
• the lipid conjugate is a PEG-lipid.
• PEG polyethylene glycol
• PEGylation helps to protect nanoparticles from the immune system and their escape from RES uptake (Nanomedicine (Lond). 2011 Jun; 6(4):715-28).
• PEGylation has been used to stabilize lipid formulations and their payloads through physical, chemical, and biological mechanisms.
• Detergent-like PEG lipids e.g., PEG-DSPE
• PEG-DSPE can enter the lipid formulation to form a hydrated layer and steric barrier on the surface.
• the surface layer can be generally divided into two types, brush-like and mushroom-like layers.
• PEG-DSPE- stabilized formulations PEG will take on the mushroom conformation at a low degree of PEGylation (usually less than 5 mol%) and will shift to brush conformation as the content of PEG-DSPE is increased past a certain level (Journal of Nanomaterials. 2011;2011:12). PEGylation leads to a significant increase in the circulation half-life of lipid formulations (Annu. Rev. Biomed. Eng. 2011 Aug 15; 13():507-30; J. Control Release. 2010 Aug 3; 145(3): 178-81).
• PEG-lipids include, but are not limited to, PEG coupled to dialkyloxypropyls (PEG-DAA), PEG coupled to diacylglycerol (PEG-DAG), methoxypolyethyleneglycol (PEG-DMG or PEG2000-DMG), PEG coupled to phospholipids such as phosphatidylethanolamine (PEG-PE), PEG conjugated to ceramides, PEG conjugated to cholesterol or a derivative thereof, and mixtures thereof.
• PEG-DAA dialkyloxypropyls
• PEG-DAG PEG coupled to diacylglycerol
• PEG-DMG or PEG2000-DMG methoxypolyethyleneglycol
• PEG-PE phosphatidylethanolamine
• PEG conjugated to ceramides PEG conjugated to cholesterol or a derivative thereof, and mixtures thereof.
• PEG is a linear, water-soluble polymer of ethylene PEG repeating units with two terminal hydroxyl groups.
• PEGs are classified by their molecular weights and include the following: monomethoxypolyethylene glycol (MePEG-OH), monomethoxypolyethylene glycol- succinate (MePEG-S), monomethoxypolyethylene glycol-succinimidyl succinate (MePEG-S-NHS), monomethoxypolyethylene glycol-amine (MePEG-NH2), monomethoxypolyethylene glycol-tresylate (MePEG-TRES), monomethoxypolyethylene glycol-imidazolyl-carbonyl (MePEG-IM), as well as such compounds containing a terminal hydroxyl group instead of a terminal methoxy group (e.g., HO-PEG-S, HO-PEG-S-NHS, HO- PEG-NH2).
• MePEG-OH monomethoxypoly
• the PEG moiety of the PEG-lipid conjugates described herein may comprise an average molecular weight ranging from about 550 daltons to about 10,000 daltons. In certain aspects, the PEG moiety has an average molecular weight of from about 750 daltons to about 5,000 daltons (e.g., from about 1,000 daltons to about 5,000 daltons, from about 1,500 daltons to about 3,000 daltons, from about 750 daltons to about 3,000 daltons, from about 750 daltons to about 2,000 daltons). In some aspects, the PEG moiety has an average molecular weight of about 2,000 daltons or about 750 daltons. The average molecular weight may be any value or subvalue within the recited ranges, including endpoints.
• the PEG can be optionally substituted by an alkyl, alkoxy, acyl, or aryl group.
• the PEG can be conjugated directly to the lipid or may be linked to the lipid via a linker moiety.
• Any linker moiety suitable for coupling the PEG to a lipid can be used including, e.g., non-ester-containing linker moieties and ester-containing linker moieties.
• the linker moiety is a non-ester-containing linker moiety.
• non-ester- containing linker moieties include, but are not limited to, amido (-C(O)NH-), amino (-NR-), carbonyl (-C(O)-), carbamate (-NHC(O)O-), urea (-NHC(O)NH-), disulfide (-S-S-), ether (-0- ), succinyl (-(0)CCH2CH2C(0)-), succinamidyl (-NHC(0)CH2CH2C(0)NH-), ether, as well as combinations thereof (such as a linker containing both a carbamate linker moiety and an amido linker moiety).
• a carbamate linker is used to couple the PEG to the lipid.
• an ester-containing linker moiety is used to couple the PEG to the lipid.
• exemplary ester-containing linker moieties include, e.g., carbonate (-OC(O)O-), succinoyl, phosphate esters (-O-(O)POH-O-), sulfonate esters, and combinations thereof.
• Phosphatidylethanolamines having a variety of acyl chain groups of varying chain lengths and degrees of saturation can be conjugated to PEG to form the lipid conjugate.
• Such phosphatidylethanolamines are commercially available or can be isolated or synthesized using conventional techniques known to those of skill in the art.
• Phosphatidylethanolamines containing saturated or unsaturated fatty acids with carbon chain lengths in the range of Cio to C20 are preferred.
• Phosphatidylethanolamines with mono- or di-unsaturated fatty acids and mixtures of saturated and unsaturated fatty acids can also be used.
• Suitable phosphatidylethanolamines include, but are not limited to, dimyristoyl- phosphatidylethanolamine (DMPE), dipalmitoyl-phosphatidylethanolamine (DPPE), dioleoyl- phosphatidylethanolamine (DOPE), and distearoyl-phosphatidylethanolamine (DSPE).
• DMPE dimyristoyl- phosphatidylethanolamine
• DPPE dipalmitoyl-phosphatidylethanolamine
• DOPE dioleoyl- phosphatidylethanolamine
• DSPE distearoyl-phosphatidylethanolamine
• the PEG-DAA conjugate is a PEG-didecyloxypropyl (CIO) conjugate, a PEG-dilauryloxypropyl (C12) conjugate, a PEG-dimyristyloxypropyl (C14) conjugate, a PEG-dipalmityloxypropyl (Cl 6) conjugate, or a PEG-distearyloxypropyl (Cl 8) conjugate.
• the PEG has an average molecular weight of about 750 or about 2,000 daltons.
• the terminal hydroxyl group of the PEG is substituted with a methyl group.
• hydrophilic polymers can be used in place of PEG.
• suitable polymers that can be used in place of PEG include, but are not limited to, polyvinylpyrrolidone, polymethyloxazoline, polyethyloxazoline, polyhydroxypropyl, methacrylamide, polymethacrylamide, and polydimethylacrylamide, polylactic acid, polyglycolic acid, and derivatized celluloses such as hydroxymethylcellulose or hydroxyethylcellulose.
• the lipid conjugate (e.g., PEG-lipid) comprises from about 0.1 mol% to about 2 mol%, from about 0.5 mol% to about 2 mol%, from about 1 mol% to about 2 mol%, from about 0.6 mol% to about 1.9 mol%, from about 0.7 mol% to about 1.8 mol%, from about 0.8 mol% to about 1.7 mol%, from about 0.9 mol% to about 1.6 mol%, from about 0.9 mol% to about 1.8 mol%, from about 1 mol% to about 1.8 mol%, from about 1 mol% to about 1.7 mol%, from about 1.2 mol% to about 1.8 mol%, from about 1.2 mol% to about 1.7 mol%, from about 1.3 mol% to about 1.6 mol%, or from about 1.4 mol% to about 1.6 mol% (or any fraction thereof or range therein) of the total lipid present in the lipid formulation.
• the lipid conjugate (e.g., PEG-lipid) comprises about 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1.0%, 1.2%, 1.3%, 1.4%, 1.5%, 1.6%, 1.7%, 1.8%, 1.9%, 2.0%, 2.5%, 3.0%, 3.5%, 4.0%, 4.5%, or 5%, (or any fraction thereof or range therein) of the total lipid present in the lipid formulation.
• the amount may be any value or subvalue within the recited ranges, including endpoints.
• the percentage of lipid conjugate (e.g., PEG-lipid) present in the lipid formulations of the disclosure is a target amount, and the actual amount of lipid conjugate present in the formulation may vary, for example, by ⁇ 0.5 mol%.
• concentration of the lipid conjugate can be varied depending on the lipid conjugate employed and the rate at which the lipid formulation is to become fusogenic.
• the lipid formulation for any of the compositions described herein comprises a lipoplex, a liposome, a lipid nanoparticle, a polymer-based particle, an exosome, a lamellar body, a micelle, or an emulsion.
• lipid formulations for the intracellular delivery of nucleic acids are designed for cellular uptake by penetrating target cells through exploitation of the target cells’ endocytic mechanisms where the contents of the lipid delivery vehicle are delivered to the cytosol of the target cell.
• nucleic Acid Therapeutics 28(3): 146-157, 2018
• functionalized ligands such as PEG-lipid at the surface of the lipid delivery vehicle are shed from the surface, which triggers internalization into the target cell.
• RNA payloads the cell’s own internal translation processes will then translate the RNA into the encoded protein.
• the encoded protein can further undergo postranslational processing, including transportation to a targeted organelle or location within the cell or excretion from the cell.
• postranslational processing including transportation to a targeted organelle or location within the cell or excretion from the cell.
• the composition and concentration of the lipid conjugate By controlling the composition and concentration of the lipid conjugate, one can control the rate at which the lipid conjugate exchanges out of the lipid formulation and, in turn, the rate at which the lipid formulation becomes fusogenic.
• other variables including, e.g., pH, temperature, or ionic strength, can be used to vary and/or control the rate at which the lipid formulation becomes fusogenic. Other methods which can be used to control the rate at which the lipid formulation becomes fusogenic will become apparent to those of skill in the art upon reading this disclosure.
• the composition and concentration of the lipid conjugate one can control the liposomal or lipid particle size.
• MLVs Multilamellar Vesicles
• LUV and SUV Small or Large Unilamellar vesicles
• Lipid formulations can also be prepared through the Double Emulsion technique, which involves lipids dissolution in a water/organic solvent mixture.
• the organic solution, containing water droplets is mixed with an excess of aqueous medium, leading to a water-in- oil-in-water (W/O/W) double emulsion formation. After mechanical vigorous shaking, part of the water droplets collapse, giving Large Unilamellar Vesicles (LUVs).
• Double Emulsion technique involves lipids dissolution in a water/organic solvent mixture.
• the organic solution containing water droplets, is mixed with an excess of aqueous medium, leading to a water-in- oil-in-water (W/O/W) double emulsion formation. After mechanical vigorous shaking, part of the water droplets collapse, giving Large Unilamellar Vesicles (LUVs).
• LUVs Large Unilamellar Vesicles
• the Reverse Phase Evaporation (REV) method also allows one to achieve LUVs loaded with nucleic acid.
• REV Reverse Phase Evaporation
• a two-phase system is formed by phospholipids dissolution in organic solvents and aqueous buffer.
• the resulting suspension is then sonicated briefly until the mixture becomes a clear one-phase dispersion.
• the lipid formulation is achieved after the organic solvent evaporation under reduced pressure. This technique has been used to encapsulate different large and small hydrophilic molecules including nucleic acids.
• the Microfluidic method unlike other bulk techniques, gives the possibility of controlling the lipid hydration process.
• the method can be classified in continuous-flow microfluidic and droplet-based microfluidic, according to the way in which the flow is manipulated.
• MHF microfluidic hydrodynamic focusing
• lipids are dissolved in isopropyl alcohol which is hydrodynamically focused in a microchannel cross junction between two aqueous buffer streams.
• Vesicles size can be controlled by modulating the flow rates, thus controlling the lipids solution/buffer dilution process.
• the method can be used for producing oligonucleotide (ON) lipid formulations by using a microfluidic device consisting of three-inlet and one-outlet ports.
• Dual Asymmetric Centrifugation differs from more common centrifugation as it uses an additional rotation around its own vertical axis. An efficient homogenization is achieved due to the two overlaying movements generated: the sample is pushed outwards, as in a normal centrifuge, and then it is pushed towards the center of the vial due to the additional rotation.
• VPC viscous vesicular phospholipid gel
• the lipid formulation size can be regulated by optimizing DAC speed, lipid concentration and homogenization time.
• the Ethanol Injection (El) method can be used for nucleic acid encapsulation.
• This method provides the rapid injection of an ethanolic solution, in which lipids are dissolved, into an aqueous medium containing nucleic acids to be encapsulated, through the use of a needle. Vesicles are spontaneously formed when the phospholipids are dispersed throughout the medium.
• the Detergent dialysis method can be used to encapsulate nucleic acids. Briefly lipid and plasmid are solubilized in a detergent solution of appropriate ionic strength, after removing the detergent by dialysis, a stabilized lipid formulation is formed. Unencapsulated nucleic acid is then removed by ion-exchange chromatography and empty vesicles by sucrose density gradient centrifugation. The technique is highly sensitive to the cationic lipid content and to the salt concentration of the dialysis buffer, and the method is also difficult to scale.
• Stable lipid formulations can also be produced through the Spontaneous Vesicle Formation by Ethanol Dilution method in which a stepwise or dropwise ethanol dilution provides the instantaneous formation of vesicles loaded with nucleic acid by the controlled addition of lipid dissolved in ethanol to a rapidly mixing aqueous buffer containing the nucleic acid.
• nucleic acids can also be obtained starting with preformed liposomes through two different methods: (1) A simple mixing of cationic liposomes with nucleic acids which gives electrostatic complexes called “lipoplexes”, where they can be successfully used to transfect cell cultures, but are characterized by their low encapsulation efficiency and poor performance in vivo; and (2) a liposomal destabilization, slowly adding absolute ethanol to a suspension of cationic vesicles up to a concentration of 40% v/v followed by the dropwise addition of nucleic acids achieving loaded vesicles; however, the two main steps characterizing the encapsulation process are too sensitive, and the particles have to be downsized.
• compositions disclosed herein can be formulated using one or more excipients to: (1) increase stability; (2) increase cell transfection; (3) permit a sustained or delayed release (e.g., from a depot formulation of the polynucleotide, primary construct, or RNA); (4) alter the biodistribution (e.g., target the polynucleotide, primary construct, or RNA to specific tissues or cell types); (5) increase the translation of encoded protein in vivo; and/or (6) alter the release profile of encoded protein in vivo.
• excipients to: (1) increase stability; (2) increase cell transfection; (3) permit a sustained or delayed release (e.g., from a depot formulation of the polynucleotide, primary construct, or RNA); (4) alter the biodistribution (e.g., target the polynucleotide, primary construct, or RNA to specific tissues or cell types); (5) increase the translation of encoded protein in vivo; and/or (6) alter the release profile of encoded protein
• compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods include the step of associating the active ingredient (i.e., nucleic acid) with an excipient and/or one or more other accessory ingredients.
• a pharmaceutical composition in accordance with the present disclosure may be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses.
• compositions may additionally comprise a pharmaceutically acceptable excipient, which, as used herein, includes, but is not limited to, any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, and the like, as suited to the particular dosage form desired.
• a pharmaceutically acceptable excipient includes, but is not limited to, any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, and the like, as suited to the particular dosage form desired.
• excipients of the present disclosure can include, without limitation, liposomes, lipid nanoparticles, polymers, lipoplexes, core-shell nanoparticles, peptides, proteins, cells transfected with primary DNA construct, or RNA (e.g., for transplantation into a subject), hyaluronidase, nanoparticle mimics and combinations thereof.
• the pharmaceutical compositions described herein can include one or more excipients, each in an amount that together increases the stability of the nucleic acid in the lipid formulation, increases cell transfection by the nucleic acid, increases the expression of the encoded protein, and/or alters the release profile of encoded proteins.
• the RNA of the present disclosure may be formulated using self-assembled nucleic acid nanoparticles.
• excipients for formulating pharmaceutical compositions and techniques for preparing the composition are known in the art (see Remington: The Science and Practice of Pharmacy, 21st Edition, A. R. Gennaro, Lippincott, Williams & Wilkins, Baltimore, Md., 2006; incorporated herein by reference in its entirety).
• compositions of this disclosure may further contain as pharmaceutically acceptable carriers substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, and wetting agents, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, and mixtures thereof.
• pharmaceutically acceptable carriers substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, and wetting agents, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, and mixtures thereof.
• RNA-lipid formulation may be administered in a time release formulation, for example in a composition which includes a slow release polymer.
• the active agent can be prepared with carriers that will protect against rapid release, for example a controlled release vehicle such as a polymer, microencapsulated delivery system, or a bioadhesive gel. Prolonged delivery of the RNA, in various compositions of the disclosure can be brought about by including in the composition agents that delay absorption, for example, aluminum monostearate hydrogels and gelatin.
• immune responses induced using the methods provided herein include an antibody response, a cellular immune response, or both an antibody response and a cellular immune response.
• Methods of inducing an immune response provided herein include administering to a subject an effective amount of any RNA or DNA molecule, i.e., nucleic acid molecule, provided herein.
• methods of inducing an immune response include administering to a subject an effective amount of any composition comprising an RNA molecule and a lipid provided herein.
• methods of inducing an immune response include administering to a subject an effective amount of any pharmaceutical composition comprising an RNA molecule and a lipid formulation provided herein.
• RNA molecules, compositions, and pharmaceutical composition provided here are vaccines that can elicit a protective or a therapeutic immune response, for example.
• the term “subject” refers to any individual or patient on which the methods disclosed herein are performed.
• the term “subject” can be used interchangeably with the term “individual” or “patient.”
• the subject can be a human, although the subject may be an animal, as will be appreciated by those in the art.
• other animals including mammals such as rodents (including mice, rats, hamsters and guinea pigs), cats, dogs, rabbits, farm animals including cows, horses, goats, sheep, pigs, etc., and primates (including monkeys, chimpanzees, orangutans and gorillas) are included within the definition of subject.
• the term “effective amount” or “therapeutically effective amount” refers to that amount of an RNA molecule, composition, or pharmaceutical composition described herein that is sufficient to effect the intended application, including but not limited to inducing an immune response and/or disease treatment, as defined herein.
• the therapeutically effective amount may vary depending upon the intended application (e.g., inducing an immune response, treatment, application in vivo), or the subject or patient and disease condition being treated, e.g., the weight and age of the subject, the species, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
• the term also applies to a dose that will induce a particular response in a target cell.
• the specific dose will vary depending on the particular RNA molecule, composition, or pharmaceutical composition chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
• Exemplary doses of nucleic molecules that can be administered include about 0.01 ⁇ g, about 0.02 ⁇ g, about 0.03 ⁇ g, about 0.04 ⁇ g, about 0.05 ⁇ g, about 0.06 ⁇ g, about 0.07 ⁇ g, about 0.08 ⁇ g, about 0.09 ⁇ g, about 0.1 ⁇ g, about 0.2 ⁇ g, about 0.3 ⁇ g, about 0.4 ⁇ g, about 0.5 ⁇ g, about 0.6 ⁇ g, about 0.7 ⁇ g, about 0.8 ⁇ g, about 0.9 ⁇ g, about 1.0 ⁇ g, about 1.5 ⁇ g, about 2.0 ⁇ g, about 2.5 ⁇ g, about 3.0 ⁇ g, about 3.5 ⁇ g, about 4.0 ⁇ g, about 4.5 ⁇ g, about 5.0 ⁇ g, about 5.5 ⁇ g, about 6.0 ⁇ g, about 6.5 ⁇ g, about 7.0 ⁇ g, about 7.5 ⁇ g, about 8.0 ⁇ g, about 8.5 ⁇ g, about
• nucleic acid molecules are RNA molecules. In another aspect, the nucleic acid molecules are DNA molecules. Nucleic acid molecules can have a unit dosage comprising about 0.01 ⁇ g to about 1,000 ⁇ g or more nucleic acid in a single dose.
• compositions provided herein that can be administered include about 0.01 ⁇ g, about 0.02 ⁇ g, about 0.03 ⁇ g, about 0.04 ⁇ g, about 0.05 ⁇ g, about 0.06 ⁇ g, about 0.07 ⁇ g, about 0.08 ⁇ g, about 0.09 ⁇ g, about 0.1 ⁇ g, about 0.2 ⁇ g, about 0.3 ⁇ g, about 0.4 ⁇ g, about 0.5 ⁇ g, about 0.6 ⁇ g, about 0.7 ⁇ g, about 0.8 ⁇ g, about 0.9 ⁇ g, about 1.0 ⁇ g, about 1.5 ⁇ g, about 2.0 ⁇ g, about 2.5 ⁇ g, about 3.0 ⁇ g, about 3.5 ⁇ g, about 4.0 ⁇ g, about 4.5 ⁇ g, about 5.0 ⁇ g, about 5.5 ⁇ g, about 6.0 ⁇ g, about 6.5 ⁇ g, about 7.0 ⁇ g, about 7.5 ⁇ g, about 8.0 ⁇ g, about 8.5 ⁇ g, about
• compositions provided herein that can be administered include about 0.01 ⁇ g, about 0.02 ⁇ g, about 0.03 ⁇ g, about 0.04 ⁇ g, about 0.05 ⁇ g, about 0.06 ⁇ g, about 0.07 ⁇ g, about 0.08 ⁇ g, about 0.09 ⁇ g, about 0.1 ⁇ g, about 0.2 ⁇ g, about 0.3 ⁇ g, about 0.4 ⁇ g, about 0.5 ⁇ g, about 0.6 ⁇ g, about 0.7 ⁇ g, about 0.8 ⁇ g, about 0.9 ⁇ g, about 1.0 ⁇ g, about 1.5 ⁇ g, about 2.0 ⁇ g, about 2.5 ⁇ g, about 3.0 ⁇ g, about 3.5 ⁇ g, about 4.0 ⁇ g, about 4.5 ⁇ g, about 5.0 ⁇ g, about 5.5 ⁇ g, about 6.0 ⁇ g, about 6.5 ⁇ g, about 7.0 ⁇ g, about 7.5 ⁇ g, about 8.0 ⁇ g, about 8.5 ⁇ g, about 9.0 ⁇
• compositions provided herein can have a unit dosage comprising about 0.01 ⁇ g to about 1,000 ⁇ g or more nucleic acid and lipid in a single dose.
• pharmaceutical compositions provided herein can have a unit dosage comprising about 0.01 ⁇ g to about 1,000 ⁇ g or more nucleic acid and lipid formulation in a single dose.
• a vaccine unit dosage can correspond to the unit dosage of nucleic acid molecules, compositions, or pharmaceutical compositions provided herein and that can be administered to a subject.
• vaccine compositions of the instant disclosure have a unit dosage comprising about 0.01 ⁇ g to about 1,000 ⁇ g or more nucleic acid and lipid formulation in a single dose.
• vaccine compositions of the instant disclosure have a unit dosage comprising about 0.01 ⁇ g to about 50 ⁇ g nucleic acid and lipid formulation in a single dose. In yet another aspect, vaccine compositions of the instant disclosure have a unit dosage comprising about 0.2 ⁇ g to about 20 ⁇ g nucleic acid and lipid formulation in a single dose.
• a dosage form of the composition of this disclosure can be solid, which can be reconstituted in a liquid prior to administration.
• the solid can be administered as a powder.
• the solid can be in the form of a capsule, tablet, or gel.
• the pharmaceutical composition comprises a nucleic acid lipid formulation that has been lyophilized.
• the lyophilized composition may comprise one or more lyoprotectants, such as, including but not necessarily limited to, glucose, trehalose, sucrose, maltose, lactose, mannitol, inositol, hydroxypropyl-P-cyclodextrin, and/or polyethylene glycol.
• the lyophilized composition comprises a poloxamer, potassium sorbate, sucrose, or any combination thereof.
• the poloxamer is poloxamer 188.
• the lyophilized compositions described herein may comprise about 0.01 to about 1.0% w/w of a poloxamer.
• the lyophilized compositions described herein may comprise about 1.0 to about 5.0% w/w of potassium sorbate. The percentages may be any value or subvalue within the recited ranges, including endpoints. [00356]
• the lyophilized composition may comprise about 0.01 to about 1.0 % w/w of the nucleic acid molecule.
• the composition may comprise about 1.0 to about 5.0 % w/w lipids. In some embodiments, the composition may comprise about 0.5 to about 2.5 % w/w of TRIS buffer. In some embodiments, the composition may comprise about 0.75 to about 2.75 % w/w of NaCl. In some embodiments, the composition may comprise about 85 to about 95 % w/w of a sugar. The percentages may be any value or subvalue within the recited ranges, including endpoints.
• the dosage form of the pharmaceutical compositions described herein can be a liquid suspension of RNA lipid nanoparticles described herein.
• the RNA of RNA lipid nanoparticles is a self-replicating RNA.
• the RNA of RNA lipid nanoparticles is an mRNA.
• the liquid suspension is in a buffered solution.
• the buffered solution comprises a buffer selected from the group consisting of HEPES, MOPS, TES, and TRIS.
• the buffer has a pH of about 7.4.
• the buffer is HEPES.
• the buffered solution further comprises a cryoprotectant.
• the cryoprotectant is selected from a sugar and glycerol or a combination of a sugar and glycerol.
• the sugar is a dimeric sugar.
• the sugar is sucrose.
• the buffer comprises HEPES, sucrose, and glycerol at a pH of 7.4.
• the composition comprises a HEPES, MOPS, TES, or TRIS buffer at a pH of about 7.0 to about 8.5.
• the HEPES, MOPS, TES, or TRIS buffer may at a concentration ranging from 7 mg/ml to about 15 mg/ml. The pH or concentration may be any value or subvalue within the recited ranges, including endpoints.
• the suspension is frozen during storage and thawed prior to administration. In some embodiments, the suspension is frozen at a temperature below about 70 °C. In some embodiments, the suspension is diluted with sterile water during intravenous administration. In some embodiments, intravenous administration comprises diluting the suspension with about 2 volumes to about 6 volumes of sterile water.
• the suspension comprises about 0.1 mg to about 3.0 mg RNA/mL, about 15 mg/mL to about 25 mg/mL of an ionizable cationic lipid, about 0.5 mg/mL to about 2.5 mg/mL of a PEG-lipid, about 1.8 mg/mL to about 3.5 mg/mL of a helper lipid, about 4.5 mg/mL to about 7.5 mg/mL of a cholesterol, about 7 mg/mL to about 15 mg/mL of a buffer, about 2.0 mg/mL to about 4.0 mg/mL of NaCl, about 70 mg/mL to about 110 mg/mL of sucrose, and about 50 mg/mL to about 70 mg/mL of glycerol.
• a lyophilized RNA-lipid nanoparticle formulation can be resuspended in a buffer as described herein.
• compositions of the disclosure are administered to a subject such that a RNA concentration of at least about 0.05 mg/kg, at least about 0.1 mg/kg, at least about 0.5 mg/kg, at least about 1.0 mg/kg, at least about 2.0 mg/kg, at least about 3.0 mg/kg, at least about 4.0 mg/kg, at least about 5.0 mg/kg of body weight is administered in a single dose or as part of single treatment cycle.
• compositions of the disclosure are administered to a subject such that a total amount of at least about 0.1 mg, at least about 0.5 mg, at least about 1.0 mg, at least about 2.0 mg, at least about 3.0 mg, at least about 4.0 mg, at least about 5.0 mg, at least about 6.0 mg, at least about 7.0 mg, at least about 8.0 mg, at least about 9.0 mg, at least about 10 mg, at least about 15 mg, at least about 20 mg, at least about 25 mg, at least about 30 mg, at least about 35 mg, at least about 40 mg, at least about 45 mg, at least about 50 mg, at least about 55 mg, at least about 60 mg, at least about 65 mg, at least about 70 mg, at least about 75 mg, at least about 80 mg, at least about 85 mg, at least about 90 mg, at least about 95 mg, at least about 100 mg, at least about 105 mg, at least about 110 mg, at least about 115 mg, at least about 120 mg, or at least about 125 mg RNA is administered in one or more
• nucleic acid molecules i.e., RNA or DNA molecules, compositions, and pharmaceutical compositions provided herein are administered intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, by aerosol, or by a pulmonary route, such as by inhalation or by nebulization, for example.
• the pharmaceutical compositions described are administered systemically.
• Suitable routes of administration include, for example, oral, rectal, vaginal, transmucosal, pulmonary including intratracheal or inhaled, or intestinal administration; parenteral delivery, including intradermal, transdermal (topical), intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, or intranasal.
• the intramuscular administration is to a muscle selected from the group consisting of skeletal muscle, smooth muscle and cardiac muscle.
• the pharmaceutical composition is administered intravenously.
• compositions may be administered to any desired tissue.
• the RNA delivered is expressed in a tissue different from the tissue in which the lipid formulation or pharmaceutical composition was administered.
• RNA is delivered and expressed in the liver.
• nucleic acid molecules i.e., RNA or DNA molecules, compositions, and pharmaceutical compositions provided herein are administered intramuscularly.
• the subject in which an immune response is induced is a healthy subject.
• the term “healthy subject” refers to a subject not having a condition or disease, including an infectious disease or cancer, for example, or not having a condition or disease against which an immune response is induced.
• a nucleic acid molecule, composition, or pharmaceutical composition provided herein is administered prophylactically to prevent an infectious disease, for example.
• a nucleic acid molecule, composition, or pharmaceutical composition provided herein can also be administered therapeutically, i.e., to treat a condition or disease, such as an infection, after the onset of the condition or disease.
• the terms “treat,” “treatment,” “therapy,” “therapeutic,” and the like refer to obtaining a desired pharmacologic and/or physiologic effect, including, but not limited to, alleviating, delaying or slowing the progression, reducing the effects or symptoms, preventing onset, inhibiting, ameliorating the onset of a diseases or disorder, obtaining a beneficial or desired result with respect to a disease, disorder, or medical condition, such as a therapeutic benefit and/or a prophylactic benefit.
• Treatment includes any treatment of a disease in a mammal, particularly in a human, and includes: (a) preventing the disease from occurring in a subject, including a subject which is predisposed to the disease or at risk of acquiring the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease.
• a therapeutic benefit includes eradication or amelioration of the underlying disorder being treated.
• a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder.
• treatment or compositions for treatment including pharmaceutical compositions, are administered to a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
• the methods of the present disclosure may be used with any mammal or other animal.
• treatment results in a decrease or cessation of symptoms.
• a prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
• Nucleic acid molecules, i.e., RNA or DNA molecules, compositions, and pharmaceutical compositions provided herein can be administered once or multiple times. Accordingly, nucleic acid molecules, compositions, and pharmaceutical compositions provided herein can be administered one, two, three, four, five, six, seven, eight, nine, ten, or more times.
• Timing between two or more administrations can be one week, two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, weeks, ten weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, 45 weeks, 46 weeks, 47 weeks, 48 weeks, 49 weeks, 50 weeks, 51 weeks, 52 weeks, or more weeks, and any number or range in between.
• timing between two or more administrations is one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, 11 months, 12 months, 13 months, 14 months, 15 months, 16 months, 17 months, 18 months, 19 months, 20 months, 21 months, 22 months, 23 months, 24 months, or more months, and any number or range in between.
• timing between two or more administrations can be one year, two years, three years, four years, five years, six years, seven years, eight years, nine years, ten years, or more years, and any number or range in between, Timing between the first and any subsequent administration can be the same or different.
• nucleic acid molecules, compositions, or pharmaceutical compositions provided herein are administered once.
• nucleic acid molecule, composition, or pharmaceutical composition can be administered in the methods provided herein.
• two or more nucleic acid molecules, compositions, or pharmaceutical compositions provided herein are administered simultaneously.
• two or more nucleic acid molecules, compositions, or pharmaceutical compositions provided herein are administered sequentially.
• Simultaneous and sequential administrations can include any number and any combination of nucleic acid molecules, compositions, or pharmaceutical compositions provided herein.
• Multiple nucleic acid molecules, compositions, or pharmaceutical compositions that are administered together or sequentially can include transgenes encoding different antigenic proteins or fragments thereof. In this manner, immune responses against different antigenic targets can be induced.
• nucleic acid molecules, compositions, or pharmaceutical compositions including transgenes encoding different antigenic proteins or fragments thereof can be administered simultaneously or sequentially. Any combination of nucleic acid molecules, compositions, and pharmaceutical compositions including any combination of transgenes can be administered simultaneously or sequentially. In some aspects, administration is simultaneous. In other aspects, administration is sequential.
• Timing between two or more administrations can be one week, two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, weeks, ten weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, 45 weeks, 46 weeks, 47 weeks, 48 weeks, 49 weeks, 50 weeks, 51 weeks, 52 weeks, or more weeks, and any number or range in between.
• timing between two or more administrations is one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, 11 months, 12 months, 13 months, 14 months, 15 months, months, 16 months, 17 months, 18 months, 19 months, 20 months, 21 months, 22 months, 23 months, 24 months, or more months, and any number or range in between.
• timing between two or more administrations can be one year, two years, three years, four years, five years, six years, seven years, eight years, nine years, ten years, or more years, and any number or range in between, Timing between the first and any subsequent administration can be the same or different.
• Nucleic acid molecules, compositions, and pharmaceutical compositions provided herein can be administered with any other vaccine or treatment.
• the protein product encoded by the RNA of the disclosure e.g., an antigen
• the amount of protein product necessary to achieve a therapeutic effect will vary depending on antibody titer necessary to generate an immunity to pathogen or disease such as COVID-19 in the patient.
• the protein product may be detectable in the target tissues at a concentration (e.g., a therapeutic concentration) of at least about 0.025-1.5 ⁇ g/ml (e.g., at least about 0.050 ⁇ g/ml, at least about 0.075 ⁇ g/ml, at least about 0.1 ⁇ g/ml, at least about 0.2 ⁇ g/ml, at least about 0.3 ⁇ g/ml, at least about 0.4 ⁇ g/ml, at least about 0.5 ⁇ g/ml, at least about 0.6 ⁇ g/ml, at least about 0.7 ⁇ g/ml, at least about 0.8 ⁇ g/ml, at least about 0.9 ⁇ g/ml, at least about 1.0 ⁇ g/ml, at least about 1.1 ⁇ g/ml, at least about 1.2 ⁇ g/ml, at least about 1.3 ⁇ g/ml, at least about 1.4 ⁇ g/ml, or at least about 1.5 ⁇ g/ml (e
• the composition described herein may be administered one time. In some embodiments, the composition described herein may be administered two times. [00369] In some embodiments, the composition may be administered in the form of a booster dose, to a subject who was previously vaccinated against coronavirus.
• a pharmaceutical composition of the present disclosure is administered to a subject once per month. In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject twice per month. In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject three times per month. In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject four times per month.
• compositions of the present disclosure may be administered in a local rather than systemic manner, for example, via injection of the pharmaceutical composition directly into a targeted tissue, preferably in a depot or sustained release formulation.
• Local delivery can be affected in various ways, depending on the tissue to be targeted.
• compositions of the present disclosure can be inhaled (for nasal, tracheal, or bronchial delivery); compositions of the present disclosure can be injected into the site of injury, disease manifestation, or pain, for example; compositions can be provided in lozenges for oral, tracheal, or esophageal application; can be supplied in liquid, tablet or capsule form for administration to the stomach or intestines, can be supplied in suppository form for rectal or vaginal application; or can even be delivered to the eye by use of creams, drops, or even injection.
• Formulations containing compositions of the present disclosure complexed with therapeutic molecules or ligands can even be surgically administered, for example in association with a polymer or other structure or substance that can allow the compositions to diffuse from the site of implantation to surrounding cells. Alternatively, they can be applied surgically without the use of polymers or supports.
• RNA such as a self-replicating RNA or mRNA provided herein, formulations thereof, or encoded proteins described herein may be used in combination with one or more other therapeutic, prophylactic, diagnostic, or imaging agents.
• combination with it is not intended to imply that the agents must be administered at the same time and/or formulated for delivery together, although these methods of delivery are within the scope of the present disclosure.
• Compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent.
• the methods of treatment of the present disclosure encompass the delivery of pharmaceutical, prophylactic, diagnostic, or imaging compositions in combination with agents that may improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body.
• an RNA molecule of the disclosure may be used in combination with a pharmaceutical agent for immunizing or vaccinating a subject.
• agents utilized in combination with the presently disclosed RNA molecules and formulations thereof be utilized at levels that do not exceed the levels at which they are utilized individually.
• the levels utilized in combination will be lower than those utilized individually.
• the combinations, each or together may be administered according to the split dosing regimens as are known in the art.
• range format any description in range format is merely for convenience and brevity and not meant to be limiting. Accordingly, the description of a range should be considered to have specifically disclosed all 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, 2.1, 2.2, 2.5, 3, 4, 4.75, 4.8, 4.85, 4.95, 5, 5.5, 5.75, 5.9, 5.00, and 6. This applies to a range of any breadth.
• FIG. 1 shows a schematic of an exemplary self- replicating RNA (not to scale) of approximately 11,860 kb.
• RNA vaccines designed for the studies described herein are typically single-stranded molecules that include a 5’ cap, a 5’ untranslated region (UTR), an open reading frame encoding the replicase polyprotein derived from Venezuela Equine Encephalitis Virus (VEEV) that includes the nsPl, nsP2, nsP3, and nsP4 proteins, a transgene 5’ UTR located in the intergenic region that also includes a part of the subgenomic promoter sequence in the negative orientation, an open reading frame of a transgene encoding the primary structure of an antigenic protein, a 3’ UTR, and a poly A tail.
• VEEV Venezuela Equine Encephalitis Virus
• the relative location of the open reading frames encoding the replicase polyprotein and a transgene, such as a SARS-CoV-2 spike glycoprotein, are shown ( Figure 1 A).
• the SARS-CoV-2 spike glycoprotein is divided into two domains, SI and S2.
• the ACE2 receptor binding domain is located within the SI domain.
• the S2 domain includes an intracellular fusion domain, a transmembrane domain, and a cytoplasmic domain.
• Self- replicating RNA vaccines are generally made from naturally occurring unmodified RNA bases: adenine, guanine, cytosine, and uracil.
• the 5’ cap of self-replicating RNA vaccines designed as described herein typically has a Capl structure (CAPl, m7G(5’)pppA(2’-OMe)pU, with U in RNA denoted as T in DNA and vice versa).
• sequences encoding the SARS-CoV-2 glycoprotein transgene included codon changes that result in prolines at positions 986 and 987 (K986P and V987P mutations), stabilizing the SARS-CoV-2 glycoprotein in a prefusion conformation and increasing immunogenicity of the SI receptor binding domain (Baden, et al., 2021, N Engl J Med 384:403- 416 & Polack, et al., 2020, N Engl J Med 383:2603-2615; Keech, et al., 2020, N Engl J Med, 383:2320-2332).
• Furin cleavage sites of SARS-CoV-2 glycoproteins were inactivated by including R682G, R683S, and R685S mutations, thereby changing the RRAR motif at the S1/S2 cleavage junction to GSAS (Wrapp, et al. 2020, Science, 367: 1260-1263).
• the RRAR motif can also be changed to RRAG or GRAR to inactivate furin cleavage.
• Transgene sequences encoding variant SARS-CoV-2 spike glycoproteins included in self-replicating RNA vaccines were as follows: SEQ ID NO: 10, encoding South Africa variant B.1.351 (Beta); SEQ ID NO: 11, encoding a SARS-CoV-2 spike glycoprotein having a D614G mutation (B.1); SEQ ID NO: 12, encoding U.K. variant B.l.1.7 (Alpha); SEQ ID NO: 13, encoding Brazil variant PI (Gamma).
• Self-replicating RNA vaccines included codon-optimized nsPl, nsP2, nsP3, and nsP4 (z ' .e., replicase) and codon-optimized transgene sequences. Codon-optimized replicase and transgene sequences were included in self-replicating RNA vaccines to increase the amount and duration of SARS-CoV-2 glycoprotein expression by increasing translation without changing the encoded amino acid sequences. For example, a sequence of SEQ ID NO:6 was obtained using an hCAI algorithm with an input sequence of SEQ ID NO:20 (nucleotides 463-7455), resulting in an intermediate sequence of SEQ ID NO: 185.
• the sequences of skeletal muscle and dendritic cell miRNA binding sites corresponding to SEQ ID NOs.:54-184 were entered into miRanda to identify putative miRNA binding sites in a self-replicating RNA target sequence that included codon- optimized nsPl, nsP2, nsP3, and nsP4 (z ' .e., replicase) sequences and a luciferase transgene (SEQ ID NO: 186). 15 putative miRNA binding sites representing targets for miRNAs in mouse and human dendritic cells and mouse and human skeletal muscle were identified (Figure IB, Table 6).
• nsPl, nsP2, nsP3, and nsP4 regions identified using miRanda are shown in Table 7. The relative positions of putative miRNA binding sites are provided, with nucleotide numbering of nsPl, nsP2, nsP3, and nsP4 serving as a reference.
• Table 7 Putative miRNA binding sites in the VEEV non-structural protein coding region.
• Symbols *, #, L , and $ indicate identical nucleotide positions for miRNAs within each of the non- structural coding sequences encoding nsPl, nsP2, nsP3, and nsP4
• Identified seed sequences of putative miRNA target sites were manually mutated in silico to synonymous codons to eliminate or reduce miRNA binding. Elimination of miRNA binding sites was confirmed using miRanda. Without being limited by theory, mutation of miRNA binding sites to eliminate or reduce miRNA binding based on predictions using miRanda should result in increased expression of sequences encoding VEEV non- structural proteins. Codon-optimized sequences encoding SARS-CoV-2 spike glycoprotein and its variants were introduced into self-replicating RNA backbones having codon-optimized nsPl- 4 sequences and mutated miRNA binding sites.
• nsPl-nsP4 coding region of self-replicating RNAs Exemplary mutations of putative miRNA binding sites in the nsPl-nsP4 coding region of self-replicating RNAs are summarized in Table 8. Mutations made in 15 putative miRNA binding sites identified in the VEEV nsPl, nsP2, nsP3, and nsP4 regions are shown. The relative positions of putative miRNA binding sites are provided, with nucleotide numbering of nsPl, nsP2, nsP3, and nsP4 serving as a reference and point mutations shown below putative miRNAs and their positions in bold italics.
• Table 8 Exemplary mutations of putative miRNA binding sites in the VEEV nsPl, nsP2, nsP3, and nsP4 regions.
• Table 9 Exemplary features of self-replicating RNA vaccines.
• Table 10 summarizes features of self-replicating RNA constructs encoding SARS- CoV-2 South Africa and D614G spike glycoprotein variants.
• Table 10 Features of self-replicating RNA constructs encoding SARS-CoV-2 South Africa and D614G spike glycoprotein variants.
• the codon optimization method reduces the number of uridines in the RNA transcript. Without being limited by theory, the purpose is to reduce innate immune activation and increase translation efficiency of open reading frames while maintaining a high level of antigen expression. These RNA sequence changes by the optimization method do not alter the amino acid sequence of the replicon or antigen upon translation of the RNA transcript.
• RNA vaccines encoding SARS-CoV-2 South Africa and D614G spike glycoprotein variants (e.g ., SEQ ID NO:l and SEQ ID NO:2, respectively, for the full-length self-replicating RNA sequence, with U in RNA shown as T in DNA and vice versa)
• self-replicating RNA vaccines encoding SARS-CoV-2 UK B. E 1.7 and Brazil P.1 spike glycoprotein variants were designed (SEQ ID NO:3 and SEQ ID NO:4, respectively, for the full-length self-replicating RNA sequence, with U in RNA shown as T in DNA and vice versa).
• Sequences of construct features such as 5’ UTR, 3’ UTR, and transgene sequences, are provided below in addition to full-length construct sequences.
• mRNA vaccines that encode an antigenic protein such as a SARS-CoV-2 spike glycoprotein or another viral glycoprotein were also designed.
• mRNA vaccines typically include a 5’ UTR, an open reading frame encoding an antigenic protein, a 3’ UTR, and a poly- A tail.
• Other sequence elements of mRNA vaccines generally include a Kozak sequence and translational enhancers located in untranslated regions, either the 5’ UTR, the 3’ UTR, or both.
• mRNA vaccines encoding SARS-CoV-2 South Africa and D614G spike glycoprotein variants were designed and constructed (SEQ ID NO:29 and SEQ ID NO:32, respectively, for the full-length mRNA sequences, with U in RNA shown as T in DNA and vice versa).
• mRNA constructs included a 5’ TEV UTR (SEQ ID NO:35) and a 3’ Xenopus beta-globin (Xbg) UTR (SEQ ID NO:36 with poly-A tail; SEQ ID NO:37 without poly-A tail).
• Self-replicating RNA and mRNA vaccines encoding any SARS-CoV-2 spike glycoprotein variant, any SARS-CoV-2 spike glycoprotein having any mutation or any combination of mutations, or any other viral glycoprotein can be designed and constructed similar to the constructs described above.
• SARS-CoV-2 spike glycoprotein variants, SARS- CoV-2 spike glycoproteins having a mutation or a combination of mutations, or any other viral glycoproteins can be included in self-replicating RNA and mRNA vaccines having a backbone that includes any combination of the features described above.
• Exemplary SARS-CoV-2 spike glycoprotein variants and SARS-CoV-2 spike glycoprotein mutations that can be encoded are shown in Table 11.
• RNA molecules that encode a hemagglutinin (HA) of influenza virus were designed and prepared, including a self-replicating RNA having a sequence of SEQ ID NO:40 and an mRNA having a sequence of SEQ ID NO:48.
• This example describes expression and potency of SARS-CoV-2 RNA vaccine constructs.
• RNAs designated with a suffix of “.1” were synthesized in the presence of N 1 - methylpseudouridine (N1MPU), resulting in 100% of the uridines being N1MPU, while RNAs designated with a suffix of “.5” did not include modified nucleotides, unless otherwise indicated.
• Cells were harvested by scraping into buffer that included 10 mM PBS and 50 mM EDTA or by trypsinization. Total protein was isolated and protein concentration determined by BCA assay performed in duplicate, with duplicates yielding comparable results. Proteins were separated by polyacrylamide gel electrophoresis and transferred to membranes at 45 V for 1.5 hours for Western blotting using an antibody detecting the SARS-CoV-2 spike glycoprotein.
• Total protein was comparable for cells transfected with SARS-CoV-2 vaccine constructs encoding either a SARS-CoV-2 Wuhan spike glycoprotein or a SARS-CoV-2 D614G spike glycoprotein variant. Similar banding patterns were observed for the self- replicating RNA vaccine construct expressing the SARS-CoV-2 Wuhan spike glycoprotein for cells harvested with or without trypsinization, with bands corresponding to full-length spike and SI and S2 domains ( Figure 2A, arrows). By contrast, bands corresponding to SI and S2 were observed for protein extracts prepared from cells harvested by trypsinization that were not observed for protein extracts prepared from cells without trypsinization ( Figure 2A) for the SARS-CoV-2 D614G spike glycoprotein variant.
• Figure 2B shows quantitation of SARS-CoV-2 spike protein expressed from the indicated construct based on SI signal using protein extracts prepared from cells that were transfected as described above and harvested without trypsinization. Comparable levels of SARS-CoV-2 spike protein was seen for the constructs expressing the SARS-CoV-2 Wuhan glycoprotein or D614G spike glycoprotein variant.
• RNA vaccines encoding SARS-CoV-2 spike glycoprotein variants in mice.
• RNA constructs encoding SARS-CoV-2 spike glycoprotein variants
• mice were administered the indicated RNA as shown in Table 16.
• Serum was obtained at day 0 (pre-bleed) and at days 14, 28, 42 and 56 after the first immunization. Serum was probed simultaneously for responses to four SARS-CoV-2 spike glycoprotein variants: SARS-CoV-2 spike (Wuhan, wild-type), SARS-CoV-2 spike (P.1, Brazil, Gamma), SARS-CoV-2 spike (B.1.351, South Africa, Beta) and SARS-CoV-2 spike (B.l.1.7, UK, Alpha).
• SARS-CoV-2 spike Wuhan, wild-type
• SARS-CoV-2 spike P.1, Brazil, Gamma
• SARS-CoV-2 spike B.1.351, South Africa, Beta
• SARS-CoV-2 spike B.l.1.7, UK, Alpha
• V-PLEX SARS-CoV-2 Panel 5 IgG and ACE2 Kits from MSD Cat# K15429U and K15432U were used for measuring serum IgG antibody levels.
• Neutralizing antibody levels upon immunization with mRNA encoding SARS-CoV-2 D614G spike glycoprotein were likewise greater as compared to neutralizing antibody levels seen upon immunization with self-replicating RNA encoding wild-type (Wuhan) SARS-CoV-2 spike glycoprotein (Figure 5B; Figures 6C-D).
• mice with self-replicating RNA or mRNA encoding SARS-CoV-2 variant D614G or variant South Africa spike glycoproteins elicits effective humoral immune responses, including neutralizing antibodies that were effective against wild-type and numerous SARS-CoV-2 variant glycoproteins.
• This example describes immunogenicity of RNA vaccines encoding SARS-CoV-2 spike glycoprotein variants in non-human primates (NHPs).
• RNA constructs encoding SARS-CoV-2 spike glycoprotein variants in NHPs were administered as shown in Table 17. Table 17. Administration of RNA Vaccines to NHPs.
• Serum was obtained at day 0 (pre-bleed) and at days 15, 29, and 43 after the first immunization. Serum was probed simultaneously for responses to four SARS-CoV-2 spike glycoprotein variants: SARS-CoV-2 spike (Wuhan, wild-type), SARS-CoV-2 spike (P.1, Brazil, Gamma), SARS-CoV-2 spike (B.1.351, South Africa, Beta) and SARS-CoV-2 spike (B.l.1.7, UK, Alpha).
• SARS-CoV-2 spike Wuhan, wild-type
• SARS-CoV-2 spike P.1, Brazil, Gamma
• SARS-CoV-2 spike B.1.351, South Africa, Beta
• SARS-CoV-2 spike B.l.1.7, UK, Alpha
• V-PLEX SARS-CoV-2 Panel 5 IgG and ACE2 Kits from MSD Cat# K15429U and K15432U were used for measuring serum IgG antibody levels.
• Neutralizing antibody levels upon immunization with mRNA encoding SARS-CoV-2 D614G spike glycoprotein were likewise greater as compared to neutralizing antibody levels seen upon immunization with self-replicating RNA encoding wild- type (Wuhan) SARS-CoV-2 spike glycoprotein ( Figure 7B; Figure 7H).
• These results show that immunization of NHPs with self-replicating RNA or mRNA encoding SARS-CoV-2 variant D614G or variant South Africa spike glycoproteins elicits effective humoral immune responses, including neutralizing antibodies that were effective against wild-type and numerous SARS-CoV-2 variant glycoproteins.
• This example describes immunogenicity of influenza hemagglutinin (HA) expressed from self-replicating RNA or mRNA.
• RNA and mRNA vaccine constructs were designed to encode the full-length hemagglutinin (HA) protein from influenza virus A/California/07/2009 (H1N1) (HA amino acid sequence: SEQ ID NOs: 47 and 53 for self-replicating RNA and mRNA, respectively; nucleic acid sequence: SEQ ID NOs: 46 and 52 for self-replicating RNA and mRNA, respectively).
• H1N1 hemagglutinin
• the mRNA vaccine construct encoding HA included a tobacco etch virus (TEV) 5’ UTR (SEQ ID NO:49) and a Xenopus beta-globin (Xbg) 3’ UTR (SEQ ID NO:50 (without poly-A tail); SEQ ID NO:52 (with poly- A tail)).
• TSV tobacco etch virus
• Xbg Xenopus beta-globin
• SEQ ID NO:50 without poly-A tail
• SEQ ID NO:52 with poly- A tail
• HAI hemagglutination inhibition
• Results in Figure 8 show that protective HAI titers were obtained with self- replicating RNA and mRNA encoding HA.
• HAI titers for the self-replicating RNA construct encoding HA were greater than HAI titers for the mRNA encoding HA at all time points.
• protective HAI titers were seen for the self-replicating RNA construct encoding HA beginning at day 14 that were maintained at least until day 56.
• mRNA encoding HA showed protective HAI titers at day 56.
• lipid nanoparticle compositions that were manufactured according to well-known processes, for example, those described in U.S. App. No. 16/823,212, the contents of which are incorporated by reference for the specific purpose of teaching lipid nanoparticle manufacturing processes.
• the lipid nanoparticle compositions and the lyophilized products were characterized for several properties. The materials and methods for these characterization processes as well as a general method of manufacturing the lipid nanoparticle compositions that were used for lyophilization experiments are provided in this example.
• Lipid nanoparticle formulations used in this example were manufactured by mixing lipids (ionizable cationic lipid (ATX-126): helper lipid: cholesterol: PEG-lipid) in ethanol with RNA dissolved in citrate buffer. The mixed material was instantaneously diluted with Phosphate Buffer. Ethanol was removed by dialysis against phosphate buffer using regenerated cellulose membrane (100 kD MWCO) or by tangential flow filtration (TFF) using modified polyethersulfone (mPES) hollow fiber membranes (100 kD MWCO).
• lipids ionizable cationic lipid (ATX-126): helper lipid: cholesterol: PEG-lipid
• the mixed material was instantaneously diluted with Phosphate Buffer. Ethanol was removed by dialysis against phosphate buffer using regenerated cellulose membrane (100 kD MWCO) or by tangential flow filtration (TFF) using modified polyethersulfone (mPE
• HEPES 4-(2-hydroxyethyl)-l- piperazineethanesulfonic acid
• 10-300 for example, 40-60
• the formulation was concentrated followed by 0.2 pm filtration using PES filters.
• the RNA concentration in the formulation was then measured by RiboGreen fluorimetric assay, and the concentration was adjusted to a final desired concentration by diluting with HEPES buffer containing 10-100 (for example 40-60) mM NaCl, 0-15% sucrose, pH 7.2-8.5 containing glycerol.
• the final formulation was then filtered through a 0.2 pm filter and filled into glass vials, stoppered, capped and placed at -70 ⁇ 5 °C.
• the lipid nanoparticles formulations were characterized for their pH and osmolality. Lipid content and RNA content were measured by high performance liquid chromatography (HPLC), and mRNA integrity by was measured by fragment analyzer. Dynamic Light Scattering
• the average particle size (z) and polydispersity index (PDI) of lipid nanoparticle formulations used in the Examples was measured by dynamic light scattering on a Malvern Zetasizer Nano ZS (United Kingdom).
• RiboGreen is a proprietary fluorescent dye (Molecular Probes/Invitrogen a division of Life Technologies, now part of Thermo Fisher Scientific of Eugene, Oregon, United States) that is used in the detection and quantification of nucleic acids, including both RNA and DNA. In its free form, RiboGreen exhibits little fluorescence and possesses a negligible absorbance signature. When bound to nucleic acids, the dye fluoresces with an intensity that is several orders of magnitude greater than the unbound form. The fluorescence can then be detected by a sensor (fluorimeter) and the nucleic acid can be quantified.
• Self-Replicating RNAs are typically larger than the average mRNA, and tests were designed to determine whether self-replicating RNA lipid nanoparticle formulations could be successfully lyophilized.
• the quality of lyophilized lipid nanoparticle formulations was assessed by analyzing the formulations post-lyophilization and comparing this to the lipid nanoparticle formulation prior to lyophilization as well as after a conventional freeze/thaw cycle (i.e., frozen at ⁇ -70 °C then allowed to thaw at room temperature).
• the analysis of the lipid nanoparticle formulations included the analysis of particle size and polydispersity (PDI) and encapsulation efficiency (%Encap).
• the particle size post- lyophilization was compared to the particle size pre-lyophilization and the difference can be reported as a delta (d).
• the various compositions tested were screened as to whether a threshold of properties was met including minimal particle size increase (d ⁇ 10 nm), the maintenance of PDI ( ⁇ 0.2), and maintenance of high encapsulation efficiency (> 85%).
• the lipid nanoparticle formulations were prepared as described above, with self- replicating RNA (SEQ ID NO: 18).
• the resulting lipid nanoparticle formulation was then processed with a buffer exchange to form a prelyophilization suspension having a concentration of 0.05 to 2.0 mg/mL self-replicating RNA, 0.01 to 0.05 M potassium sorbate, 0.01 to 0.10 % w/v Poloxamer 188 (Kolliphor®), 14 to 18% w/v sucrose, 25 to 75 mM NaCl, and 15 to 25 mM pH 8.0 Tris buffer.
• the prelyophilization formulation was then lyophilized in a Millrock Revo Freeze Dryer (Model No. RV85S4), using aliquots of 2.0 mL of suspension and the lyophilization cycle provided in Table 18 below.
• lyophilized particles prepared following the methods described above were reconstituted in 2 mL of water and characterized using DLS and RiboGreen.
• the results provided in Table 19 below show that the lyophilized compositions were found to produce lyophilized lipid nanoparticle formulations with adequate size, polydispersity, and delta values ( ⁇ 5.3 nm) upon reconstitution.
• Any self-replicating RNA and any mRNA can be prepared as a lyophilized formulation using the processes described above, including any self-replicating RNA and any mRNA delivering antigenic proteins provided herein. Furthermore, lyophilized formulations can be administered to induce immune responses to encoded antigenic proteins, such as SARS- CoV-2 spike glycoproteins and variants thereof.
• This example describes immunogenicity of liquid and lyophilized self-replicating RNA formulations.
• Test formulations were administered intramuscularly (IM) and serum was collected at various timepoints (Days 10, 19, 31 for the first study and Days 10, 20, 30 for the second study) post-immunization to measure the production of anti-SARS-CoV-2 spike protein IgG using a Luminex bead fluorescent assay.
• the liquid and lyophilized formulations of a self-replicating RNA vaccine showed comparable immunogenicity.
• the vaccine can induce effective, adaptive humoral (neutralizing antibodies) and cellular (CD8+) immune responses targeting the SARS-CoV-2 spike (S) glycoprotein.
• the vaccine also elicited induction of antispike glycoprotein antibodies (IgG) levels that were higher than those seen for a conventional mRNA vaccine and induced production of IgG antibodies at a faster rate than a conventional mRNA vaccine. It continued to elicit increasing levels of IgG up to 50 days post vaccination whereas the conventional mRNA vaccine plateaued by day 10 post vaccination. It produced an RNA dose-dependent increase in CD8+ T lymphocytes and a balanced, Thl dominant CD4+ T helper cell immune response with no skew towards a Th2 response.
• AGGAC ATCCC AAT GGAC AGGTTCGT GAT GGACCTGAAGAGGGACGT GAAGGT GA
• CTGAAC AT GCTGC AGGAC ATCCC AAT GGAC AGGTTCGT GAT GGACCTGAAGAGG

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