Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N15/86—Viral vectors
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
  • A61K31/52—Purines, e.g. adenine
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
  • A61K35/66—Microorganisms or materials therefrom
  • A61K35/76—Viruses; Subviral particles; Bacteriophages
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • A61K48/0008—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'non-active' part of the composition delivered, e.g. wherein such 'non-active' part is not delivered simultaneously with the 'active' part of the composition
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/10—Type of nucleic acid
  • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
  • C12N2310/141—MicroRNAs, miRNAs
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
  • C12N2750/00011—Details
  • C12N2750/14011—Parvoviridae
  • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
  • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
  • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
  • C12N2750/00011—Details
  • C12N2750/14011—Parvoviridae
  • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
  • C12N2750/14151—Methods of production or purification of viral material
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2800/00—Nucleic acids vectors
  • C12N2800/10—Plasmid DNA
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2830/00—Vector systems having a special element relevant for transcription
  • C12N2830/50—Vector systems having a special element relevant for transcription regulating RNA stability, not being an intron, e.g. poly A signal

Definitions

• This invention is directed to methods and compositions for inhibition of an innate immune response associated with AAV transduction.
• Adeno-associated virus (AAV) vectors have been successfully applied in clinical trials in patients with hemophilia and blindness disorders.
• FIX AAV vector encoding factor IX
• FIX AAV vector encoding factor IX
• AAV is a single-stranded DNA virus. Its genome comprises the rep and cap sequences flanked by two inverted terminal repeats (ITR). Replacement of the rep and the cap genes with a therapeutic cassette (comprising a promoter, one or more therapeutic transgene and a poly(A) (“pA”) tail) results in an AAV vector construct.
• the AAV ITR has been shown to have a promoter function, which implicates that the plus strand RNA transcribed from the 5’ ITR and the minus strand RNA transcribed from the 3’ ITR could be generated in AAV transduced cells.
• MDA5 and RIG-I are cytoplasmic viral RNA sensors capable of activating type I interferon signaling pathways after virus infection, so they play a critical role in antiviral innate immunity.
• MDA5 and RIG-I share high sequence similarity and a common signaling adaptor, mitochondrial antiviral signaling (MAVS), but they play non-redundant functions in antiviral immunity by recognizing different viruses or viral RNA.
• RIG-I recognizes 5'- triphosphorylated (PPP) blunt-ended double-stranded RNA (dsRNA) or single-stranded RNA hairpins that are often present in a variety of positive and negative strand viruses.
• MDA5 recognizes relatively long dsRNA in the genome of dsRNA viruses or dsRNA replication intermediates of positive-strand viruses, such as encephalomyocarditis virus (EMCV) and poliovirus.
• EMCV encephalomyocarditis virus
• the present invention overcomes previous shortcomings in the art by providing compositions and methods of their use in inhibiting an innate immune response associated with AAV transduction in a subject.
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) 5’ inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the recombinant nucleic acid molecule further comprises: a) a poly(A) (pA) sequence downstream of the 5’ ITR and upstream of the promoter, in 3’ to 5’ orientation and a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; b) a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; c) a first pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation and a second pA sequence downstream of the first pA sequence and upstream of the 3’ ITR, in a 5’
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) vector cassette of a first AAV serotype, comprising an AAV 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the recombinant nucleic acid molecule comprises an AAV 5’ ITR and/or an AAV 3’ ITR from a second AAV serotype that is different than the first AAV serotype and replaces the 5’ ITR and/or 3’ ITR of the first AAV serotype and in particular embodiments, wherein the ITR of second AAV serotype has no promoter function or reduced promoter function as compared with the promoter function of the ITR of the first AAV serotype.
• AAV adeno-associated virus
• ITR AAV 5' inverted terminal repeat
• NOI nucleotide sequence of interest
• the first AAV serotype can be any AAV serotype now known or later identified and the second AAV serotype that is different that the first AAV serotype can be any AAV serotype now known or later identified.
• the first AAV serotype is AAV2 and the ITR of the second AAV serotype is AAV5.
• the recombinant nucleic acid molecule can comprise an AAV vector cassette of AAV2, said cassette of AAV2 comprising a 5’ and/or 3’ ITR of AAV5.
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the 5’ ITR and/or the 3’ ITR that is modified (e.g., by substitution, insertion and/or deletion) to diminish or eliminate promoter activity from the 5’ ITR and/or the 3’ ITR.
• AAV adeno-associated virus
• ITR inverted terminal repeat
• NOI nucleotide sequence of interest
• the present invention provides a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, an NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR, wherein the NOI sequence is fused with (e.g., in frame with; upstream and/or downstream of) one or more than one nucleotide sequence that encodes an interfering RNA sequence that targets one or more than one cytoplasmic dsRNA sensor.
• the present invention provides A) a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, an NOI operably associated with a first promoter, a first pA sequence in 3’ to 5’ orientation, a nucleotide sequence that encodes an interfering RNA sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, a second pA sequence and an AAV 3’ ITR; B) A recombinant nucleic acid molecule, comprising an AAV 5’ ITR, a NOI operably associated with a first promoter, a pA sequence in 3’ to 5’ orientation, a short hairpin RNA (shRNA) sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, and an AAV 3’ ITR; C) a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, a shRNA that targets a
• composition comprising a first recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR and a second recombinant nucleic acid molecule comprising an interfering RNA sequence that targets a cytoplasmic dsRNA sensor.
• Nonlimiting examples of a cytoplasmic dsRNA of this invention include MDA5, MAVS, RIG-l, TRAF6, TRAF5, RIP1, FADD, IRF, TRAF3, NAP1, TBK1, IKK, IKB,
• Nonlimiting examples of an interfering RNA (RNAi) of this invention include small interfering RNA (siRNA), short hairpin RNA (shRNA), microRNA (miRNA), long double stranded RNA (long dsRNA), antisense RNA, ribozymes, etc., as are known in the art, as well as any other interfering RNA or inhibitory RNA now known or later identified.
• siRNA small interfering RNA
• shRNA short hairpin RNA
• miRNA microRNA
• long stranded RNA long stranded RNA
• antisense RNA ribozymes
• the present invention further provides a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, an NOI and an inhibitor of MAVS signaling, both operably associated with a promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR.
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a first promoter, a first pA sequence in 3’ to 5’ orientation, an inhibitor of MAVS signaling operably associated with a second promoter, a second pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR.
• the present invention provides a composition comprising a first recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR and a second recombinant nucleic acid molecule comprising an inhibitor of MAVS signaling and a pA sequence in 3’ to 5’ orientation.
• Nonlimiting examples of an inhibitor of MAVS signaling include a serine protease NS3-4A from hepatitis C virus, proteases from Hepatitis A virus and GB virus B, and hepatitis B virus (HBV) X protein, poly(rC)-binding protein 2, the 20S proteasomal subunit PSMA7, and mitofusin 2, as well as any other inhibitor of MAVS signaling now known or later identified.
• a serine protease NS3-4A from hepatitis C virus proteases from Hepatitis A virus and GB virus B
• HBV hepatitis B virus
• a method is also provided herein, of enhancing transduction of an AAV vector in cells of a subject, comprising administering to the subject an AAV vector and an agent that interferes with dsRNA activation pathways in cells of the subject.
• Nonlimiting examples of an agent that interferes with dsRNA activation pathways include 2-aminopurine, a steroid (e.g., hydrocortisone as shown in Figures 28 and 29), and any other agent that interferes with dsRNA activation pathways in a cell as now known or later identified.
• the AAV vector and the agent(s) of this invention can be administered to the subject simultaneously and/or subsequently, in any order and in any time interval (e.g., hours, days, weeks, etc.)
• Figures 1A and IB show IFN-b inhibited AAV transgene expression in the HeLa cell line.
• HeLa cells were transduced with 5xl0 3 particles of AAV2/luciferase per cell.
• IB Recombinant human IFN-b was added to the medium every day at 0.5ng/mL.
• Transgene expression was detected by luciferase assay at dayl, 2, 4 and 6. *** p ⁇ 0.00J when compared to no IFN-b treatment.
• Figure 2 shows Poly(I:C) inhibited AAV transgene expression in cell lines.
• HeLa or Huh7 cells were transduced with 5x10 3 particles of AAV2/luciferase per cell. 2pg/mL poly(I:C) was added at different time points: l8h before AAV transduction, day 0 or day 3. Luciferase expression was detected 3 days after poly(I:C) transfection.
• Figures 3A-3E show that the dsRNA immune response is activated at a later time point after AAV transduction.
• HeLa cells were transduced with 5xl0 3 particles of
• MDA5 3 A
• RIG-I 3B
• IFN-b 3C
• the data represents the average and standard deviation from 3 experiments.
• PBS or AAV infected group contain 2 or 3 wells of cells.
• Q-PCR data analysis one sample from PBS group was normalized to 1 in each timepoint of each experiment.
• MDA5 expression in HeLa cells in each group were detected by western blot 8 days after dsAAV2/GFP transduction (3D). The relative level of MDA5 expression was calculated based on the intensity of b-actin protein (3E). *** p ⁇ 0.00J when compared to the PBS group.
• FIGS 4A and 4B show the dsRNA response profile in different cell lines.
• 4A Huh7, HEK293 and HepG2 cells were transduced with 5x10 3 particles of AAV2/GFP per cell. The expression of MDA5, RIG-I and IFN-b was detected by Q-PCR at day 7. *p ⁇ 0.05, **p ⁇ 0.0J when compared to the PBS group.
• 4B AAV2 with different transgenes was added to HeLa cells with 5x10 3 particles per cell. The expression of MDA5, RIG-I and IFN-b was detected by Q-PCR at day 7 after AAV transduction. For Q-PCR data analysis, samples from PBS group were normalized to 1 in each experiment.
• Figures 5A and 5B show the dsRNA innate immune response in human primary hepatocytes after dsAAV2/GFP transduction.
• Fresh human primary hepatocytes from 12 individuals were transduced by AAV2/GFP with 5x10 3 particles per cell.
• the expression of MDA5, RIG-I and IFN-b was detected by Q-PCR at different time points after AAV transduction.
• the gene expression of PBS group in each timepoint was normalized to 1, which was not shown in graph.
• Figures 6A and 6B show the dsRNA innate immune response in human primary hepatocytes after dsAAV2/ hFIX-opt transduction.
• Fresh human primary hepatocytes from 10 individuals were transduced by dsAAV8/hFIX-opt with 5x10 3 particles per cell.
• the expression of MDA5, RIG-I and IFN-b was detected by Q-PCR at different time points after AAV transduction.
• the gene expression of PBS group in each timepoint was normalized to 1, which was not shown in graph.
• Figures 7A-7C show the dsRNA response in human hepatocytes from xenografted mice after dsAAV8/ hFIX-opt transduction.
• 7 A 2 human hepatocytes from xenografted mice were injected with 3x10 1 1 particles of AAV8/hFIX-opt.
• the expression of MDA5, RIG- I and IFN-b of human hepatocytes in mice were detected by Q-PCR at 8 weeks after AAV transduction.
• MDA5 protein in mice liver was detected by western blot after 8 weeks, the band intensity were measured to show the relative MDA5 expression based on b-actin, in which the data was from 3 separate experiments. **p ⁇ 0.0J when compared to the control group.
• mice with human hepatocytes from another donor were injected with a dose of dsAAV8/hFIX-opt.
• the expression of MDA5, RIG-I and IFN-b of human hepatocytes in mice was detected by Q-PCR at 4 and 8 weeks after AAV transduction.
• MDA5 protein in mice liver was detected by western blot after 4 or 8 weeks, the relative expression level of MDA5 were calculated based on b-actin intensity, *p ⁇ 0.05, when compared to the control group.
• Figures 8A-8E show knockdown of dsRNA activation pathway increased AAV transgene expression.
• 8 A HeLa cells were transfected with siControl, siMDA5 or siMAVS. The knock down efficiency was detected by western blot and Q-PCR.
• 8B At day 0, HeLa cells were transduced with 5x10 3 particles of AAV2/luciferase per cell. SiRNA was transfected to HeLa cells at day4, and luciferase expression was detected 48h or 72h later. As control, 2pg/mL poly(LC) was added at day 3 and siRNA were transfected to HeLa cells at day 4. *p ⁇ 0.05, **p ⁇ 0.0J **p ⁇ 0.001, when compared to the PBS group.
• Figure 9 shows the effect of 3’-ITR on transgene expression lxl 0 5 of 293 cells/well were plated in a 24 well plate. Twenty four hours later, 0.5 up of human alpha-l antitrypsin (AAT) expression plasmids flanked by two AAV ITRs (2TR) or with 3TTR deletion (up/TR) or with poly(A) at reversed orientation between transgene and 3’-ITR (2TR/down-poly A-R) were transfected into 293 cells using lipofectamine 2000. At 48 hr post-transfection, AAT level in the supernatant was detected using ELISA. *p ⁇ 0.05, **p ⁇ 0.0l, when compared to 2TR plasmid.
• AAT human alpha-l antitrypsin
• Figures 10A-10B show diagrams of cassettes with (10A) single poly(A) blocking and (10B) multiple poly(A) blocking.
• Figure 11 shows a diagram of ITRs from AAV2 and AAV5.
• Figure 12 shows GFP expression from AAV ITR promoters. 5ug of pTR/GFP were cotransfected with lug of pCMV/lacZ into 293 cells in a 6 well plate. Two days later, 293 cells were visualized under fluorescence microscopy and stained for LacZ expression.
• Figure 13 shows AAT expression from AAV ITR promoters. 2ug of pTR/AAT were transfected into different cells in a l2well plates. Two days later, supernatant was harvested for AAT detection using ELISA.
• Figure 14 shows AAT expression from AAV/ITR-AAT vectors.
• lxl0e9 particles of AAV/ITR/AAT vectors were added lxl 0e5 293 cells in a 48 well plate. Two days later, supernatant was harvested for AAT expression.
• Figure 15 shows lxl Oel 1 particles of AAV/ITR/AAT vectors were administered via muscular injection in C57BL mice. Four weeks later, the blood was harvested and AAT expression was detected by ELISA.
• Figure 16 shows diagrams A-F of locations for shRNA or miRNA.
• Figure 17 shows diagrams A-C of cassettes for inhibitor expression.
• Figure 18 shows the effect of hydrocortisone on AAV transduction at later time point. Hela cells were transduced with AAV2/luc and lOug hydrocortisone was added to culture at day 5 post AAV transduction. 24 hr or 48 hr later after addition of hydrocortisone, luciferase activity from cell lysate was measured.
• Figure 19 shows the effect of hydrocortisone on innate immune response from AAV transduction at later time point.
• Hela cells were transduced with AAV2/luc and lOug hydrocortisone was added to culture at day 5 post AAV transduction. 24 hr later after addition of hydrocortisone, cells were harvested for analysis of MDA5 (top panel) and IFN-b (bottom panel) expression at transcription level by quantitative RT-PCR.
• Figures 20A-20B show strand transcript generation in AAV-transduced cells.
• RNA was used as a template to eliminate the possibility of AAV genome DNA contamination in extracted RNA.
• cDNA in different orientations was diluted to 20-, 200-, or 2,000-fold as PCR templates.
• Figure 21 shows high AAV transduction in human hepatocytes with MAVS deficiency.
• Human hepatocyte cell lines PH5CH8 and PH5CH8 with MAVS knockdown were transduced with different doses per cell of AAV2/luc vectors. Top panel: 200 vg/cell dose; middle panel: 5000 vg/cell dose; bottom panel: 5000 vg/cell dose. Transgene expression was analyzed at indicated time points.
• Figures 22A-22B show shRNAs used and a western blot for MAVS shRNA knockdown efficiency.
• Five different MAVS shRNAs were transfected into Hela cells, and 48 hrs later, cells were collected for cell lysate preparation. Cell lysate was loaded onto a SDS-PAGE gel, and afterward transferred to a nitrocellulose membrane and stained with MAVS antibody and GAPDH antibody. Signal was detected using ECL Western Blotting Detection Reagent (GE).
• GE ECL Western Blotting Detection Reagent
• MAVS shRNA #29 SEQ ID NO:36; MAVS shRNA #30: SEQ ID NO:37; MAVS shRNA #31 : SEQ ID NO:38; MAVS shRNA #32: SEQ ID NO:39; MAVS shRNA #68: SEQ ID NO:40.
• Figure 23 shows that knockdown of MAVS with shRNA increases AAV
• a can mean one or more than one.
• a cell can mean a single cell or a multiplicity of cells.
• and/or refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of
• a measurable value such as an amount of dose (e.g., an amount of a non- viral vector) and the like, is meant to encompass variations of ⁇ 20%, ⁇ 10%, ⁇ 5%, ⁇ 1%, ⁇ 0.5%, or even ⁇ 0.1% of the specified amount.
• aspects of the invention relate to the finding that AAV administration induces an innate immune response in a subject resulting from long term AAV transduction.
• This innate immune response is late in the infection stage.
• the innate immune response is triggered, at least in part, by the presence of double stranded RNA that results from viral infection and/or replication, triggering the cytoplasmic ds RNA recognition pathway.
• the innate immune response is activated when high amounts of minus stranded RNA are synthesized by the AAV (e.g., at the late phase of AAV transduction). This may be at its peak around week 6 of the transduction.
• This innate immune response involves, at least in part, increased production of type I IFN-b, and/or increased dsRNA sensors (e.g., MDA5 and MAVS) in the recipient cell or subject.
• Inhibition of the innate immune response at a late phase following AAV transduction such as by inhibiting the expression and/or activity of dsRNA sensors, increases AAV transgene expression in the cell or subject.
• One aspect of the invention relates to a nucleic acid molecule cassette designed to reduce the generation of dsRNA in AAV transduction to thereby reduce provocation of the innate immune response, and/or to inhibit an innate immune response that may be generated (e.g., by expressing RNAi, such as siRNA, that specifically targets mediators of the response, such as MDA5 and/or MAVS).
• RNAi such as siRNA
• MDA5 and/or MAVS mediators of the response
• Another aspect of the invention relates to an rAAV vector genome that comprises a nucleic acid molecule cassette as described herein (e.g., shown in Figure 10A and/or Figure 10B and/or Figure 16 and/or Figure 17).
• the AAV genome that contains the nucleic acid molecule cassette may be further packaged into a viral capsid to form a rAAV particle.
• Another aspect of the invention relates to a pharmaceutical formulation comprising an rAAV vector genome or AAV particle that comprises a nucleic acid molecule cassette as described herein.
• infection with the rAAV viral particle comprising the nucleic acid molecule cassette results in significant reduction in the innate immune response in the recipient cell or subject, at the late phase of viral transduction, compared to an otherwise identical rAAV viral particle that lacks the cassette elements described herein. In one embodiment, infection with the rAAV viral particle comprising the nucleic acid molecule cassette results in a significant increase in expression of a transgene in a recipient cell or subject, at the late phase of viral transduction, compared to an otherwise identical control rAAV viral particle that lacks the cassette elements described herein.
• a significant increase is any reproducible, statistically significant increase, such as by the methods used in the examples section herein (e.g., 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 50%, 60%, 75%, 90%, 100%, 2X, 3X, 4X, 5X, 10X, or more increase over the control).
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the recombinant nucleic acid molecule further comprises: a) a poly(A) (pA) sequence downstream of the 5’ ITR and upstream of the promoter, in 3’ to 5’ orientation and a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; b) a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; c) a first pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation and a second pA sequence downstream of the first pA sequence and upstream of the 3’ ITR, in a 5’
• the recombinant nucleic acid molecule comprising an adeno- associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, further comprises: a) a poly A (pA) sequence downstream of the 5’ ITR and upstream of the promoter, in 3’ to 5’ orientation and a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; b) a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; c) a first pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation and a second pA sequence downstream of the first pA sequence and upstream of the 3’ ITR, in a 5’ to 3’ orientation; d) a first pA sequence upstream of the 3’
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the recombinant nucleic acid molecule further comprises one or more of : a) a poly A (pA) sequence downstream of the 5’ ITR and upstream of the promoter, in 3’ to 5’ orientation and a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; b) a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; c) a first pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation and a second pA sequence downstream of the first pA sequence and upstream of the 3’ ITR, in
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the recombinant nucleic acid molecule further comprises at least one of : a) a poly A (pA) sequence downstream of the 5’ ITR and upstream of the promoter, in 3’ to 5’ orientation and a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; b) a pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation; c) a first pA sequence upstream of the 3’ ITR and downstream of the NOI, in 3’ to 5’ orientation and a second pA sequence downstream of the first pA sequence and upstream of the 3’ ITR, in
• Nonlimiting examples of embodiments of this invention include the individual cassettes (i.e., recombinant nucleic acid molecules) as shown in Figures 10A, 10B, 16 and 17, as well as any cassette having any combination of elements (e.g., poly(A) sequences) and/or any combination of orientations as shown in the respective cassettes.
• Poly (A) sequences that can be utilized in the invention are known in the art and can be determined by the skilled practitioner.
• These cassettes and recombinant nucleic acid molecules can be present in a composition or population singly or in any combination and/or in any ratio.
• a composition or population of this invention can also comprise, consist essentially of or consist of a single cassette or recombinant nucleic acid molecule of this invention.
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) vector cassette of a first AAV serotype, comprising an AAV 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the AAV 5’ ITR and/or an AAV 3’ ITR from a second AAV serotype that is different than the first AAV serotype.
• the 5’ ITR and/or 3’ ITR of the first AAV serotype can be replaced with a 5’ ITR and/or a 3’ ITR from the second AAV serotype.
• the ITR of the second AAV serotype has no promoter function or reduced promoter function as compared with the promoter function of the ITR of the first AAV serotype.
• the first AAV serotype can be any AAV serotype now known or later identified and the second AAV serotype that is different that the first AAV serotype can be any AAV serotype now known or later identified.
• the first AAV serotype is AAV2 and the ITR of the second AAV serotype is AAV5.
• the recombinant nucleic acid molecule can comprise an AAV vector cassette of AAV2, said cassette of AAV2 comprising a 5’ ITR and/or a 3’ ITR of AAV5.
• the present invention provides a recombinant nucleic acid molecule, comprising an adeno-associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the 5’ ITR and/or the 3’ ITR that is modified (e.g., by substitution, insertion and/or deletion) to diminish or eliminate promoter activity from the 5’ ITR and/or the 3’ ITR.
• AAV adeno-associated virus
• ITR inverted terminal repeat
• NOI nucleotide sequence of interest
• the present invention provides a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, an NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR, wherein the NOI sequence is fused with (e.g., in frame with; upstream and/or downstream of) one or more than one nucleotide sequence that encodes an interfering RNA sequence that targets one or more than one cytoplasmic dsRNA sensor.
• the present invention provides A) a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, an NOI operably associated with a first promoter, a first pA sequence in 3’ to 5’ orientation, a nucleotide sequence that encodes an interfering RNA sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, a second pA sequence and an AAV 3’ ITR; B) A recombinant nucleic acid molecule, comprising an AAV 5’ ITR, a NOI operably associated with a first promoter, a pA sequence in 3’ to 5’ orientation, a short hairpin RNA (shRNA) sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, and an AAV 3’
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, an NOI operably associated with a first promoter, a p
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, a shRNA that targets a cytoplasmic dsRNA sensor, operably associated with a first promoter, a NOI operably associated with a second promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR;
• a recombinant nucleic acid molecule comprising, in the following order; an AAV 5’ ITR, a miRNA that targets a cytoplasmic dsRNA sensor and a NOI, both operably associated with a promoter, a
• composition comprising a first recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR and a second recombinant nucleic acid molecule comprising an interfering RNA sequence that targets a cytoplasmic dsRNA sensor.
• Nonlimiting examples of a cytoplasmic dsRNA of this invention include MDA5, MAVS, RIG-l, TRAF6, TRAF5, RIP1, FADD, IRF, TRAF3, NAP1, TBK1, IKK, IKB, TANK and any other molecules involved in MAVS downstream signaling, in any combination and order in a recombinant nucleic acid molecule of this invention.
• Nonlimiting examples of an interfering RNA (RNAi) of this invention include small interfering RNA (siRNA), short hairpin RNA (shRNA), microRNA (miRNA), long double stranded RNA (long dsRNA), antisense RNA, ribozymes, etc., as are known in the art, as well as any other interfering RNA or inhibitory RNA now known or later identified.
• siRNA small interfering RNA
• shRNA short hairpin RNA
• miRNA microRNA
• long stranded RNA long stranded RNA
• antisense RNA ribozymes
• the present invention further provides a recombinant nucleic acid molecule, comprising an AAV 5’ ITR, an NOI and an inhibitor of MAVS signaling, both operably associated with a promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR.
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a first promoter, a first pA sequence in 3’ to 5’ orientation, an inhibitor of MAVS signaling operably associated with a second promoter, a second pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR.
• the present invention provides a composition comprising a first recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR and a second recombinant nucleic acid molecule comprising an inhibitor of MAVS signaling and a pA sequence in 3’ to 5’ orientation.
• Nonlimiting examples of an inhibitor of MAVS signaling include a serine protease NS3-4A from hepatitis C virus, proteases from Hepatitis A virus and GB virus B, hepatitis B virus (HBV) X protein, poly(rC) -binding protein 2, the 20S proteasomal subunit PSMA7, and/or mitofusin 2, as well as any other inhibitor of MAVS signaling now known or later identified.
• a method is also provided herein, of enhancing transduction of an AAV vector in cells of a subject, comprising administering to the subject an AAV vector and an agent that interferes with dsRNA activation pathways in cells of the subject.
• Nonlimiting examples of an agent that interferes with dsRNA activation pathways include 2-aminopurine, a steroid (e.g., hydrocortisone), and any other agent that interferes with dsRNA activation pathways in a cell as now known or later identified.
• the AAV vector and the agent(s) of this invention can be administered to the subject simultaneously and/or subsequently, in any order and in any time interval (e.g., hours, days, weeks, etc.)
• the AAV vector is administered first, and the agent is administered following that.
• the agent is administered first, and the AAV vector is administered following that.
• the agent is administered in one or more interval.
• the agent is administered in intervals (e.g., days such as every 1, 2, 3, 4, 5, 6, days,, or weeks such as every 1, 2, 3, 4, 5, 6 weeks or more) following administration of the AAV vector.
• amino acid can be selected from any subset of these amino acid(s) for example A, G, I or L; A, G, I or V; A or G; only L; etc. as if each such subcombination is expressly set forth herein.
• amino acid can be disclaimed (e.g., by negative proviso).
• the amino acid is not A, G or I; is not A; is not G or V; etc. as if each such possible disclaimer is expressly set forth herein.
• capsid subunits can be expressed independently to achieve modification in only one or two of the capsid subunits (VP1, VP2, VP3, VP1 + VP2, VP1+VP3, or VP2 +VP3).
• the terms“reduce,”“reduces,”“reduction,”“diminish.”“inhibit” and similar terms mean a decrease of at least about 5%, 10%, 15%; 20%, 25%, 35%, 50%, 75%, 80%, 85%, 90%, 95%, 97% or more.
• the terms“enhance,”“enhances,”“enhancement” and similar terms indicate an increase of at least about 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400%, 500% or more.
• parvovirus encompasses the family Parvoviridae, including autonomously replicating parvoviruses and dependo viruses.
• the autonomous parvoviruses include members of the genera Parvovirus, Erythrovirus, Densovirus, Iteravirus, and
• Exemplary autonomous parvoviruses include, but are not limited to, minute virus of mouse, bovine parvovirus, canine parvovirus, chicken parvovirus, feline
• panleukopenia virus feline parvovirus, goose parvovirus, Hl parvovirus, muscovy duck parvovirus, B19 virus, and any other autonomous parvovirus now known or later discovered.
• Other autonomous parvoviruses are known to those skilled in the art. See, e.g., BERNARD N. FIELDS et al., VIROLOGY, Volume 2, Chapter 69 (4th ed., Lippincott-Raven
• AAV adeno-associated virus
• AAV type 1 AAV type 2, AAV type 3 (including types 3 A and 3B), AAV type 4, AAV type 5, AAV type 6, AAV type 7, AAV type 8, AAV type 9, AAV type 10, AAV type 11, avian AAV, bovine AAV, canine AAV, equine AAV, ovine AAV, and any other AAV now known or later discovered. See, e.g., BERNARD N. FIELDS et ah, VIROLOGY, volume 2, chapter 69 (4th ed., Lippincott-Raven Publishers).
• a number of additional AAV serotypes and clades have been identified ⁇ see, e.g., Gao et al., (2004) J. Virology 78:6381-6388; Moris et al., (2004) Virology 33-:375-383; and Table 3).
• parvoviruses as well as the sequences of the native terminal repeats (TRs), Rep proteins, and capsid subunits are known in the art. Such sequences may be found in the literature or in public databases such as GenBank. See, e.g., GenBank Accession Numbers NC 002077,
• tropism refers to preferential entry of the virus into certain cells or tissues, optionally followed by expression (e.g., transcription and, optionally, translation) of a sequence(s) carried by the viral genome in the cell, e.g., for a recombinant virus, expression of a heterologous nucleic acid(s) of interest.
• efficient transduction or “efficient tropism,” or similar terms, can be determined by reference to a suitable control (e.g., at least about 50%, 60%, 70%, 80%, 85%, 90%, 95%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 350%, 400%, 500% or more of the transduction or tropism, respectively, of the control).
• the virus vector efficiently transduces or has efficient tropism for neuronal cells and cardiomyocytes.
• Suitable controls will depend on a variety of factors including the desired tropism and/or transduction profile.
• virus“does not efficiently transduce” or“does not have efficient tropism” for a target tissue or similar terms, by reference to a suitable control.
• the virus vector does not efficiently transduce (i.e., has does not have efficient tropism) for liver, kidney, gonads and/or germ cells.
• transduction e.g., undesirable transduction
• tissue(s) e.g., liver
• transduction e.g., undesirable transduction
• tissue(s) e.g., liver
• the level of transduction of the desired target tissue(s) e.g., skeletal muscle, diaphragm muscle, cardiac muscle and/or cells of the central nervous system.
• polypeptide encompasses both peptides and proteins, unless indicated otherwise.
• A“polynucleotide” is a sequence of nucleotide bases, and may be RNA, DNA or DNA-RNA hybrid sequences (including both naturally occurring and non-naturally occurring nucleotides), but in representative embodiments are either single or double stranded DNA sequences.
• an“isolated” polynucleotide e.g, an“isolated DNA” or an“isolated RNA
• an“isolated” nucleotide means a polynucleotide at least partially separated from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polynucleotide.
• an "isolated” nucleotide is enriched by at least about 10-fold, lOO-fold, 1000-fold, 10,000-fold or more as compared with the starting material.
• an“isolated” polypeptide means a polypeptide that is at least partially separated from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polypeptide.
• an "isolated” polypeptide is enriched by at least about 10-fold, lOO-fold, 1000-fold, 10,000-fold or more as compared with the starting material.
• an“isolated cell” refers to a cell that is separated from other components with which it is normally associated in its natural state.
• an isolated cell can be a cell in culture medium and/or a cell in a pharmaceutically acceptable carrier of this invention.
• an isolated cell can be delivered to and/or introduced into a subject.
• an isolated cell can be a cell that is removed from a subject and manipulated as described herein ex vivo and then returned to the subject.
• virus vector or virus particle or population of virus particles it is meant that the virus vector or virus particle or population of virus particles is at least partially separated from at least some of the other components in the starting material.
• purified virus vector or virus particle or population of virus particles is enriched by at least about 10-fold, lOO-fold, 1000-fold, 10,000-fold or more as compared with the starting material.
• A“therapeutic polypeptide” is a polypeptide that can alleviate, reduce, prevent, delay and/or stabilize symptoms that result from an absence or defect in a protein in a cell or subject and/or is a polypeptide that otherwise confers a benefit to a subject, e.g., anti-cancer effects or improvement in transplant survivability or induction of an immune response.
• “treat,”“treating” or“treatment of’ it is meant that the severity of the subject’s condition is reduced, at least partially improved or stabilized and/or that some alleviation, mitigation, decrease or stabilization in at least one clinical symptom is achieved and/or there is a delay in the progression of the disease or disorder.
• prevent refers to prevention and/or delay of the onset of a disease, disorder and/or a clinical symptom(s) in a subject and/or a reduction in the severity of the onset of the disease, disorder and/or clinical symptom(s) relative to what would occur in the absence of the methods of the invention.
• the prevention can be complete, e.g., the total absence of the disease, disorder and/or clinical symptom(s).
• the prevention can also be partial, such that the occurrence of the disease, disorder and/or clinical symptom (s) in the subject and/or the severity of onset is substantially less than what would occur in the absence of the present invention.
• A“treatment effective” amount as used herein is an amount that is sufficient to provide some improvement or benefit to the subject.
• a“treatment effective” amount is an amount that will provide some alleviation, mitigation, decrease or stabilization in at least one clinical symptom in the subject.
• the therapeutic effects need not be complete or curative, as long as some benefit is provided to the subject.
• prevention effective amount is an amount that is sufficient to prevent and/or delay the onset of a disease, disorder and/or clinical symptoms in a subject and/or to reduce and/or delay the severity of the onset of a disease, disorder and/or clinical symptoms in a subject relative to what would occur in the absence of the methods of the invention.
• level of prevention need not be complete, as long as some preventative benefit is provided to the subject.
• nucleotide sequence of interest “NOI),”“heterologous nucleotide sequence” and“heterologous nucleic acid molecule” are used interchangeably herein and refer to a nucleic acid sequence that is not naturally occurring in the virus.
• NOI, heterologous nucleic acid molecule or heterologous nucleotide sequence comprises an open reading frame that encodes a polypeptide and/or nontranslated RNA of interest (e.g., for delivery to a cell and/or subject).
• virus vector e.g., AAV
• vector genome e.g., viral DNA [vDNA]
• vector may be used to refer to the vector genome/vDNA alone.
• A“recombinant nucleotide sequence,”“recombinant nucleic acid molecule,”“rAAV vector genome” or“rAAV genome” is an AAV genome (i.e., vDNA) that comprises one or more heterologous nucleic acid sequences.
• terminal repeat or “TR” or“inverted terminal repeat (ITR)” includes any viral terminal repeat or synthetic sequence that forms a hairpin structure and functions as an inverted terminal repeat (i.e., mediates the desired functions such as replication, virus packaging, integration and/or provirus rescue, and the like).
• the TR can be an AAV TR or a non-AAV TR.
• a non-AAV TR sequence such as those of other parvoviruses (e.g ., canine parvovirus (CPV), mouse parvovirus (MVM), human parvovirus B-19) or any other suitable virus sequence (e.g., the SV40 hairpin that serves as the origin of SV40 replication) can be used as a TR, which can further be modified by truncation, substitution, deletion, insertion and/or addition.
• the TR can be partially or completely synthetic, such as the“double-D sequence” as described in United States Patent No. 5,478,745 to Samulski et al.
• An“AAV terminal repeat” or “AAV TR” may be from any AAV, including but not limited to serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 or any other AAV now known or later discovered (see, e.g., Table 3).
• An AAV terminal repeat need not have the native terminal repeat sequence (e.g., a native AAV TR sequence may be altered by insertion, deletion, truncation and/or missense mutations), as long as the terminal repeat mediates the desired functions, e.g., replication, virus packaging, integration, and/or provirus rescue, and the like.
• AAV proteins VP1, VP2 and VP3 are capsid proteins that interact together to form an AAV capsid of an icosahedral symmetry.
• VP1.5 is an AAV capsid protein described in US Publication No. 2014/0037585.
• virus vectors of the invention can further be“targeted” virus vectors (e.g., having a directed tropism) and/or a“hybrid” parvovirus (i.e., in which the viral TRs and viral capsid are from different parvoviruses) as described in international patent publication WO
• the virus vectors of the invention can further be duplexed parvovirus particles as described in international patent publication WO 01/92551 (the disclosure of which is incorporated herein by reference in its entirety).
• double stranded (duplex) genomes can be packaged into the virus capsids of the invention.
• viral capsid or genomic elements can contain other modifications, including insertions, deletions and/or substitutions.
• A“chimeric’ capsid protein as used herein means an AAV capsid protein that has been modified by substitutions in one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) amino acid residues in the amino acid sequence of the capsid protein relative to wild type, as well as insertions and/or deletions of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) amino acid residues in the amino acid sequence relative to wild type.
• complete or partial domains, functional regions, epitopes, etc., from one AAV serotype can replace the corresponding wild type domain, functional region, epitope, etc.
• a chimeric capsid protein of this invention can be produced according to protocols well known in the art and a large number of chimeric capsid proteins are described in the literature as well as herein that can be included in the capsid of this invention.
• amino acid or“amino acid residue” encompasses any naturally occurring amino acid, modified forms thereof, and synthetic amino acids.
• the amino acid can be a modified amino acid residue (nonlimiting examples are shown in Table 6) and/or can be an amino acid that is modified by post translation modification (e.g., acetylation, amidation, formylation, hydroxylation,
• non-naturally occurring amino acid can be an "unnatural" amino acid as described by Wang et al., Annu Rev Biophys Biomol Struct. 35:225-49 (2006). These unnatural amino acids can advantageously be used to chemically link molecules of interest to the AAV capsid protein.
• the AAV vector of this invention can be a synthetic viral vector designed to display a range of desirable phenotypes that are suitable for different in vitro and in vivo applications.
• the present invention provides an AAV particle comprising an adeno-associated virus (AAV) capsid, wherein the capsid comprises capsid protein VP1, wherein said capsid protein VP1 is from one or more than one first AAV serotype and capsid protein VP3, wherein said capsid protein VP3 is from one or more than one second AAV serotype and wherein at least one of said first AAV serotype is different from at least one of said second AAV serotype, in any combination.
• AAV adeno-associated virus
• the AAV particle can comprise a capsid that comprises capsid protein VP2, wherein said capsid protein VP2 is from one or more than one third AAV serotype, wherein at least one of said one or more than one third AAV serotype is different from said first AAV serotype and/or said second AAV serotype, in any combination ln some embodiments, the AAV capsid described herein can comprise capsid protein VP1.5.
• VP 1.5 is described in US Patent Publication No. 20140037585 and the amino acid sequence of VP 1.5 is provided herein.
• the AAV particle of this invention can comprise a capsid that comprises capsid protein VP1.5, wherein said capsid protein VP1.5 is from one or more than one fourth AAV serotype, wherein at least one of said one or more than one fourth AAV serotype is different from said first AAV serotype and/or said second AAV serotype, in any combination.
• the AAV capsid protein described herein can comprise capsid protein VP2.
• the present invention also provides an AAV vector of this invention, comprising an AAV capsid wherein the capsid comprises capsid protein VP1, wherein said capsid protein VP1 is from one or more than one first AAV serotype and capsid protein VP2, wherein said capsid protein VP2 is from one or more than one second AAV serotype and wherein at least one of said first AAV serotype is different from at least one of said second AAV serotype, in any combination.
• an AAV vector of this invention comprising an AAV capsid wherein the capsid comprises capsid protein VP1, wherein said capsid protein VP1 is from one or more than one first AAV serotype and capsid protein VP2, wherein said capsid protein VP2 is from one or more than one second AAV serotype and wherein at least one of said first AAV serotype is different from at least one of said second AAV serotype, in any combination.
• the AAV vector of this invention can comprise a capsid that comprises capsid protein VP3, wherein said capsid protein VP3 is from one or more than one third AAV serotype, wherein at least one of said one or more than one third AAV serotype is different from said first AAV serotype and/or said second AAV serotype, in any
• the AAV capsid described herein can comprise capsid protein VP 1.5.
• the present invention further provides an AAV vector that comprises an adeno- associated virus (AAV) capsid, wherein the capsid comprises capsid protein VP1, wherein said capsid protein VP1 is from one or more than one first AAV serotype and capsid protein VP1.5, wherein said capsid protein VP1.5 is from one or more than one second AAV serotype and wherein at least one of said first AAV serotype is different from at least one of said second AAV serotype, in any combination.
• AAV adeno- associated virus
• the AAV vector of this invention can comprise a capsid that comprises capsid protein VP3, wherein said capsid protein VP3 is from one or more than one third AAV serotype, wherein at least one of said one or more than one third AAV serotype is different from said first AAV serotype and/or said second AAV serotype, in any
• the AAV capsid protein described herein can comprise capsid protein VP2.
• said one or more than one first AAV serotype, said one or more than one second AAV serotype, said one or more than one third AAV serotype and said one or more than one fourth AAV serotype are selected from the group consisting of the AAV serotypes listed in Table 3, in any combination
• the AAV capsid described herein lacks capsid protein VP2.
• the capsid can comprise a chimeric capsid VP1 protein, a chimeric capsid VP2 protein, a chimeric capsid VP3 protein and/or a chimeric capsid VP1.5 protein.
• the present invention further provides a composition, which can be a pharmaceutical formulation comprising the virus vector or AAV particle of this invention and a
• transduction by the AAV particles of this invention of cells is at least about five-fold, ten-fold, 50-fold, lOO-fold, 1000-fold or higher than transduction levels by AAV particles that induce a dsRNA mediated immune response as described herein.
• Heterologous molecules e.g ., nucleic acid, proteins, peptides, etc.
• therapeutically useful molecules can be associated with a transgene for transfer of the molecules into host target cells.
• Such associated molecules can include DNA and/or RNA.
• the modified capsid proteins and capsids can further comprise any other
• the corresponding modification will be an insertion and/or a substitution, depending on whether the corresponding amino acid positions are partially or completely present in the virus or, alternatively, are completely absent.
• the specific amino acid position(s) may be different than the position in AAV2 (see, e.g., Table 5).
• the corresponding amino acid position(s) will be readily apparent to those skilled in the art using well-known techniques. Nonlimiting examples of corresponding positions in a number of other AAV are shown in Table 5 (Position 2).
• the virus vector of this invention is a recombinant virus vector comprising a heterologous nucleic acid encoding a polypeptide and/or a functional RNA of interest. Recombinant virus vectors are described in more detail below.
• the capsid proteins, virus capsids, virus vectors and AAV particles of the invention exclude those capsid proteins, capsids, virus vectors and AAV particles as they would be present or found in their native state.
• the present invention further provides methods of producing the AAV particles and vectors of this invention.
• the present invention provides a method of making an AAV particle, comprising: a) transfecting a host cell with one or more plasmids that provide, in combination all functions and genes needed to assemble AAV particles; b) introducing one or more nucleic acid constructs into a packaging cell line or producer cell line to provide, in combination, all functions and genes needed to assemble AAV particles; c) introducing into a host cell one or more recombinant baculovirus vectors that provide in combination all functions and genes needed to assemble AAV particles; and/or d) introducing into a host cell one or more recombinant herpesvirus vectors that provide in combination all functions and genes needed to assemble AAV particles.
• Nonlimiting examples of various methods of making the virus vectors of this invention are described in Clement and Greiger
• the present invention provides a method of producing an AAV particle, the method comprising providing to a cell: (a) a nucleic acid template comprising at least one TR sequence (e.g., AAV TR sequence), and (b) AAV sequences sufficient for replication of the nucleic acid template and encapsidation into AAV capsids (e.g., AAV rep sequences and AAV cap sequences encoding the AAV capsids of the invention).
• the nucleic acid template further comprises at least one heterologous nucleic acid sequence.
• the nucleic acid template comprises two AAV ITR sequences, which are located 5’ and 3’ to the heterologous nucleic acid sequence (if present), although they need not be directly contiguous thereto.
• the nucleic acid template and AAV rep and cap sequences are provided under conditions such that virus vector comprising the nucleic acid template packaged within the AAV capsid is produced in the cell.
• the method can further comprise the step of collecting the virus vector from the cell.
• the virus vector can be collected from the medium and/or by lysing the cells.
• the cell can be a cell that is permissive for AAV viral replication. Any suitable cell known in the art may be employed. In particular embodiments, the cell is a mammalian cell. As another option, the cell can be a / mv-complementing packaging cell line that provides functions deleted from a replication-defective helper virus, e.g., 293 cells or other El a trans- complementing cells.
• a replication-defective helper virus e.g., 293 cells or other El a trans- complementing cells.
• the AAV replication and capsid sequences may be provided by any method known in the art. Current protocols typically express the AAV rep/ cap genes on a single plasmid. The AAV replication and packaging sequences need not be provided together, although it may be convenient to do so.
• the AAV rep and/or cap sequences may be provided by any viral or non- viral vector.
• the rep! cap sequences may be provided by a hybrid adenovirus or herpesvirus vector (e.g., inserted into the El a or E3 regions of a deleted adenovirus vector). Epstein Barr virus (EBV) vectors may also be employed to express the AAV cap and rep genes.
• EBV Epstein Barr virus
• EBV vectors are episomal, yet will maintain a high copy number throughout successive cell divisions (i.e., are stably integrated into the cell as extra-chromosomal elements, designated as an“EBV based nuclear episome,” see Margolski, (1992) Curr. Top. Microbiol. Immun. 158:67).
• the rep/ cap sequences may be stably incorporated into a cell.
• AAV rep/ cap sequences will not be flanked by the TRs, to prevent rescue and/or packaging of these sequences.
• the nucleic acid template can be provided to the cell using any method known in the art.
• the template can be supplied by a non-viral (e.g., plasmid) or viral vector.
• the nucleic acid template is supplied by a herpesvirus or adenovirus vector (e.g, inserted into the El a or E3 regions of a deleted adenovirus).
• a herpesvirus or adenovirus vector e.g, inserted into the El a or E3 regions of a deleted adenovirus.
• Palombo et al., J. Virology 72:5025 (1998) describes a baculovirus vector carrying a reporter gene flanked by the AAV TRs.
• EBV vectors may also be employed to deliver the template, as described above with respect to the rep/ cap genes.
• the nucleic acid template is provided by a replicating rAAV virus.
• an AAV provirus comprising the nucleic acid template is stably integrated into the chromosome of the cell.
• helper virus functions e.g, adenovirus or herpesvirus
• helper virus sequences necessary for AAV replication are known in the art. Typically, these sequences will be provided by a helper adenovirus or herpesvirus vector.
• the adenovirus or herpesvirus sequences can be provided by another non-viral or viral vector, e.g, as a non- infectious adenovirus miniplasmid that carries all of the helper genes that promote efficient AAV production as described by Ferrari et al., (1997) Nature Med. 3:1295, and U.S. Patent Nos. 6,040,183 and 6,093,570.
• helper virus functions may be provided by a packaging cell with the helper sequences embedded in the chromosome or maintained as a stable extrachromosomal element.
• the helper virus sequences cannot be packaged into AAV virions, e.g., are not flanked by TRs.
• helper construct may be a non- viral or viral construct.
• the helper construct can be a hybrid adenovirus or hybrid herpesvirus comprising the AAV rep I cap genes.
• the AAV replcap sequences and the adenovirus helper sequences are supplied by a single adenovirus helper vector.
• This vector can further comprise the nucleic acid template.
• the AAV replcap sequences and/or the rAAV template can be inserted into a deleted region (e.g., the El a or E3 regions) of the adenovirus.
• the AAV replcap sequences and the adenovirus helper sequences are supplied by a single adenovirus helper vector.
• the rAAV template can be provided as a plasmid template.
• the AAV rep/ cap sequences and adenovirus helper sequences are provided by a single adenovirus helper vector, and the rAAV template is integrated into the cell as a provirus.
• the rAAV template is provided by an EBV vector that is maintained within the cell as an extrachromosomal element (e.g., as an EBV based nuclear episome).
• the AAV replcap sequences and adenovirus helper sequences are provided by a single adenovirus helper.
• the rAAV template can be provided as a separate replicating viral vector.
• the rAAV template can be provided by a rAAV particle or a second recombinant adenovirus particle.
• the hybrid adenovirus vector typically comprises the adenovirus 5’ and 3’ cis sequences sufficient for adenovirus replication and packaging (i.e., the adenovirus terminal repeats and PAC sequence).
• the AAV replcap sequences and if present the rAAV template are embedded in the adenovirus backbone and are flanked by the 5' and 3' cis sequences, so that these sequences may be packaged into adenovirus capsids.
• the adenovirus helper sequences and the AAV replcap sequences are generally not flanked by TRs so that these sequences are not packaged into the AAV virions.
• Zhang et al., ((2001) Gene Ther. 18:704-12) describe a chimeric helper comprising both adenovirus and the AAV rep and cap genes.
• Herpesvirus may also be used as a helper virus in AAV packaging methods.
• Hybrid herpesviruses encoding the AAV Rep protein(s) may advantageously facilitate scalable AAV vector production schemes.
• a hybrid herpes simplex virus type I (HSV-l) vector expressing the AAV-2 rep and cap genes has been described (Conway et al., (1999) Gene Therapy 6:986 and WO 00/17377.
• virus vectors of the invention can be produced in insect cells using baculovirus vectors to deliver the rep! cap genes and rAAV template as described, for example, by Urabe et al., (2002) Human Gene Therapy 13:1935-43.
• AAV vector stocks free of contaminating helper virus may be obtained by any method known in the art.
• AAV and helper virus may be readily differentiated based on size.
• AAV may also be separated away from helper virus based on affinity for a heparin substrate (Zolotukhin et al. (1999) Gene Therapy 6:973).
• Deleted replication-defective helper viruses can be used so that any contaminating helper virus is not replication competent.
• an adenovirus helper lacking late gene expression may be employed, as only adenovirus early gene expression is required to mediate packaging of AAV virus.
• Adenovirus mutants defective for late gene expression are known in the art (e.g., tslOOK and tsl49 adenovirus mutants).
• the present invention provides a method of administering a nucleic acid molecule to a cell, the method comprising contacting the cell with the virus vector, the AAV particle, the composition and/or the pharmaceutical formulation of this invention.
• the present invention further provides a method of delivering a nucleic acid to a subject, the method comprising administering to the subject the virus vector, the AAV particle, the composition and/or the pharmaceutical formulation of this invention.
• the subject of this invention can be any animal and in some embodiments, the subject is a mammal and in some embodiments, the subject is a human. In some embodiments, the subject has or is at risk for a disorder that can be treated by immunotherapy and/or gene therapy protocols.
• Nonlimiting examples of such disorders include a muscular dystrophy including Duchenne or Becker muscular dystrophy, hemophilia A, hemophilia B, multiple sclerosis, diabetes mellitus, Gaucher disease, Fabry disease, Pompe disease, cancer, arthritis, muscle wasting, heart disease including congestive heart failure or peripheral artery disease, intimal hyperplasia, a neurological disorder including epilepsy, Huntington's disease, Parkinson's disease or Alzheimer's disease, an autoimmune disease, cystic fibrosis, thalassemia, Hurler's Syndrome, Sly syndrome, Scheie Syndrome, Hurler-Scheie Syndrome, Hunter's Syndrome, Sanfilippo Syndrome A, B, C, D, Morquio Syndrome, Maroteaux-Lamy Syndrome, Krabbe's disease, phenylketonuria, Batten's disease, spinal cerebral ataxia, LDL receptor deficiency, hyperammonemia, anemia, arthritis, a retinal degenerative disorder including macular degeneration, adenosine deaminas
• virus vector, the AAV particle and/or the composition or pharmaceutical formulation of this invention can be administered/delivered to a subject of this invention via a systemic route (e.g., intravenously, intraarterially,
• virus vector and/or composition can be administered to the subject via an intracerebroventrical, intracistemal, intraparenchymal, intracranial and/or intrathecal route.
• virus vectors of the present invention are useful for the delivery of nucleic acid molecules to cells in vitro, ex vivo, and in vivo.
• the virus vectors can be advantageously employed to deliver or transfer nucleic acid molecules to animal cells, including mammalian cells.
• Nucleic acid molecules of interest include nucleic acid molecules encoding polypeptides, including therapeutic (e.g., for medical or veterinary uses) and/or immunogenic (e.g., for vaccines) polypeptides.
• Therapeutic polypeptides include, but are not limited to, cystic fibrosis
• CTR transmembrane regulator protein
• dystrophin including mini- and micro-dystrophins, see, e.g., Vincent et ah, (1993) Nature Genetics 5:130; U.S. Patent Publication No.
• myostatin propeptide myostatin propeptide, follistatin, activin type II soluble receptor, IGF-l, anti-inflammatory polypeptides such as the Ikappa B dominant mutant, sarcospan, utrophin (Tinsley et al., (1996) Nature 384:349), mini-utrophin, clotting factors (e.g., Factor VIII, Factor IX, Factor X, etc.), erythropoietin, angiostatin, endostatin, catalase, tyrosine hydroxylase, superoxide dismutase, leptin, the LDL receptor, lipoprotein lipase, ornithine transcarbamylase, b-globin, a-globin, spectrin, ai-antitrypsin, adenosine deaminase, hypoxanthine guanine phosphoribosyl transferase, b-glucocere
• angiogenesis inhibitors such as Yasohibins and other VEGF inhibitors (e.g., Vasohibin 2 [see, WO JP2006/073052]).
• Other illustrative heterologous nucleic acid sequences encode suicide gene products (e.g., thymidine kinase, cytosine deaminase, diphtheria toxin, and tumor necrosis factor), proteins conferring resistance to a drug used in cancer therapy, tumor suppressor gene products (e.g., p53, Rb, Wt-l), TRAIL, FAS-ligand, and any other polypeptide that has a therapeutic effect in a subject in need thereof.
• AAV vectors can also be used to deliver monoclonal antibodies and antibody fragments, for example, an antibody or antibody fragment directed against myostatin (see, e.g., Fang et al., Nature Biotechnology 23:584-590 (2005)).
• Heterologous nucleic acid sequences encoding polypeptides include those encoding reporter polypeptides (e.g., an enzyme). Reporter polypeptides are known in the art and include, but are not limited to, Green Fluorescent Protein (GFP), luciferase, b-galactosidase, alkaline phosphatase, luciferase, and chloramphenicol acetyltransferase gene.
• GFP Green Fluorescent Protein
• luciferase luciferase
• b-galactosidase alkaline phosphatase
• luciferase e.g., luciferase
• chloramphenicol acetyltransferase gene e.g., chloramphenicol acetyltransferase gene.
• the heterologous nucleic acid molecule encodes a secreted polypeptide (e.g., a polypeptide that is a secreted polypeptide in its native state or that has been engineered to be secreted, for example, by operable association with a secretory signal sequence as is known in the art).
• a secreted polypeptide e.g., a polypeptide that is a secreted polypeptide in its native state or that has been engineered to be secreted, for example, by operable association with a secretory signal sequence as is known in the art.
• the heterologous nucleic acid molecule may encode an antisense nucleic acid molecule, a ribozyme (e.g., as described in U.S. Patent No. 5,877,022), RNAs that effect spliceosome-mediated /n v-splicing (see, Puttaraju et al, (1999) Nature Biotech. 17:246; U.S. Patent No. 6,013,487; U.S. Patent No.
• RNAi interfering RNAs
• siRNA siRNA
• shRNA or miRNA that mediate gene silencing
• other non-translated RNAs such as“guide” RNAs (Gorman et al, (1998) Proc. Nat. Acad. Sci. USA 95:4929; U.S. Patent No. 5,869,248 to Yuan et al), and the like.
• RNAi against a multiple drug resistance (MDR) gene product e.g., to treat and/or prevent tumors and/or for administration to the heart to prevent damage by chemotherapy
• MDR multiple drug resistance
• myostatin e.g., for Duchenne muscular dystrophy
• VEGF e.g., to treat and/or prevent tumors
• RNAi against phospholamban e.g., to treat cardiovascular disease, see, e.g., Andino et al., J. Gene Med. 10:132-142 (2008) and Li et al., Acta Pharmacol Sin.
• phospholamban inhibitory or dominant-negative molecules such as phospholamban S16E (e.g., to treat cardiovascular disease, see, e.g., Hoshijima et al. Nat. Med. 8:864-871 (2002)), RNAi to adenosine kinase (e.g., for epilepsy), and RNAi directed against pathogenic organisms and viruses (e.g., hepatitis B and/or C virus, human immunodeficiency virus, CMV, herpes simplex virus, human papilloma virus, etc.).
• pathogenic organisms and viruses e.g., hepatitis B and/or C virus, human immunodeficiency virus, CMV, herpes simplex virus, human papilloma virus, etc.
• a nucleic acid sequence that directs alternative splicing can be delivered.
• an antisense sequence (or other inhibitory sequence) complementary to the 5' and/or 3' splice site of dystrophin exon 51 can be delivered in conjunction with a Ul or U7 small nuclear (sn) RNA promoter to induce skipping of this exon.
• a DNA sequence comprising a Ul or U7 snRNA promoter located 5' to the antisense/inhibitory sequence(s) can be packaged and delivered in a modified capsid of the invention.
• the virus vector may also comprise a heterologous nucleic acid molecule that shares homology with and recombines with a locus on a host cell chromosome. This approach can be utilized, for example, to correct a genetic defect in the host cell.
• the present invention also provides virus vectors that express an immunogenic polypeptide, peptide and/or epitope, e.g., for vaccination.
• the nucleic acid molecule may encode any immunogen of interest known in the art including, but not limited to,
• HAV human immunodeficiency virus
• SIV simian immunodeficiency virus
• influenza virus HIV or SIV gag proteins
• tumor antigens cancer antigens
• bacterial antigens bacterial antigens
• viral antigens and the like.
• parvoviruses as vaccine vectors is known in the art (see, e.g., Miyamura et al, (1994) Proc. Nat. Acad. Sci USA 91 :8507; U.S. Patent No. 5,916,563 to Young et al,
• the immunogen or antigen may be expressed from a heterologous nucleic acid molecule introduced into a recombinant vector genome.
• Any immunogen or antigen of interest as described herein and/or as is known in the art can be provided by the virus vector of the present invention.
• An immunogenic polypeptide can be any polypeptide, peptide, and/or epitope suitable for eliciting an immune response and/or protecting the subject against an infection and/or disease, including, but not limited to, microbial, bacterial, protozoal, parasitic, fungal and/or viral infections and diseases.
• the immunogenic polypeptide can be an orthomyxovirus immunogen (e.g ., an influenza virus immunogen, such as the influenza virus hemagglutinin (HA) surface protein or the influenza virus nucleoprotein, or an equine influenza virus immunogen) or a lentivirus immunogen (e.g., an equine infectious anemia virus immunogen, a Simian Immunodeficiency Virus (SIV) immunogen, or a Human Immunodeficiency Virus (HIV) immunogen, such as the HIV or SIV envelope GP160 protein, the HIV or SIV matrix/capsid proteins, and the HIV or SIV gag, pol and env genes products).
• an influenza virus immunogen such as the influenza virus hemagglutinin (HA) surface protein or the influenza virus nucleoprotein, or an equine influenza virus immunogen
• a lentivirus immunogen e.g., an equine infectious anemia virus immunogen, a Simian Immunode
• the immunogenic polypeptide can also be an arenavirus immunogen (e.g., Lassa fever virus immunogen, such as the Lassa fever virus nucleocapsid protein and the Lassa fever envelope glycoprotein), a poxvirus immunogen (e.g., a vaccinia virus immunogen, such as the vaccinia Ll or L8 gene products), a flavivirus immunogen (e.g., a yellow fever virus immunogen or a Japanese encephalitis virus immunogen), a filovirus immunogen (e.g, an Ebola virus immunogen, or a Marburg virus immunogen, such as NP and GP gene products), a bunyavirus immunogen (e.g, RVFV, CCHF, and/or SFS virus immunogens), or a coronavirus immunogen (e.g., an infectious human coronavirus immunogen, such as the human coronavirus envelope glycoprotein, or a porcine transmissible gastroenteritis virus immunogen, or an avian infectious
• the immunogenic polypeptide can further be a polio immunogen, a herpes immunogen (e.g, CMV, EBV, HSV immunogens) a mumps immunogen, a measles immunogen, a rubella immunogen, a diphtheria toxin or other diphtheria immunogen, a pertussis antigen, a hepatitis (e.g, hepatitis A, hepatitis B, hepatitis C, etc.) immunogen, and/or any other vaccine immunogen now known in the art or later identified as an immunogen.
• a herpes immunogen e.g, CMV, EBV, HSV immunogens
• a mumps immunogen e.g, a mumps immunogen
• measles immunogen e.g., a measles immunogen
• a rubella immunogen e.g., a diphtheria toxin or other diphtheria immunogen
• the immunogenic polypeptide can be any tumor or cancer cell antigen.
• the tumor or cancer antigen is expressed on the surface of the cancer cell.
• cancer and tumor cell antigens are described in S.A. Rosenberg (Immunity 10:281 (1991)).
• Other illustrative cancer and tumor antigens include, but are not limited to: BRCA1 gene product, BRCA2 gene product, gplOO, tyrosinase, GAGE- 1/2, BAGE, RAGE, LAGE, NY-ESO-l, CDK-4, b-catenin, MUM-l, Caspase-8, KIAA0205, HPVE, SART-l, PRAME, pl5, melanoma tumor antigens (Kawakami et al., (1994) Proc. Natl. Acad. Sci. USA 91 :3515; Kawakami et al., (1994) J. Exp. Med., 180:347; Kawakami et al., (1994) Cancer Res.
• telomerases telomerases
• nuclear matrix proteins prostatic acid phosphatase
• papilloma virus antigens and/or antigens now known or later discovered to be associated with the following cancers: melanoma, adenocarcinoma, thymoma, lymphoma (e.g ., non-Hodgkin’s lymphoma,
• heterologous nucleic acid molecule can encode any polypeptide, peptide and/or epitope that is desirably produced in a cell in vitro, ex vivo, or in vivo.
• virus vectors may be introduced into cultured cells and the expressed gene product isolated therefrom.
• heterologous nucleic acid molecule(s) of interest can be operably associated with appropriate control sequences.
• the heterologous nucleic acid molecule can be operably associated with expression control elements, such as transcription/translation control signals, origins of replication, polyadenylation signals, internal ribosome entry sites (IRES), promoters, and/or enhancers, and the like.
• expression control elements such as transcription/translation control signals, origins of replication, polyadenylation signals, internal ribosome entry sites (IRES), promoters, and/or enhancers, and the like.
• heterologous nucleic acid molecule(s) of interest can be achieved at the post-transcriptional level, e.g., by regulating selective splicing of different introns by the presence or absence of an oligonucleotide, small molecule and/or other compound that selectively blocks splicing activity at specific sites (e.g., as described in WO 2006/119137).
• oligonucleotide, small molecule and/or other compound that selectively blocks splicing activity at specific sites e.g., as described in WO 2006/119137.
• promoter/enhancer elements can be used depending on the level and tissue-specific expression desired.
• promoter/enhancer can be constitutive or inducible, depending on the pattern of expression desired.
• the promoter/enhancer can be native or foreign and can be a natural or a synthetic sequence. By foreign, it is intended that the transcriptional initiation region is not found in the wild-type host into which the transcriptional initiation region is introduced.
• the promoter/enhancer elements can be native to the target cell or subject to be treated.
• the promoters/enhancer element can be native to the heterologous nucleic acid sequence.
• the promoter/enhancer element is generally chosen so that it functions in the target cell(s) of interest. Further, in particular embodiments the promoter/enhancer element is a mammalian promo ter/enhancer element.
• the promoter/enhancer element may be constitutive or inducible.
• Inducible expression control elements are typically advantageous in those applications in which it is desirable to provide regulation over expression of the heterologous nucleic acid sequence(s).
• Inducible promoters/enhancer elements for gene delivery can be tissue-specific or -preferred promoter/enhancer elements, and include muscle specific or preferred
• inducible promoter/enhancer elements include hormone-inducible and metal-inducible elements.
• exemplary inducible promoters/enhancer elements include, but are not limited to, a Tet on/off element, a RU486-inducible promoter, an ecdysone-inducible promoter, a rapamycin-inducible promoter, and a metallothionein promoter.
• heterologous nucleic acid sequence(s) is transcribed and then translated in the target cells
• specific initiation signals are generally included for efficient translation of inserted protein coding sequences.
• exogenous translational control sequences which may include the ATG initiation codon and adjacent sequences, can be of a variety of origins, both natural and synthetic.
• the virus vectors according to the present invention provide a means for delivering heterologous nucleic acid molecules into a broad range of cells, including dividing and nondividing cells.
• the virus vectors can be employed to deliver a nucleic acid molecule of interest to a cell in vitro , e.g., to produce a polypeptide in vitro or for ex vivo or in vivo gene therapy.
• the virus vectors are additionally useful in a method of delivering a nucleic acid to a subject in need thereof, e.g., to express an immunogenic or therapeutic polypeptide or a functional RNA. In this manner, the polypeptide or functional RNA can be produced in vivo in the subject.
• the subject can be in need of the polypeptide because the subject has a deficiency of the polypeptide.
• the method can be practiced because the production of the polypeptide or functional RNA in the subject may impart some beneficial effect.
• the virus vectors can also be used to produce a polypeptide of interest or functional RNA in cultured cells or in a subject (e.g., using the subject as a bioreactor to produce the polypeptide or to observe the effects of the functional RNA on the subject, for example, in connection with screening methods).
• virus vectors of the present invention can be employed to deliver a heterologous nucleic acid molecule encoding a polypeptide or functional RNA to treat and/or prevent any disorder or disease state for which it is beneficial to deliver a therapeutic polypeptide or functional RNA.
• Illustrative disease states include, but are not limited to: cystic fibrosis (cystic fibrosis transmembrane regulator protein) and other diseases of the lung, hemophilia A (Factor VIII), hemophilia B (Factor IX), thalassemia (B-globin), anemia (erythropoietin) and other blood disorders, Alzheimer’s disease (GDF; neprilysin), multiple sclerosis (B-interferon), Parkinson’s disease (glial-cell line derived neurotrophic factor
• GDNF Huntington’s disease
• RNAi to remove repeats
• amyotrophic lateral sclerosis epilepsy
• epilepsy galanin, neurotrophic factors
• cancer endostatin, angiostatin, TRAIL, FAS-ligand, cytokines including interferons
• RNAi including RNAi against VEGF or the multiple drug resistance gene product, mir-26a [e.g., for hepatocellular carcinoma]
• diabetes mellitus insulin
• muscular dystrophies including Duchenne
• strophin mini-dystrophin, insulin-like growth factor I, a sarcoglycan [e.g, a, b, g], RNAi against myostatin, myostatin propeptide, follistatin, activin type II soluble receptor, anti- inflammatory polypeptides such as the Ikappa B dominant mutant, sarcospan, utrophin, mini- utrophin, antisense or RNAi against splice junctions in the dystrophin gene to induce exon skipping [see, e.g., WO/2003/095647], antisense against U7 snRNAs to induce exon skipping [see, e.g., WO/2006/021724], and antibodies or antibody fragments against myostatin or myostatin propeptide) and Becker, Gaucher disease (glucocerebrosidase), Hurler’s disease (a- L-iduronidase), adenosine dea
• GDNF astrocytomas [endostatin, angiostatin and/or RNAi against VEGF], glioblastomas [endostatin, angiostatin and/or RNAi against VEGF]), liver, kidney, heart including congestive heart failure or peripheral artery disease (PAD)
• PAD peripheral artery disease
• protein phosphatase inhibitor I (1-1) and fragments thereof (e.g., I1C), serca2a zinc finger proteins that regulate the phospholamban gene, Barkct, p2-adrenergic receptor, b2- adrenergic receptor kinase (BARK), phosphoinositide-3 kinase (PI3 kinase), S100A1, parvalbumin, adenylyl cyclase type 6, a molecule that effects G-protein coupled receptor kinase type 2 knockdown such as a truncated constitutively active bARKct; calsarcin, RNAi against
• the invention can further be used following organ transplantation to increase the success of the transplant and/or to reduce the negative side effects of organ transplantation or adjunct therapies (e.g., by administering immunosuppressant agents or inhibitory nucleic acids to block cytokine production).
• organ transplantation or adjunct therapies e.g., by administering immunosuppressant agents or inhibitory nucleic acids to block cytokine production.
• bone morpho genic proteins including BNP 2, 7, etc., RANKL and/or VEGF
• the invention can also be used to produce induced pluripotent stem cells (iPS).
• a virus vector of the invention can be used to deliver stem cell associated nucleic acid(s) into a non-pluripotent cell, such as adult fibroblasts, skin cells, liver cells, renal cells, adipose cells, cardiac cells, neural cells, epithelial cells, endothelial cells, and the like.
• Nucleic acids encoding factors associated with stem cells are known in the art.
• Nonlimiting examples of such factors associated with stem cells and pluripotency include Oct-3/4, the SOX family (e.g., SOX1, SOX2, SOX3 and/or SOX15), the Klf family (e.g, Klfl, Klf2, Klf4 and/or Klf5), the Myc family (e.g., C-myc, L-myc and/or N-myc), NANOG and/or LIN28.
• SOX family e.g., SOX1, SOX2, SOX3 and/or SOX15
• the Klf family e.g, Klfl, Klf2, Klf4 and/or Klf5
• the Myc family e.g., C-myc, L-myc and/or N-myc
• NANOG e.g., NANOG and/or LIN28.
• the invention can also be practiced to treat and/or prevent a metabolic disorder such as diabetes (e.g., insulin), hemophilia (e.g., Factor IX or Factor VIII), a lysosomal storage disorder such as a mucopolysaccharidosis disorder (e.g, Sly syndrome [b-glucuronidase], Hurler Syndrome [a-L-iduronidase], Scheie Syndrome [a-L-iduronidase], Hurler-Scheie Syndrome [a-L-iduronidase], Hunter's Syndrome [iduronate sulfatase], Sanfilippo Syndrome A [heparan sulfamidase], B [N-acetylglucosaminidase], C [acetyl-CoA:a-glucosaminide acetyltransferase], D [N-acetylglucosamine 6-sulfatase], Morquio Syndrome A [galactose-6- sulfate sulfat
• deficiency states usually of enzymes, which are generally inherited in a recessive manner, and unbalanced states, which may involve regulatory or structural proteins, and which are typically inherited in a dominant manner.
• gene transfer can be used to bring a normal gene into affected tissues for replacement therapy, as well as to create animal models for the disease using antisense mutations.
• gene transfer can be used to create a disease state in a model system, which can then be used in efforts to counteract the disease state.
• virus vectors according to the present invention permit the treatment and/or prevention of genetic diseases.
• the virus vectors according to the present invention may also be employed to provide a functional RNA to a cell in vitro or in vivo.
• Expression of the functional RNA in the cell can diminish expression of a particular target protein by the cell.
• functional RNA can be administered to decrease expression of a particular protein in a subject in need thereof.
• Functional RNA can also be administered to cells in vitro to regulate gene expression and/or cell physiology, e.g., to optimize cell or tissue culture systems or in screening methods.
• virus vectors according to the instant invention find use in diagnostic and screening methods, whereby a nucleic acid of interest is transiently or stably expressed in a cell culture system, or alternatively, a transgenic animal model.
• the virus vectors of the present invention can also be used for various non-therapeutic purposes, including but not limited to use in protocols to assess gene targeting, clearance, transcription, translation, etc., as would be apparent to one skilled in the art.
• the virus vectors can also be used for the purpose of evaluating safety (spread, toxicity,
• virus vectors of the present invention may be used to produce an immune response in a subject.
• a virus vector comprising a heterologous nucleic acid sequence encoding an immunogenic polypeptide can be
• Immunogenic polypeptides are as described hereinabove. In some embodiments, a protective immune response is elicited.
• An“active immune response” or“active immunity” is characterized by“participation of host tissues and cells after an encounter with the immunogen. It involves differentiation and proliferation of immunocompetent cells in lymphoreticular tissues, which lead to synthesis of antibody or the development of cell-mediated reactivity, or both.” Herbert B. Herscowitz, Immunophysiology: Cell Function and Cellular Interactions in Antibody
• an active immune response is mounted by the host after exposure to an immunogen by infection or by vaccination.
• Active immunity can be contrasted with passive immunity, which is acquired through the“transfer of preformed substances (antibody, transfer factor, thymic graft, interleukin-2) from an actively immunized host to a non-immune host.” Id.
• A“protective” immune response or“protective” immunity as used herein indicates that the immune response confers some benefit to the subject in that it prevents or reduces the incidence of disease.
• a protective immune response or protective immunity may be useful in the treatment and/or prevention of disease, in particular cancer or tumors (e.g., by preventing cancer or tumor formation, by causing regression of a cancer or tumor and/or by preventing metastasis and/or by preventing growth of metastatic nodules).
• the protective effects may be complete or partial, as long as the benefits of the treatment outweigh any disadvantages thereof.
• the virus vector or cell comprising the heterologous nucleic acid molecule can be administered in an immunogenically effective amount, as described below.
• the virus vectors of the present invention can also be administered for cancer immunotherapy by administration of a virus vector expressing one or more cancer cell antigens (or an immunologically similar molecule) or any other immunogen that produces an immune response against a cancer cell.
• a virus vector expressing one or more cancer cell antigens (or an immunologically similar molecule) or any other immunogen that produces an immune response against a cancer cell.
• an immune response can be produced against a cancer cell antigen in a subject by administering a virus vector comprising a heterologous nucleic acid encoding the cancer cell antigen, for example to treat a patient with cancer and/or to prevent cancer from developing in the subject.
• the virus vector may be administered to a subject in vivo or by using ex vivo methods, as described herein.
• cancer antigen can be expressed as part of the virus capsid or be otherwise associated with the virus capsid (e.g., as described above).
• any other therapeutic nucleic acid e.g., RNAi
• polypeptide e.g., cytokine
• cancer encompasses tumor-forming cancers.
• cancer tissue encompasses tumors.
• A“cancer cell antigen” encompasses tumor antigens.
• cancer has its understood meaning in the art, for example, an uncontrolled growth of tissue that has the potential to spread to distant sites of the body (i.e., metastasize).
• exemplary cancers include, but are not limited to melanoma, adenocarcinoma, thymoma, lymphoma (e.g, non-Hodgkin’s lymphoma, Hodgkin’s lymphoma), sarcoma, lung cancer, liver cancer, colon cancer, leukemia, uterine cancer, breast cancer, prostate cancer, ovarian cancer, cervical cancer, bladder cancer, kidney cancer, pancreatic cancer, brain cancer and any other cancer or malignant condition now known or later identified.
• the invention provides a method of treating and/or preventing tumor- forming cancers.
• Tumor is also understood in the art, for example, as an abnormal mass of undifferentiated cells within a multicellular organism. Tumors can be malignant or benign. In representative embodiments, the methods disclosed herein are used to prevent and treat malignant tumors.
• “treating cancer,”“treatment of cancer” and equivalent terms it is intended that the severity of the cancer is reduced or at least partially eliminated and/or the progression of the disease is slowed and/or controlled and/or the disease is stabilized.
• these terms indicate that metastasis of the cancer is prevented or reduced or at least partially eliminated and/or that growth of metastatic nodules is prevented or reduced or at least partially eliminated.
• prevention of cancer or“preventing cancer” and equivalent terms it is intended that the methods at least partially eliminate or reduce and/or delay the incidence and/or severity of the onset of cancer.
• the onset of cancer in the subject may be reduced in likelihood or probability and/or delayed.
• immunomodulatory cytokines e.g., a-interferon, b-interferon, g-interferon, w-interferon, x-interferon, interleukin- la, interleukin- 1b, interleukin-2, interleukin-3, interleukin-4, interleukin 5, interleukin-6, interleukin-7, interleukin- 8, interleukin-9, interleukin- 10, interleukin-l l, interleukin 12, interleukin- 13, interleukin- 14, interleukin-l8, B cell Growth factor, CD40 Ligand, tumor necrosis factor-a, tumor necrosis factor-b, monocyte chemoattractant protein-l, granulocyte- macrophage colony stimulating factor, and lymphotoxin).
• immunomodulatory cytokines preferably, CTL inductive cytokines
• Cytokines may be administered by any method known in the art. Exogenous cytokines may be administered to the subject, or alternatively, a nucleic acid encoding a cytokine may be delivered to the subject using a suitable vector, and the cytokine produced in vivo.
• Virus vectors and AAV particles according to the present invention find use in both veterinary and medical applications. Suitable subjects include both avians and mammals.
• avian as used herein includes, but is not limited to, chickens, ducks, geese, quail, turkeys, pheasant, parrots, parakeets, and the like.
• mamal as used herein includes, but is not limited to, humans, non-human primates, bovines, ovines, caprines, equines, felines, canines, lagomorphs, etc. Human subjects include neonates, infants, juveniles, adults and geriatric subjects.
• the subject is "in need of' the methods of the invention.
• the present invention provides a pharmaceutical composition
• a pharmaceutical composition comprising a virus vector and/or capsid and/or AAV particle of the invention in a pharmaceutically acceptable carrier and, optionally, other medicinal agents, pharmaceutical agents, stabilizing agents, buffers, carriers, adjuvants, diluents, etc.
• the carrier will typically be a liquid.
• the carrier may be either solid or liquid.
• the carrier will be respirable, and optionally can be in solid or liquid particulate form.
• the carrier will be sterile and/or physiologically compatible.
• pharmaceutically acceptable it is meant a material that is not toxic or otherwise undesirable, i.e., the material may be administered to a subject without causing any undesirable biological effects.
• the virus vector may be introduced into the cells at the appropriate multiplicity of infection according to standard transduction methods suitable for the particular target cells.
• Titers of virus vector to administer can vary, depending upon the target cell type and number, and the particular virus vector, and can be determined by those of skill in the art without undue experimentation.
• at least about 10 infectious units, optionally at least about 10 5 infectious units are introduced to the cell.
• the cell(s) into which the virus vector is introduced can be of any type, including but not limited to neural cells (including cells of the peripheral and central nervous systems, in particular, brain cells such as neurons and oligodendricytes), lung cells, cells of the eye (including retinal cells, retinal pigment epithelium, and corneal cells), epithelial cells (e.g., gut and respiratory epithelial cells), muscle cells (e.g., skeletal muscle cells, cardiac muscle cells, smooth muscle cells and/or diaphragm muscle cells), dendritic cells, pancreatic cells (including islet cells), hepatic cells, myocardial cells, bone cells (e.g., bone marrow stem cells), hematopoietic stem cells, spleen cells, keratinocytes, fibroblasts, endothelial cells, prostate cells, germ cells, and the like.
• neural cells including cells of the peripheral and central nervous systems, in particular, brain cells such as neurons and oligodendricytes
• lung cells
• the cell can be any progenitor cell.
• the cell can be a stem cell (e.g., neural stem cell, liver stem cell).
• the cell can be a cancer or tumor cell.
• the cell can be from any species of origin, as indicated above.
• the virus vector can be introduced into cells in vitro for the purpose of administering the modified cell to a subject.
• the cells have been removed from a subject, the virus vector is introduced therein, and the cells are then administered back into the subject.
• Methods of removing cells from subject for manipulation ex vivo, followed by introduction back into the subject are known in the art (see, e.g., U.S. patent No. 5,399,346).
• the recombinant virus vector can be introduced into cells from a donor subject, into cultured cells, or into cells from any other suitable source, and the cells are administered to a subject in need thereof (i.e., a "recipient" subject).
• Suitable cells for ex vivo nucleic acid delivery are as described above. Dosages of the cells to administer to a subject will vary upon the age, condition and species of the subject, the type of cell, the nucleic acid being expressed by the cell, the mode of administration, and the like. Typically, at least about 10 2 to about 10 8 cells or at least about 10 3 to about 10 6 cells will be administered per dose in a pharmaceutically acceptable carrier. In particular embodiments, the cells transduced with the virus vector are administered to the subject in a treatment effective or prevention effective amount in combination with a pharmaceutical carrier.
• the virus vector is introduced into a cell and the cell can be administered to a subject to elicit an immunogenic response against the delivered polypeptide (e.g., expressed as a transgene or in the capsid).
• an immunogenic response against the delivered polypeptide e.g., expressed as a transgene or in the capsid.
• An“immunogenically effective amount” is an amount of the expressed polypeptide that is sufficient to evoke an active immune response against the polypeptide in the subject to which the pharmaceutical formulation is administered.
• the dosage is sufficient to produce a protective immune response (as defined above). The degree of protection conferred need not be complete or permanent, as long as the benefits of administering the immunogenic polypeptide outweigh any disadvantages thereof.
• a further aspect of the invention is a method of administering the virus vector and/or virus capsid to subjects.
• Administration of the virus vectors and/or capsids according to the present invention to a human subject or an animal in need thereof can be by any means known in the art.
• the virus vector and/or capsid is delivered in a treatment effective or prevention effective dose in a pharmaceutically acceptable carrier.
• the virus vectors and/or capsids of the invention can further be administered to elicit an immunogenic response (e.g., as a vaccine).
• immunogenic compositions of the present invention comprise an immunogenically effective amount of virus vector and/or capsid in combination with a pharmaceutically acceptable carrier.
• the dosage is sufficient to produce a protective immune response (as defined above).
• the degree of protection conferred need not be complete or permanent, as long as the benefits of administering the immunogenic polypeptide outweigh any disadvantages thereof.
• Subjects and immunogens are as described above.
• Dosages of the virus vector and/or capsid to be administered to a subject depend upon the mode of administration, the disease or condition to be treated and/or prevented, the individual subject’s condition, the particular virus vector or capsid, and the nucleic acid to be delivered, and the like, and can be determined in a routine manner.
• Exemplary doses for achieving therapeutic effects are titers of at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 3 , 10 14 , 10 15 transducing units, optionally about l0 8 to about 10 13 transducing units.
• more than one administration may be employed to achieve the desired level of gene expression over a period of various intervals, e.g., hourly, daily, weekly, monthly, yearly, etc.
• Exemplary modes of administration include oral, rectal, transmucosal, intranasal, inhalation (e.g, via an aerosol), buccal (e.g., sublingual), vaginal, intrathecal, intraocular, transdermal, in utero (or in ovo ), parenteral (e.g., intravenous, subcutaneous, intradermal, intramuscular [including administration to skeletal, diaphragm and/or cardiac muscle], intradermal, intrapleural, intracerebral, and intraarticular), topical (e.g, to both skin and mucosal surfaces, including airway surfaces, and transdermal administration), intralymphatic, and the like, as well as direct tissue or organ injection (e.g, to liver, skeletal muscle, cardiac muscle, diaphragm muscle or brain).
• Administration can also be to a tumor (e.g, in or near a tumor or a lymph node). The most suitable route in any given case will depend on the nature and severity of the condition being treated and
• the virus vector and/or capsid can be delivered by intravenous administration, intraarterial administration, intraperitoneal administration, limb perfusion, (optionally, isolated limb perfusion of a leg and/or arm; see, e.g. Arruda et al., (2005) Blood 105: 3458-3464), and/or direct intramuscular injection.
• the virus vector and/or capsid is administered to a limb (arm and/or leg) of a subject (e.g., a subject with muscular dystrophy such as DMD) by limb perfusion, optionally isolated limb perfusion (e.g., by intravenous or intra-articular administration).
• the virus vectors and/or capsids of the invention can advantageously be administered without employing“hydrodynamic” techniques.
• Tissue delivery (e.g., to muscle) of prior art vectors is often enhanced by hydrodynamic techniques (e.g, intravenous/intravenous administration in a large volume), which increase pressure in the vasculature and facilitate the ability of the vector to cross the endothelial cell barrier.
• the viral vectors and/or capsids of the invention can be administered in the absence of hydrodynamic techniques such as high volume infusions and/or elevated intravascular pressure (e.g., greater than normal systolic pressure, for example, less than or equal to a 5%, 10%, 15%, 20%, 25% increase in intravascular pressure over normal systolic pressure).
• hydrodynamic techniques such as high volume infusions and/or elevated intravascular pressure (e.g., greater than normal systolic pressure, for example, less than or equal to a 5%, 10%, 15%, 20%, 25% increase in intravascular pressure over normal systolic pressure).
• the invention can also be practiced to produce antisense RNA, RNAi or other functional RNA (e.g., a ribozyme) for systemic delivery.
• Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions.
• one may administer the virus vector and/or virus capsids of the invention in a local rather than systemic manner, for example, in a depot or sustained-release formulation.
• the virus vector and/or virus capsid can be delivered adhered to a surgically implantable matrix (e.g., as described in U.S. Patent Publication No. US-2004- 0013645-A1).
• the delivery vectors of the invention may be administered to treat diseases of the CNS, including genetic disorders, neurodegenerative disorders, psychiatric disorders and tumors.
• diseases of the CNS include, but are not limited to Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Canavan disease, Leigh's disease, Refsum disease, Tourette syndrome, primary lateral sclerosis, amyotrophic lateral sclerosis, progressive muscular atrophy, Pick's disease, muscular dystrophy, multiple sclerosis, myasthenia gravis, Binswanger's disease, trauma due to spinal cord or head injury, Tay Sachs disease, Lesch-Nyan disease, epilepsy, cerebral infarcts, psychiatric disorders including mood disorders (e.g., depression, bipolar affective disorder, persistent affective disorder, secondary mood disorder), schizophrenia, drug dependency (e.g., alcoholism and other substance dependencies), neuroses (e.g., anxiety, obsessional disorder, somatoform disorder, dissoci
• mood disorders e
• disorders of the CNS include ophthalmic disorders involving the retina, posterior tract, and optic nerve (e.g., retinitis pigmentosa, diabetic retinopathy and other retinal degenerative diseases, uveitis, age-related macular degeneration, glaucoma).
• optic nerve e.g., retinitis pigmentosa, diabetic retinopathy and other retinal degenerative diseases, uveitis, age-related macular degeneration, glaucoma.
• ophthalmic diseases and disorders are associated with one or more of three types of indications: (1) angiogenesis, (2) inflammation, and (3) degeneration.
• the delivery vectors of the present invention can be employed to deliver anti-angiogenic factors; anti-inflammatory factors; factors that retard cell degeneration, promote cell sparing, or promote cell growth and combinations of the foregoing.
• Diabetic retinopathy for example, is characterized by angiogenesis. Diabetic retinopathy can be treated by delivering one or more anti-angiogenic factors either intraocularly ( e.g ., in the vitreous) or periocularly (e.g., in the sub-Tenon's region). One or more neurotrophic factors may also be co-delivered, either intraocularly (e.g., intravitreally) or periocularly.
• Uveitis involves inflammation.
• One or more anti-inflammatory factors can be administered by intraocular (e.g., vitreous or anterior chamber) administration of a delivery vector of the invention.
• Retinitis pigmentosa by comparison, is characterized by retinal degeneration.
• retinitis pigmentosa can be treated by intraocular (e.g., vitreal administration) of a delivery vector encoding one or more neurotrophic factors.
• Age-related macular degeneration involves both angiogenesis and retinal
• This disorder can be treated by administering the inventive deliver vectors encoding one or more neurotrophic factors intraocularly (e.g., vitreous) and/or one or more anti-angiogenic factors intraocularly or periocularly (e.g., in the sub-Tenon's region).
• one or more neurotrophic factors intraocularly (e.g., vitreous) and/or one or more anti-angiogenic factors intraocularly or periocularly (e.g., in the sub-Tenon's region).
• Glaucoma is characterized by increased ocular pressure and loss of retinal ganglion cells.
• Treatments for glaucoma include administration of one or more neuroprotective agents that protect cells from excitotoxic damage using the inventive delivery vectors.
• Such agents include N-methyl-D-aspartate (NMD A) antagonists, cytokines, and neurotrophic factors, delivered intraocularly, optionally intravitreally.
• NMD A N-methyl-D-aspartate
• cytokines cytokines
• neurotrophic factors delivered intraocularly, optionally intravitreally.
• the present invention may be used to treat seizures, e.g., to reduce the onset, incidence or severity of seizures.
• the efficacy of a therapeutic treatment for seizures can be assessed by behavioral (e.g., shaking, ticks of the eye or mouth) and/or electrographic means (most seizures have signature electrographic abnormalities).
• the invention can also be used to treat epilepsy, which is marked by multiple seizures over time.
• somatostatin (or an active fragment thereof) is administered to the brain using a delivery vector of the invention to treat a pituitary tumor.
• the delivery vector encoding somatostatin (or an active fragment thereof) is administered by microinfusion into the pituitary.
• such treatment can be used to treat acromegaly (abnormal growth hormone secretion from the pituitary).
• the nucleic acid e.g., GenBank Accession No. J00306) and amino acid (e.g, GenBank Accession No. P01166; contains processed active peptides somatostatin-28 and somatostatin- 14) sequences of somatostatins are known in the art.
• the vector can comprise a secretory signal as described in U.S. Patent No. 7,071,172.
• the virus vector and/or virus capsid is delivered to the CNS (e.g., to the brain or to the eye) after systemic administration.
• the virus vector and/or capsid may be introduced into the spinal cord, brainstem (medulla oblongata, pons), midbrain (hypothalamus, thalamus, epithalamus, pituitary gland, substantia nigra, pineal gland), cerebellum, telencephalon (corpus striatum, cerebrum including the occipital, temporal, parietal and frontal lobes cortex, basal ganglia, hippocampus and portaamygdala), limbic system, neocortex, corpus striatum, cerebrum, and inferior colliculus.
• the virus vector and/or capsid may also be delivered to different regions of the eye such as the retina, cornea and/or optic nerve after peripheral administration.
• the virus vector and/or capsid may be delivered into the cerebrospinal fluid (e.g., by lumbar puncture) for more disperse administration of the delivery vector.
• the virus vector and/or capsid may further be administered intravascularly to the CNS in situations in which the blood-brain barrier has been perturbed (e.g., brain tumor or cerebral infarct).
• the virus vector and/or capsid can be administered to the desired region(s) of the body by any route known in the art, including but not limited to, intrathecal, intra-ocular, intracerebral, intraventricular, intravenous (e.g., in the presence of a sugar such as mannitol), intranasal, intra-aural, intra-ocular (e.g, intra-vitreous, sub-retinal, anterior chamber) and peri-ocular (e.g., sub-Tenon's region) delivery as well as intramuscular delivery with retrograde delivery to motor neurons.
• intrathecal intra-ocular, intracerebral, intraventricular, intravenous (e.g., in the presence of a sugar such as mannitol), intranasal, intra-aural, intra-ocular (e.g, intra-vitreous, sub-retinal, anterior chamber) and peri-ocular (e.g., sub-Tenon's region) delivery as well as intra
• the virus vector is administered in a liquid formulation by direct injection (e.g, stereotactic injection) to the desired region or compartment in the CNS.
• direct injection e.g, stereotactic injection
• the virus vector and/or capsid may be provided by topical application to the desired region or by intra-nasal administration of an aerosol formulation.
• virus vector and/or capsid may be administered as a solid, slow-release formulation (see, e.g., U.S. Patent No. 7,201,898).
• the virus vector can be used for retrograde transport to treat and/or prevent diseases and disorders involving motor neurons (e.g., amyotrophic lateral sclerosis (ALS); spinal muscular atrophy (SMA), etc.).
• the virus vector can be delivered to muscle tissue from which it can migrate into neurons.
• the present invention may be as defined in any one of the following numbered paragraphs:
• a recombinant nucleic acid molecule comprising an adeno-associated virus (AAV) 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the recombinant nucleic acid molecule further comprises:
• a recombinant nucleic acid molecule comprising an adeno-associated virus (AAV) vector cassette of a first AAV serotype comprising an AAV 5' inverted terminal repeat (ITR), a nucleotide sequence of interest (NOI) operably associated with a promoter and an AAV 3’ ITR, wherein the AAV 5’ ITR and/or the AAV 3’ ITR is from a second AAV serotype that is different than the first AAV serotype.
• AAV adeno-associated virus
• ITR AAV 5' inverted terminal repeat
• NOI nucleotide sequence of interest
• a recombinant nucleic acid molecule of paragraph 2 wherein the first AAV serotype is AAV2 and the second AAV serotype is AAV5. 4.
• AAV adeno-associated virus
• NOI nucleotide sequence of interest
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, an NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR, wherein the NOI sequence is fused with one or more than one nucleotide sequence that encodes an interfering RNA sequence that targets a cytoplasmic dsRNA sensor.
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, an NOI operably associated with a first promoter, a first pA sequence in 3’ to 5’ orientation, a nucleotide sequence that encodes an interfering RNA sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, a second pA sequence and an AAV 3’ ITR.
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a first promoter, a pA sequence in 3’ to 5’ orientation, a short hairpin RNA (shRNA) sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, and an AAV 3’ ITR.
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a first promoter, a pA sequence in 3’ to 5’ orientation, a short hairpin RNA (shRNA) sequence that targets a cytoplasmic dsRNA sensor, operably associated with a second promoter, and an AAV 3’ ITR.
• shRNA short hairpin RNA
• a recombinant nucleic acid molecule comprising an AAV 5’ ITR, a shRNA that targets a cytoplasmic dsRNA sensor, operably associated with a first promoter, a NOI operably associated with a second promoter, a pA sequence in 3’ to 5’ orientation and an AAV 3’ ITR.
• a recombinant nucleic acid molecule comprising, in the following order: an AAV 5’ ITR, a NOI and a micro RNA (miRNA) sequence that targets a cytoplasmic dsRNA sensor, both operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR.
• an AAV 5’ ITR a NOI and a micro RNA (miRNA) sequence that targets a cytoplasmic dsRNA sensor, both operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR.
• miRNA micro RNA
• a recombinant nucleic acid molecule comprising, in the following order: an AAV 5’ ITR, a miRNA that targets a cytoplasmic dsRNA sensor and a NOI, both operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR.
• a recombinant nucleic acid molecule comprising, in the following order: an AAV 5’ ITR, a NOI comprising a miRNA intron sequence within the NOI, the NOI being operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR.
• a composition comprising a first recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR and a second recombinant nucleic acid molecule comprising an interfering RNA sequence that targets a cytoplasmic dsRNA sensor.
• composition of paragraph 12, wherein the interfering RNA sequence is shRNA.
• a recombinant nucleic acid molecule comprising:
• aNOI and an inhibitor of MAVS signaling both operably associated with a promoter; a pA sequence in 3’ to 5’ orientation;
• inhibitor of MAVS signaling is selected from the group consisting of: a serine protease NS3-4A from hepatitis C virus, a protease from Hepatitis A virus, a protease from GB virus B, hepatitis B virus (HBV) X protein, poly(rC) -binding protein 2, the 20S proteasomal subunit PSMA7, mitofusin 2, and any combination thereof.
• a recombinant nucleic acid molecule comprising:
• an inhibitor of MAVS signaling operably associated with a second promoter
• a rAAV vector genome comprising the recombinant nucleic acid molecule of any one of paragraphs 1-12 and 13-16.
• a rAAV particle comprising the rAAV genome of paragraph 17.
• composition comprising the rAAV particle of paragraph 18.
• a composition comprising a first recombinant nucleic acid molecule comprising an AAV 5’ ITR, a NOI operably associated with a promoter, a pA sequence in 3’ to 5’ orientation, and an AAV 3’ ITR and a second recombinant nucleic acid molecule comprising an inhibitor of MAVS signaling and a pA sequence in 3’ to 5’ orientation.
• a method of enhancing transduction of an AAV vector in cells of a subject comprising administering to the subject an AAV vector and an agent that interferes with dsRNA activation pathways in cells of the subject.
• HeLa cells 293 cells, Huh7 cells and HepG2 cells were grown in Dulbecco's Modified Eagle's Medium with 10% FBS and 1% penicillin-streptomycin at 37°C in 5%
• Human primary hepatocytes were purchased from Triangle Research Labs. The information regarding fresh human primary hepatocytes is listed in Table 1. Primary hepatocytes were plated in Williams' E Medium with Hepatocyte Thawing and Plating Supplement Pack (Thermo Fisher Scientific) and maintained in Williams' E Medium with Hepatocyte Maintenance Supplement Pack and HepExtendTM Supplement (Thermo Fisher Scientific).
• AAV virus production was described before using the triple plasmid transfection. Briefly, HEK-293 cells were transfected with an AAV transgene plasmid (single-stranded (ss) pTR-CBA-Luciferase, double-stranded (ds) pTR-CBh-GFP, ss pTR-CMV-GFP, sspTR-CBA-AAT, dspTR-shRNA-scramble and dspTR-TTR-FIX-opt), a Rep and Cap AAV helper plasmid, and an adenovirus helper plasmid pXX6-80. 48 hours post-transfection, cells were harvested. After lysis of HEK-293 cells, AAV virus was purified by cesium chloride (CsCl) gradient density centrifugation. The virus titer was determined by Q-PCR.
• CsCl cesium chloride
• mice Human xenografted mice with 70% human hepatocyte repopulation were purchased from Yecuris company. Mice were maintained in a specific pathogen-free facility at the University of North Carolina at Chapel Hill. The University of North Carolina
• HeLa, Huh7, 293 or HepG2 cells were transduced by 5 x 10 3 particles of AAV vector per cell. Transduced cells were harvested at different time points.
• mice Human hepatocytes from xenografted mice were administered with 3xl0 u particles of AAV8/FIX-opt via retro-orbital injection. At weeks 4 or 8 post AAV injection, mice were sacrificed and livers were harvested for RNA extraction and Protein analysis with Western Blot.
• Luciferase assay Cells transduced by AAV2/luciferase were treated with passive lysis buffer (Promega) for 20min. Luciferase activity was measured with Luciferase Assay Reagent (Promega) following the manufacturer's instructions. Luciferase activity was measured with a Wallac 1420 Victor3 plate reader.
• siRNA transfection at day 3 post-transduction of AAV vector, HeLa cells were split, and 24h later, cells were transfected with lpg siRNA (siMDA5:
• siMAVS AUACAACUGACCCUGUGGG (SEQ ID NO:2)
• siMAVS-2 AUACAACUGACCCUGUGGG
• RNA isolation and Real-time PCR RNA isolation and Real-time PCR. RNA from cultured cells or mouse liver tissues was isolated using TRIzol Reagent (Invitrogen). Synthesis of first strand cDNA from RNA templates was performed using RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific). Real-time PCR was performed by LightCycler 480 instrument (Roche). Primers used in real-time PCR are listed in Table 2.
• IFN-b promoter reporter assay 1 x 10 5 HeLa cells were transduced by 5 x 10 3 particles of AAV2/GFP per cell in 6 well plate. Cells were split in 1 :5 at day 3 post-transduction. Twenty four h later, cells were co-transfected with IFN-b promoter reporter plasmid and siRNA. Then luciferase activity was measured after 72h of transfection.
• IFN-b inhibits transgene expression from AAV transduced cells.
• Type I IFN-b expression is the hallmark of innate immune activation.
• poly(I:C) polyinosinic-polycytidylic acid
• FIG. 2 The data indicates that the innate immune response triggered from dsRNA impacts AAV transduction.
• Double-stranded RNA innate immune response is triggered from late AA V transduction in HeLa cells.
• AAV transduction activates the innate immune response triggered by dsRNA
• MDA5 the up- regulation of MDA5 was observed at day 6 post scAAV/GFP vector transduction in HeLa cells.
• RIG1 expression had not increased during AAV transduction in HeLa cells ( Figure 3B). No IFN-b had increased during day 3-6, however high IFN-b expression was obtained at day 8
• AA V transduction mediated dsRNA innate immune response activation is cell specific and transgene dependent.
• transgene FIX was driven by the liver specific promoter and mainly expressed in the hepatocytes.
• the results from the studies above have demonstrated that the dsRNA immune response is triggered at a later time after AAV transduction in HeLa cells, a non-hepatocyte cell line.
• AAV2/shRNA-scramble but not with AAV2/AAT ( Figure 4B).
• IFN-b expression was up-regulated in all AAV2 vector transduced cells regardless of transgenes.
• the dsRNA innate immune response is induced in AA V/GFP transduced primary human hepatocytes. It has been shown that AAV transduction triggered the dsRNA innate immune response in the human hepatocyte cell line, Huh7 cells, and as stated above, we answered whether the finding was applicable to human primary hepatocytes. It has been demonstrated that AAV2 can efficiently transduce primary human hepatocytes in vitro. We used scAAV2/GFP vectors to transduce primary human hepatocytes from 6 different subjects. At different time points after AAV2 transduction, RNA from human hepatocytes was harvested for transcriptional expression of MDA5, RIG1 and IFN-b.
• MDA5 was up- regulated in 6 out of 12 subjects beyond day 5 after AAV transduction (Figure 5A), in which higher expression of RIG1 was only observed in 3 subjects (sub 1, 5 and 12). Another 6 subjects didn’t show the expression change of MDA5 or RIG-I ( Figure 5B). However, higher expression of IFN-b was detected in all subjects after AAV transduction ( Figure 5). MDA5 expression reached the peak at day 5 or later after AAV transduction and then decreased to the baseline. There was no specific pattern for high expression of IFN-b, and in most cases, the increased IFN-b expression was accompanied with MDA5 expression at a late time point (>5 days) post AAV transduction.
• the dsRNA innate immune response is induced in AA V/FIX-opt transduced primary human hepatocytes.
• AAV vectors to deliver the therapeutic transgene FIX also triggered the dsRNA innate immune response.
• hFIX-R338L-opt enhanced coagulation activity
• MDA5 and IFN-b was up-regulated in 5 out of 10 subjects at day 5 or beyond after AAV infection
• mice The activation of the dsRNA innate immune response in human hepatocytes from AA V transduction in humanized mice. All of the above results support that the cytosolic dsRNA innate immune response in human cells is activated at a late time following AAV transduction in vitro.
• Blockage of the dsRNA activation pathway increases transgene expression and inhibits IFN-b expression from AAV transduced cells, inhibits IFN-b expression from AA V transduced cells.
• induction of the innate immune response and addition of IFN-b decreased AAV transduction.
• siRNAs specific to MDA5, and MAVS siRNAs specific to MDA5 and MAVS, a common adaptor for MDA5 and RIG1, to knockdown their expression, and studied the transgene expression and IFN-b expression.
• siRNA The transfection of siRNA was able to efficiently inhibit transcription expression of MDA5 and MAVS (Figure 8A).
• Figure 8A The transfection of siRNA was able to efficiently inhibit transcription expression of MDA5 and MAVS.
• siRNA At day 3 post AAV2/luc transduction, poly(LC) was added.
• siRNA was transfected.
• the transgene expression was measured.
• the luciferase expression was significantly increased at both 48 and 72 hrs when siRNA to MDA5 or MAVS was used.
• siRNA was transfected and IFN-b expression was measured 48 and 72 hrs later. Similar to the finding from poly(I:C) application, higher luciferase expression was achieved with administration of siRNA.
• the innate immune response system is the first line of defense against pathogens and its activation in AAV transduction has been studied. Compared to other pathogenic viruses, adeno-associated virus (AAV) infection or its recombinant vector transduction only induces transient and low innate immunity following AAV transduction. Also, all studies about innate immune response to virus have focused on the earlier time points after virus infection. In this study, we, for the first time, demonstrated that innate immune response was triggered at a late time point after long-term AAV transduction. The late innate immune response activation occurred in different cell lines and human primary hepatocytes. Most importantly, the late innate immune response was also detected in human hepatocytes from the liver of human xenografted mice after AAV transduction. The late innate immune response was mediated via the dsRNA activation pathway. Blocking of the dsRNA sensor or adaptor was able to blunt innate immune response and increase AAV transduction.
• AAV adeno-associated virus
• PRRs pattern recognition receptors
• TLRs Toll-like receptors
• RLRs RIG-I like receptors
• NLRs NOD-like receptors
• CLRs C-type lectin receptors
• AIM2-like receptors AIM2-like receptors
• cytosol DNA sensors Previous studies have demonstrated that innate immune responses are induced from AAV infection through the TLR9-MyD88 pathway in plasmacytoid DCs and TLR2 in human nonparenchymal liver cells. Another study has shown that increased TLR9 signaling was observed in the liver when AAV vectors were administered in mice via systemic administration. From these studies, the innate immune response was detected within 24 hrs.
• IFN-b The high expression of IFN-b at day 1 of AAV transduction in some primary human hepatocytes may result from the TLR9 mediated innate immune response but not from the TLR2 pathway as suggested from early studies.
• the mechanism of IFN-b up-regulation at later time points after AAV transduction has not been investigated. It is unlikely that the activation of the innate immune response at the late phase is triggered by the same mechanism as that at the early phase after AAV transduction.
• TLR9 recognition of the dsAAV genome or TLR2 recognition of the AAV capsid plays a major role in pDC or nonparenchymal liver cells for activation of the innate immune response, respectively.
• TLRs only sense PRRs localized on the cell surface or in the endosomes. After long-term AAV transduction, if PRRs from AAV vector (dsDNA AAV genome or AAV capsid protein) still remain in the endosomes, TLRs should continue to recognize these PRRs and induce a sustained IFN-b expression. This assumption is contrary to what we observed in this study that IFN-b expression was at baseline level during day 2-4 post AAV transduction in HeLa cells. Therefore, some other mechanisms should involve the activation of innate immune response at a late phase after AAV transduction.
• cytoplasmic PRRs may also detect viral nucleic acids or proteins from virus infection. Generally, RIG-I and MDA5 are able to sense cytosolic dsRNA from RNA viruses, and several DNA sensors in cytoplasm have been identified. NLR proteins are also involved in the innate immune response to virus infection.
• AAV ITRs have promoter function and the 3’ITR may transcribe minus-stranded RNA, which serves as antisense to inhibit transgene expression (Figure 9).
• This antisense RNA may bind to sense RNA to form dsRNA via annealing in the cytoplasm.
• the dsRNA generated from AAV vector transduction has potential to trigger the dsRNA innate immune response by modulation of RIG- 1 and MDA5 expression.
• MDA-5 and RIG-l bind to the common adaptor, MAVS, to promote direct or indirect transcriptional induction of many genes via activation of a few essential transcription factors including interferon-regulatory factors (IRFs) and NF-kB to produce IFN-b and inflammatory cytokines.
• IRFs interferon-regulatory factors
• NF-kB to produce IFN-b and inflammatory cytokines.
• dsRNA mediated activation of innate immune response is only detected at later phase of AAV transduction
• the promoter of AAV ITR is very weak. Therefore, it takes a relatively long time to generate enough antisense RNA from AAV 3’ITR to reach the threshold and form dsRNA.
• the biology of AAV vector transduction may play a role in dsRNA formation at the late phase of AAV transduction. Unlike adenovirus vector, the transgene expression reaches its peak at week 6 in preclinical and clinical trials and remains persistent for long term after AAV vector administration.
• Block AAV ITR promoter function The exact mechanism for dsRNA induced innate immune response from AAV transduction is unknown. One of the possibilities is the promoter function of the ITR and potential bi-directional function of the promoter for transgene expression.
• the minus strand RNA transcribed from the 3’ -ITR or the promoter, and plus strand RNA from the promoter or 5’-ITR may form double-stranded RNA which triggers an innate immune response.
• a poly(A) in the downstream of 5’-ITR or upstream of the promoter and 3’-ITR to block long RNA transcripts.
• the poly(A) can be placed as a single stretch (Figure 10A) or in a combination ( Figure 10B) at the different locations.
• ITR5/AAT or ITR2/AAT into AAV2 or AAV5 capsids After transduction of 293 cells, consistent to the result from plasmid transfection, lower AAT expression was observed from AAV/ITR5/AAT transduction regardless of different capsids ( Figure 14). After muscular injection of these vectors, AAT expression in the blood was measured at week 4 post AAV administration. Similar to in vitro transduction data, ITR5 induced much lower AAT expression than AAV2 ( Figure 15). Collectively, these results implicate that the AAV5 ITR has a weaker promoter function than that of the AAV2 ITR. It is possible that ITRs from other serotypes or variants may have no promoter function. These ITRs without promoter function will be used to generate an AAV cassette.
• RNA polymerase III or miRNA driven by the same RNA polymerase II for transgene expression for specific sensors can be applied using a separate vector ( Figure 16, diagram A) or as a single vector linked with a transgene cassette. When a single vector is used, shRNA or miRNA can be placed at different locations.
• Cytosolic viral RNA is recognized by receptors RIG-I and MDA5, which activate mitochondrial antiviral signaling protein (MAVS) through caspase-recruitment domain (CARD)-CARD interactions.
• MAVS recruits various signaling molecules to trigger downstream signaling, such as TNF receptor-associated factor 6 (TRAF6) and TRAF5.
• TRAF6 along with other intracellular proteins activates NF-KB signaling via receptor interacting protein 1 (RIP1) and FAS-associated death domain protein (FADD).
• the NF-KB signaling phosphorylates NF-KB inhibitor-a (IkBa) and initiates pro-inflammatory cytokine gene expression.
• MAVS also activate interferon regulatory factor (IRF) signaling. Utilization of the same strategy as described above to knockdown MAVS or molecules involved in MAVS downstream signaling will block the dsRNA innate immune response.
• IRF interferon regulatory factor
• MAVS signaling can also be inhibited by various molecules from virus infection.
• virus infection a serine protease NS3-4A from hepatitis C virus, the proteases from Hepatitis A virus and GB virus B, and hepatitis B virus (HBV) X protein.
• HBV hepatitis B virus
• some endogenous proteins such as poly(rC)-binding protein 2, the 20S proteasomal subunit PSMA7, and mitofusin 2, can inhibit MAVS signaling.
• proteins can be expressed with a different vector ( Figure 17, diagram A) or in a single vector fused to a transgene ( Figure 17, diagram B) or driven by a different promoter ( Figure 17, diagram C) to block dsRNA immune response during therapeutic transgene expression.
• PKR is phosphorylated and activated by dsRNA and contributes to the induction of type I interferons, such as IFN-b, which can further increase its expression.
• 2-aminopurine (2-AP) is a potent inhibitor of double-stranded RNA (dsRNA)-activated protein kinase (PKR).
• dsRNA double-stranded RNA
• PSR protein kinase
• AAV transduction is able to be achieved when the target cells are deficient for MAVS.
• This result indicates that integration of MAVS shRNA into AAV cassettes can induce higher AAV transduction by blocking dsRNA mediated activation of innate immune response.
• Table 1 Information about human primary hepatocyte subjects

Landscapes

• Health & Medical Sciences (AREA)
• Life Sciences & Earth Sciences (AREA)
• Genetics & Genomics (AREA)
• Engineering & Computer Science (AREA)
• Chemical & Material Sciences (AREA)
• Biomedical Technology (AREA)
• Zoology (AREA)
• Biotechnology (AREA)
• Organic Chemistry (AREA)
• Bioinformatics & Cheminformatics (AREA)
• Wood Science & Technology (AREA)
• General Health & Medical Sciences (AREA)
• General Engineering & Computer Science (AREA)
• Molecular Biology (AREA)
• Microbiology (AREA)
• Medicinal Chemistry (AREA)
• Virology (AREA)
• Biochemistry (AREA)
• Public Health (AREA)
• Pharmacology & Pharmacy (AREA)
• Epidemiology (AREA)
• Animal Behavior & Ethology (AREA)
• Veterinary Medicine (AREA)
• Physics & Mathematics (AREA)
• Biophysics (AREA)
• Plant Pathology (AREA)
• Immunology (AREA)
• Mycology (AREA)
• Micro-Organisms Or Cultivation Processes Thereof (AREA)
• Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
• Medicines Containing Plant Substances (AREA)

Priority Applications (6)

Applications Claiming Priority (2)

Publications (2)

Family

ID=67301987

Family Applications (1)

Country Status (7)

Cited By (3)

Families Citing this family (4)

Family Cites Families (6)

• 2019
  • 2019-01-18 US US16/963,023 patent/US20200340013A1/en active Pending
  • 2019-01-18 CA CA3088538A patent/CA3088538A1/en active Pending
  • 2019-01-18 AU AU2019210190A patent/AU2019210190B2/en active Active
  • 2019-01-18 WO PCT/US2019/014211 patent/WO2019143950A2/en not_active Ceased
  • 2019-01-18 JP JP2020539080A patent/JP7504458B2/ja active Active
  • 2019-01-18 CN CN201980020389.7A patent/CN111918966B/zh active Active
  • 2019-01-18 EP EP19741946.8A patent/EP3740572A4/en active Pending

Also Published As

Similar Documents

Legal Events