WO2018134168A1 - Methods of expressing a polynucleotide of interest in the cone photoreceptors - Google Patents

Abstract

Intraocular injection of adeno-associated viral (AAV) vectors has been an evident route for delivering gene drugs into the retina. Currently, the vectors need to be injected into the subretinal space in order to provide gene delivery to cones. In this approach, gene delivery is limited to cells that contact the local "bleb" of injected fluid. Furthermore, retinal detachment that occurs during subretinal injections is a concern in eyes with retinal degeneration. Here, the inventors establish several new vector-promoter combinations to overcome the limitations associated with AAV-mediated cone transduction in the fovea with supporting studies in mouse models, human induced pluripotent stem cell-derived organoids, post-mortem human retinal explants and living macaques. They show that an engineered AAV2 variant provides gene delivery to foveal cones with a well-tolerated dose administered intravitreally. The delivery modality relies on a cone-specific promoter and result in high-level transgene expression compatible with optogenetic vision restoration. Accordingly, the present invention relates to method of expressing a polynucleotide of interest in the cone photoreceptors of a subject comprising intravitreal delivery of a therapeutically effective amount of a recombinant AAV2-derived vector comprising a VP1 capsid protein as set forth in SEQ ID NO: 1 and the polynucleotide of interest under the control of the PR1.7 promoter as set forth in SEQ ID NO:2.

Description

METHODS OF EXPRESSING A POLYNUCLEOTIDE OF INTEREST IN THE

CONE PHOTORECEPTORS

FIELD OF THE INVENTION:

The present inventions relate to methods of expressing a polynucleotide of interest in the cone photoreceptors of a subject comprising the intravitreal delivery of a therapeutically effective amount of a recombinant AAV2-derived vector.

BACKGROUND OF THE INVENTION:

The fovea -located at the center of the macula- is a specialized region of the retina that dominates the visual perception of primates by providing high acuity color vision (1). The highest density of cones is found at the center of the fovea (<0.3 mm from the foveal center), devoid of rod photoreceptors (2). Cone density decreases by up to 100 fold with distance from the fovea (3). Cone cells in the fovea are the primary targets of gene therapies aiming to treat inherited retinal diseases like mid-stage retinitis pigmentosa (4, 5) and achromatopsia (6). Currently, viral vectors encoding therapeutic proteins need to be injected into the subretinal space between the photoreceptors and the retinal pigment epithelium (RPE) cells in order to provide gene delivery to cones. In this approach, gene delivery is limited to cells that contact the local "bleb" of injected fluid. Furthermore, retinal detachment that occurs during subretinal injections is a concern in eyes with retinal degeneration. The earliest clinical trials using subretinal delivery of adeno-associated virus (AAV) to deliver a healthy RPE65 gene in Leber's Congenital Amaurosis patients (7-9) led to some improvements in vision despite the detachment of the macula to deliver the viral vector (10, 11). However, the treatment was in certain cases complicated by macular holes and increased macular thinning in the case of sub-foveal injections (11). Furthermore, contrary to the surrounding regions, there were no treatment benefits in the fovea (12). Gene therapy using AAV has also been studied for patients with choroideremia in which the macula was the target for gene delivery (13). The 6 month follow up results from this latter study thus far suggest that sub-foveal retinal detachment does not cause vision reduction in this region but, one of the patients in this trial had visual acuity loss in the treated eye compared to his untreated eye (13). With more gene therapies reaching clinical stages of application there is a growing need to find new methods for delivering gene therapy to the fovea without detaching this brittle region (14). This can be achieved by engineering the viral vectors to permit gene delivery away from the injection site. AAV capsids that can provide gene delivery to foveal cones after injection into the vitreous humor are one possible option.

SUMMARY OF THE INVENTION:

The present inventions relates to methods of expressing a polynucleotide of interest in the cone photoreceptors of a subject comprising the intravitreal delivery of a therapeutically effective amount of a recombinant AAV2 -variant vector. In particular, the present invention is defined by the claims.

DETAILED DESCRIPTION OF THE INVENTION:

Intraocular injection of adeno-associated viral (AAV) vectors has been an evident route for delivering gene drugs into the retina. However, gaps in our understanding of AAV transduction patterns within the anatomically unique environments of the intravitreal space of the primate eye impeded the establishment of non-invasive and efficient gene delivery to foveal cones in the clinic. Here, the inventors establish several new vector-promoter combinations to overcome the limitations associated with AAV-mediated cone transduction in the fovea with supporting studies in mouse models, human induced pluripotent stem cell- derived organoids, post-mortem human retinal explants and living macaques. They show that an engineered AAV2 variant provides gene delivery to foveal cones with a well-tolerated dose administered intravitreally . This delivery modality relies on a cone-specific promoter and result in high-level transgene expression compatible with optogenetic vision restoration.

Accordingly the first object of the present invention relates to a method of expressing a polynucleotide of interest in the cone photoreceptors of a subject comprising the intravitreal delivery of a therapeutically effective amount of a recombinant AAV2-variant vector comprising the VP1 capsid protein as set forth in SEQ ID NO: l encoding a polynucleotide of interest under the control of the PR1.7 promoter as set forth in SEQ ID NO:2.

As used herein, the term "subject" is typically intended for a human. Typically the subject is affected or likely to be affected with a retinal disease affecting cone photoreceptors. Accordingly a wide variety of retinal diseases impacting retinal cone photoreceptors may thus be treated given the teachings provided herein and typically include age-related macular degeneration, Bassen-kornzweig syndrome, choroideremia, gyrate atrophy, Refsum syndrome, Usher syndrome, color blindness, blue cone monochromacy, achromatopsia, incomplete achromatopsia, oligocone trichromacy, retinitis pigmentosa (RP), macular degeneration, Stargardt's Disease, Bardet-Biedl syndrome, Bornholm eye disease, Best's Disease and Leber's congenital amaurosis. Accordingly, a further object of this invention is to provide a method for treating a retinal disease affecting cone photoreceptors in a subject in need thereof comprising the intravitreal delivery of a therapeutically effective amount of a recombinant AAV2 -variant vector comprising the VP1 capsid protein as set forth in SEQ ID NO: l and the polynucleotide of interest under the control of the PR1.7 promoter as set forth in SEQ ID NO:2 wherein the polynucleotide of interest which when expressed in cone photoreceptor has a beneficial effect on the retinal disease.

As used herein, the term "treatment" or "treat" refer to both prophylactic or preventive treatment as well as curative or disease modifying treatment, including treatment of patient at risk of contracting the disease or suspected to have contracted the disease as well as patients who are ill or have been diagnosed as suffering from a disease or medical condition, and includes suppression of clinical relapse. The treatment may be administered to a subject having a medical disorder or who ultimately may acquire the disorder, in order to prevent, cure, delay the onset of, reduce the severity of, or ameliorate one or more symptoms of a disorder or recurring disorder. By "therapeutic regimen" is meant the pattern of treatment of an illness, e.g., the pattern of dosing used during therapy. A therapeutic regimen may include an induction regimen and a maintenance regimen. The phrase "induction regimen" or "induction period" refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the initial treatment of a disease. The general goal of an induction regimen is to provide a high level of drug to a patient during the initial period of a treatment regimen. An induction regimen may employ (in part or in whole) a "loading regimen", which may include administering a greater dose of the drug than a physician would employ during a maintenance regimen, administering a drug more frequently than a physician would administer the drug during a maintenance regimen, or both. The phrase "maintenance regimen" or "maintenance period" refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the maintenance of a patient during treatment of an illness, e.g., to keep the patient in remission for long periods of time (months or years). A maintenance regimen may employ continuous therapy (e.g., administering a drug at regular intervals, e.g., weekly, monthly, yearly, etc.) or intermittent therapy (e.g., interrupted treatment, intermittent treatment, treatment at relapse, or treatment upon achievement of a particular predetermined criteria [e.g., disease manifestation, etc.]).

As used herein, the term "cone photoreceptors" has its general meaning in the art and are one of three types of photoreceptor cells in the retina of mammalian eyes. They are responsible for color vision and function best in relatively bright light, as opposed to rod cells, which work better in dim light. The combination between the specific vector and the PR1.7 promoter specially drives the expression of the polynucleotide of interest in cone photoreceptors.

As used herein, the term "intravitreal delivery" refers to the administration of the vector directly into the vitreous humour (also called vitreous body or simply vitreous) which is the clear gel that fills the space between the lens and the retina of the eyeball of humans and other vertebrates.

As used herein, the term "polynucleotide of interest" herein designates any nucleotide sequence coding for any polypeptide, structural protein, enzyme etc., the expression of which is wanted in a target cell, for any kind of reason. It can also designate a non-coding sequence, for example an antisense sequence or the sequence of an interfering RNA aimed at decreasing the expression of a gene. One skilled in the art knows, by its knowledge of the scientific literature in his field, which are the polynucleotides that may be more appropriate to treat a specific retinal disease.

Gene therapy can be performed either by introducing in cone photoreceptor a functional copy of a polynucleotide of interest (e.g. a gene) that is deficient therein (gene replacement therapy), or by delivering to cone photoreceptors a polynucleotide of interest which will have a beneficial effect on the eye disease to be treated (symptomatic therapy). Examples of polynucleotides of interest that can be used for gene replacement therapy are genes that are specifically or preferentially expressed in cone photoreceptors, such as retinitis pigmentosa GTPase regulator (RPGRORF15) (refs: 1. B. S. Pawlyk, O. V. Bulgakov, X. Sun, M. Adamian, X. Shu, A. J. Smith, E. L. Berson, R. R. Ali, S. Khani, A. F. Wright, M. A. Sandberg, T. Li, Photoreceptor rescue by an abbreviated human RPGR gene in a murine model of X-linked retinitis pigmentosa. Gene Ther 23, 196-204 (2016).; 2. D. H. Hong, B. S. Pawlyk, M. Adamian, M. A. Sandberg, T. Li, A single, abbreviated RPGR-ORF15 variant reconstitutes RPGR function in vivo. Invest Ophthalmol Vis Sci 46, 435-441 (2005).; 3. W. A. Beltran, A. V. Cideciyan, A. S. Lewin, W. W. Hauswirth, S. G. Jacobson, G. D. Aguirre, Gene augmentation for X-linked retinitis pigmentosa caused by mutations in RPGR. Cold Spring Harbor perspectives in medicine 5, a017392 (2014).; 4. W. T. Deng, F. M. Dyka, A. Dinculescu, J. Li, P. Zhu, V. A. Chiodo, S. L. Boye, T. J. Conlon, K. Erger, T. Cossette, W. W. Hauswirth, Stability and Safety of an AAV Vector for Treating RPGR-ORF15 X-Linked Retinitis Pigmentosa. Hum Gene Ther 26, 593-602 (2015). 5. Z. Wu, S. Hiriyanna, H. Qian, S. Mookherjee, M. M. Campos, C. Gao, R. Fariss, P. A. Sieving, T. Li, P. Colosi, A. Swaroop, A long-term efficacy study of gene replacement therapy for RPGR-associated retinal degeneration. Hum Mol Genet 24, 3956-3970 (2015).; 6. W. A. Beltran, A. V. Cideciyan, A. S. Lewin, S. Iwabe, H. Khanna, A. Sumaroka, V. A. Chiodo, D. S. Fajardo, A. J. Roman, W.-T. Deng, M. Swider, T. S. Aleman, S. L. Boye, S. Genini, A. Swaroop, W. W. Hauswirth, S. G. Jacobson, G. D. Aguirre, in Proc. Natl. Acad. Sci. U.S.A. (2012), vol. 109, pp. 2132-2137), CNGB3 (beta subunit of the cone cyclic nucleotide-gated cation channel) (see, e.g., Kohl et al.(2005) Eur J Hum Genet. 13(3):302), GNAT2 (cone specific alpha subunit of transducin) and CNGA3 (alpha subunit of the cone cyclic nucleotide-gated cation channel) (see, e.g., GenBank Accession No. NP 001289; and Booij et al. (2011) Ophthalmology 118: 160-167).

In some embodiments, the polynucleotide of interest may encode for a neurotrophic factor. As used herein, the "neurotrophic factor" is a generic term of proteins having a physiological action such as survival and maintenance of nerve cells, promotion of neuronal differentiation. In some embodiments, the neurotrophic factor is RdCVF. As used herein the term "RdCVF" has its general meaning in the art and refers to rod-derived cone viability factor (Leveillard T, Mohand-Sa^'id S, Lorentz O, Hicks D, Fintz A C, Clerin E et al. Identification and characterization of rod-derived cone viability factor. Nat Genet 2004; 36: 755-759.). The polynucleotide of interest encodes both a long form (RdCVF-L, 217 aa, Q8VC33) having a putative thiol-oxydoreductase activity (JEFFERY, Trends Biochem. Sci., vol.24(l):8-l 1, 1999; JEFFERY, Trends Genet, vol.19(8) :415-417, 2003) and a short form (RdCVF-S, 109 aa, Q91W38) with trophic activity for cones but no redox activity. In some embodiments, the neurotrophic factor is RdCVF2, which shares many similarities with RdCVF in terms of gene structure, expression in a rod-dependent manner and protein 3D structure (see e.g. WO2008148860 and Chalmel F, Leveillard T, Jaillard C, Lardenois A, Berdugo N, Morel E, Koehl P, Lambrou G, Holmgren A, Sahel JA, Poch O. Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential. BMC Mol Biol. 2007 Aug 31;8:74.). Like RdCVF, the RdCVF2 short isoform exhibits cone rescue activity that is independent of its putative thiol-oxydoreductase activity. In some embodiments, the polynucleotide of interest encodes for RdCVFL2.

In some embodiments, the polynucleotide product of interest is an opsin. The opsin sequence can be derived from any suitable single- or multicellular- organism, including human, algae and bacteria. In some embodiments, the opsin is rhodopsin, photopsin, L/M wavelength (red/green) cone-opsin, or short wavelength (S) cone-opsin (blue). In some embodiments, the opsin is channelrhodopsin or halorhodopsin or cruxhalorhodopsin. In some embodiments, the opsin is a light-responsive opsin as described in U.S. Patent Publication No. 2007/0261127 (e.g., ChR2; Chop2); U.S. Patent Publication No. 2001/0086421; U.S. Patent Publication No. 2010/0015095; and Diester et al. (2011) Nat. Neurosci. 14:387. Other examples of opsins include NpHR, eNpHR 1.0, eNpHR 2.0, eNpHR 3.0, SwiChR, SwiChR 2.0, SwiChR 3.0, Mac, Mac 3.0, Arch, ArchT, Arch 3.0, ArchT 3.0, iChR, ChR2, C1V1-T, C1V1-TT, Chronos, Chrimson, ChrimsonR, CatCh, VChRl-SFO, ChR2-SFO, ChR2-SSFO, ChEF, ChlEF, Jaws, ChloC, Slow ChloC, iClC2, iClC2 2.0, and iClC2 3.0. In some embodiments, the opsin consists of the amino acid sequence as set forth in SEQ ID NO: 3 or SEQ ID NO:4, or SEQ ID NO:5.

In some embodiments, the polynucleotide product of interest is a site-specific endonuclease that provides for site-specific knock-down of gene function, e.g., where the endonuclease knocks out an allele associated with a retinal disease. For example, where a dominant allele encodes a defective copy of a gene that, when wild-type, is a retinal structural protein and/or provides for normal retinal function, a site-specific endonuclease can be targeted to the defective allele and knock out the defective allele. In some embodiments, the vector thus comprises a polynucleotide that encodes a site-specific endonuclease; and a polynucleotide that encodes a functional copy of a defective allele, where the functional copy encodes a functional retinal protein. Site-specific endonucleases that are suitable for use include, e.g., zinc finger nucleases (ZFNs); transcription activator-like effector nucleases (TALENs), and CRISPR-associated endonuclease. As used herein, the term "CRISPR- associated endonuclease" has its general meaning in the art and refers to clustered regularly interspaced short palindromic repeats associated which are the segments of prokaryotic DNA containing short repetitions of base sequences. In particular, the CRISPR-associated endonuclease is Cas9 or a derivative thereof. The Cas9 nuclease can have a nucleotide sequence identical to the wild type Streptococcus pyrogenes sequence. Alternatively, the wild type Streptococcus pyrogenes Cas9 sequence can be modified. For instance, the Cas9 nuclease sequence can be for example, the sequence contained within a commercially available vector such as PX330 or PX260 from Addgene (Cambridge, MA). In some embodiments, the Cas9 endonuclease can have an amino acid sequence that is a variant or a fragment of any of the Cas9 endonuclease sequences of Genbank accession numbers KM099231.1 GL669193757; KM099232.1; GL669193761; or KM099233.1 GL669193765 or Cas9 amino acid sequence of PX330 or PX260 (Addgene, Cambridge, MA). The Cas9 nucleotide sequence can be modified to encode biologically active variants of Cas9, and these variants can have or can include, for example, an amino acid sequence that differs from a wild type Cas9 by virtue of containing one or more mutations (e.g., an addition, deletion, or substitution mutation or a combination of such mutations). For example the Cas9 nuclease can be mutated in the conserved FiNH and RuvC domains, which are involved in strand specific cleavage. For example, an aspartate-to-alanine (D10A) mutation in the RuvC catalytic domain allows the Cas9 nickase mutant (Cas9n) to nick rather than cleave DNA to yield single - stranded breaks, and the subsequent preferential repair through HDR can potentially decrease the frequency of unwanted indel mutations from off-target double-stranded breaks. In some embodiments, the vector comprises one or more guide RNA. As used herein, the term "one or more guide RNA" refers to the RNAs that guide the insertion or deletion of residues. In the context of the invention, the guide RNA is used for recruiting Cas9 to specific genomic loci. In some embodiments, the guide RNA can be a sequence complementary to a coding or a non-coding sequence. In some embodiments, the subject is administered with a combination of at least one vectors comprising one polynucleotide encoding for a Cas9 endonuclease and at least one vector comprising the guide RNA.

In some embodiments, the polynucleotide product is an interfering RNA (RNAi), in particular a siRNA. A "small interfering" or "short interfering RNA" or siRNA is a RNA duplex of nucleotides that is targeted to a gene interest (a "target gene"). An "RNA duplex" refers to the structure formed by the complementary pairing between two regions of a RNA molecule. siRNA is "targeted" to a gene in that the nucleotide sequence of the duplex portion of the siRNA is complementary to a nucleotide sequence of the targeted gene. In some embodiments, the length of the duplex of siRNAs is less than 30 nucleotides.

In some embodiments, the polynucleotide product is an antisense oligonucleotide. As used herein, the term "antisense oligonucleotide" is understood to refer to a nucleotide sequence which is substantially complementary to a target nucleotide sequence in a pre- mRNA molecule, hnRNA (heterogenous nuclear RNA) or mRNA molecule. The degree of complementarity (or substantial complementarity) of the antisense sequence is preferably such that a molecule comprising the antisense sequence can form a stable hybrid with the target nucleotide sequence in the RNA molecule under physiological conditions.

As used herein the term "AAV" refers to more than 30 naturally occurring and available adeno-associated viruses, as well as artificial AAVs. Typically the AAV capsid, ITRs, and other selected AAV components described herein, may be readily selected from among any AAV, including, without limitation, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, rhlO, AAVrh64Rl, AAVrh64R2, rh8, variants of any of the known or mentioned AAVs or AAVs yet to be discovered or variants or mixtures thereof. See, e.g., WO 2005/033321. The genomic and proteic sequences of various serotypes of AAV, as well as the sequences of the native terminal repeats (TRs), Rep proteins, and capsid subunits including VPl protein are known in the art. Such sequences may be found in the literature or in public databases such as GenBank or Protein Data Bank (PDB). See, e.g., GenBank and PDB Accession Numbers NC_002077 and 3NG9 (AAV-1), AF043303 and 1LP3 (AAV-2), NC_001729 (AAV-3), U89790 and 2G8G (AAV- 4), NC_006152 and 3NTT (AAV-5), 30AH (AAV6), AF513851 (AAV-7), NC_006261 and 2QA0 (AAV-8), AY530579 and 3UX1 (AAV-9 (isolate hu.14)); the disclosures of which are incorporated by reference herein for teaching AAV nucleic acid and amino acid sequences. See also, e.g., Srivistava et al. (1983) J. Virology 45:555; Chiorini et al. (1998) J. Virology 71 :6823; Chiorini et al. (1999) J. Virology 73: 1309; Bantel-Schaal et al. (1999) J. Virology 73:939; Xiao et al. (1999) J. Virology 73:3994; Muramatsu et al. (1996) Virology 221 :208; Shade et al.,(1986) J. Virol. 58:921; Gao et al. (2002) Proc. Nat. Acad. Sci. USA 99: 11854; Moris et al. (2004) Virology 33:375-383; international patent publications WO 00/28061, WO 99/61601, WO 98/11244; and U.S. Pat. No. 6,156,303 and US7906111.

As used herein the term "recombinant AAV2-derived vector" refers to an AAV2 -based vector comprising the VPl capsid protein as set forth in SEQ ID NO: l and the polynucleotide sequence of interest (i.e., a polynucleotide heterologous to AAV). Thus, in the recombinant AAV2-derived vector of the present invention the native VPl capsid protein of AAV2 is substituted by the VPl capsid protein as set forth in SEQ ID NO: l . The recombinant AAV2- derived vector of the present invention typically comprises 5' and 3' adeno-associated virus inverted terminal repeats (ITRs), the polynucleotide of interest (i.e a heterologous polynucleotide) operatively linked to the promoter PR1.7. The vectors of the invention are produced using methods known in the art. In short, the methods generally involve (a) the introduction of the DNA necessary for AAV replication and synthesis of the capsid, (b) the introduction of a helper construct into the producer cell line, wherein the helper construct comprises the viral functions missing from the AAV vector (c) introducing a helper virus into the producer cell line, (d) the plasmid construct containing the genome of the AAV vector, e.g. ITRs, promoter and transgene sequences, etc.... All functions for AAV virion replication and packaging need to be present, to achieve replication and packaging of the AAV vector into AAV virions. The introduction into the producer host cell can be carried out using standard virology techniques simultaneously or sequentially. Finally, the host cells are cultured to produce AAV virions and are purified using standard techniques such as iodixanol or CsCl gradients or other purification methods. The purified AAV virion is then ready for use in the methods. As used herein, the term "promoter" has its general meaning in the art and refers to a nucleic acid fragment that controls the transcription of one or more genes, located upstream with respect to the direction of transcription of the transcription initiation site of the gene, and is structurally identified by the presence of a binding site for DNA-dependent R A polymerase, transcription initiation sites and any other DNA sequences, including, but not limited to transcription factor binding sites, repressor and activator protein binding sites, and any other sequences of nucleotides known to one of skill in the art to act directly or indirectly to regulate the amount of transcription from the promoter. As used herein, the term "PR1.7 promoter" refers to the 1.7-kb L-opsin promoter described in Hum Gene Ther. 2016 Jan;27(l):72-82 and characterized by the nucleic acid sequence as set forth in SEQ ID NO:2. The promoter and the polynucleotide of interest are operatively linked. As used herein, the term "operably linked" refers to two or more nucleic acid or amino acid sequence elements that are physically linked in such a way that they are in a functional relationship with each other. For instance, a promoter is operably linked to a coding sequence if the promoter is able to initiate or otherwise control/regulate the transcription and/or expression of a coding sequence, in which case the coding sequence should be understood as being "under the control of the promoter. Generally, when two nucleic acid sequences are operably linked, they will be in the same orientation and usually also in the same reading frame. They will usually also be essentially contiguous, although this may not be required.

By a "therapeutically effective amount" is meant a sufficient amount of the vector to treat the retinal disease at a reasonable benefit/risk ratio. It will be understood that the total daily usage of the vector will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient will depend upon a variety of factors including the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific polypeptide employed; and like factors well known in the medical arts. For example, it is well known within the skill of the art to start doses of the compound at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. Thus, the doses of vectors may be adapted depending on the disease condition, the subject (for example, according to his weight, metabolism, etc.), the treatment schedule, etc. A preferred effective dose within the context of this invention is a dose allowing an optimal transduction of the cone photoreceptors. Typically, from 10⁸ to 10¹⁰ viral genomes (vg) are administered per dose in mice. Typically, the doses of AAV vectors to be administered in humans may range from 10⁹ to 10¹² vg.

The vector of the invention is thus formulated into pharmaceutical compositions. These compositions may comprise, in addition to the vector, a pharmaceutically acceptable excipient, carrier, buffer, stabiliser or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient (i.e. the vector of the invention). The precise nature of the carrier or other material may be determined by the skilled person according to the route of administration, i.e. here intravitreal injection. The pharmaceutical composition is typically in liquid form. Liquid pharmaceutical compositions generally include a liquid carrier such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil. Physiological saline solution, magnesium chloride, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may be included. For injection, the active ingredient will be in the form of an aqueous solution, which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilisers, buffers, antioxidants and/or other additives may be included, as required. For delayed release, the vector may be included in a pharmaceutical composition, which is formulated for slow release, such as in microcapsules formed from biocompatible polymers or in liposomal carrier systems according to methods known in the art. Typically, the pharmaceutical composition of the present invention is supplied in a prefilled syringe. A "ready- to-use syringe" or "prefilled syringe" is a syringe which is supplied in a filled state, i.e. the pharmaceutical composition to be administered is already present in the syringe and ready for administration. Prefilled syringes have many benefits compared to separately provided syringe and vial, such as improved convenience, affordability, accuracy, sterility, and safety. The use of prefilled syringes results in greater dose precision, in a reduction of the potential for needle sticks injuries that can occur while drawing medication from vials, in pre- measured dosage reducing dosing errors due to the need to reconstituting and/or drawing medication into a syringe, and in less overfilling of the syringe helping to reduce costs by minimising drug waste. In some embodiments the pH of the liquid pharmaceutical composition of the present invention is in the range of 5.0 to 7.0, 5.1 to 6.9, 5.2 to 6.8, 5.3 to 6.7 or 5.4 to 6.6. The invention will be further illustrated by the following figures and examples. However, these examples and figures should not be interpreted in any way as limiting the scope of the present invention. FIGURES:

Figure 1: Expression in all layers of the mouse retina is obtained with the combination of AAV2-7m8-GFP and the mouse cone arrestin (mCAR) promoter (A), PR2.1 promoter (B) while most cone-specific expression pattern is achieved with PR1.7 promoter (C) -after intravitreal injections.

Figure 2: Cone-specific expression in the retinal degeneration 10 (rdlO) mouse model for Retinitis Pigmentosa. AAV2-7m8-PR1.7-GFP expression pattern on a retinal flatmount (A) and observed specifically in cones with a higher magnification (B) after intravitreal injections.

Figure 3: Reporter gene expression pattern using ubiquitous versus cone-specific promoter in vivo in monkeys after intravitreal injections. Retinal flatmount images showing that AAV2-7m8-CMV leads to pan-retinal GFP expression (A) while it is foveal cone- specific with AAV2-7m8-PR1.7 (B). Close up to the fovea with AAV2-7m8-CMV (C, left) and AAV2-7m8-PR1.7 (C, right).

Figure 4: Foveal cone-specific expression of Jaws-GFP under the control of PR1.7 promoter in combination with AAV2-7m8 capsid in the non-human primate, after intravitreal injections. (A) In vivo eye fundus image showing foveal expression, (B) flatmount image of a half fovea (arrow: foveola), (C) retinal cryosections at the level of the fovea.

Figure 5: Cone-specific expression of GFP under the control of PR1.7 promoter and with AAV2-7m8 capsid in human tissue. (A) Retinal organoids derived from human induced pluripotent stem cells expres GFP; (B) GFP-expressing cells in the organoids are exclusively cones (cryosections), (C) expression in cones of a human post-mortem retinal explant (cryosections).

EXAMPLE:

Material & Methods:

AAV production

AAV vectors were produced as previously described using the co-transfection method and purified by iodixanol gradient ultracentrifugation (49). AAV vector stocks were titered by quantitative PCR (50) using SYBR Green (Thermo Fischer Scientific). Animals and intraocular injections

Wild-type C57BL6/j or rdlO mice, and cynomolgus macaques were used for this study. For eye injections (n=6 eyes/condition), mice were anesthetized by isofluorane inhalation. Pupils were dilated and a 33 -gauge needle was inserted into the eye to deliver 2 μΐ, of AAV vector solution intravitreally or ΙμΙ_^ subretinally. Regarding macaque eye injections, macaques were first selected based on absence neutralizing antibody titers against AAV. Primates were anesthetized with 10: 1 mg/kg ketamine/xylazine. After subretinal or intravitreal vector administration, opthtalmic steroid and antibiotic ointment were applied to the corneas post injections.

In vivo macaque eye imaging

After pupil dilation, a Spectralis HRA+OCT system (Heidelberg Engineering, Germany) was used to acquire OCT images, and fluorescent images of GFP using the "Fundus Autofluoresence mode" which consists of and excitation wavelength of 488 nm and barrier filter of 500 nm.

Two-photon imaging and ex-vivo electrophysiological recordings of macaque retinas

A two-photon microscope equipped with a 40x water immersion objective (LUMPLFLN40x/W/0.80, Olympus) with a pulsed femto-second laser (InSight™ DeepSee™ - Newport Corporation) was used for imaging GFP-positive retinal cells from whole-mount retinas (with photoreceptor-cell-side up) or retina slices (vertical sections). AAV-treated macaque retinas were isolated and later imaged in oxygenized (95% 02, 5% C02) Ames medium (Sigma-Aldrich). For live two-photon imaging, retinas were placed in the recording chamber of the microscope, and z-stacks were acquired using the excitation laser at a wavelength of 930 nm. Images were processed offline using Image J. For whole-cell patch- clamp recordings, an Axon Multiclamp 700B amplifier was used. Electrodes were made from borosilicate glass (BF100- 50-10, Sutter Instruments) and pulled to 6-9 ΜΩ. Pipettes were filled with 115 mM K Gluconate, 10 mM KC1, 1 mM MgC12, 0.5 mM CaC12, 1.5 mM EGTA, 10 mM HEPES, and 4 mM ATP-Na2 (pH 7.2). Cells were clamped at a potential of -40 mV in voltage-clamp configuration, or recorded in current-clamp (current zero) configuration. Retinas were dark-adapted at least half an hour in the recording chamber prior to recordings.

Human iPSC cultures

We have generated retinal organoids from human iPSCs based on a previously published protocol (37). Clone hiPSC-2 was expanded and differentiated on fibroblast feeders from postnatal human foreskins (ATCC CRL 2429) in "proneural medium" as already described (37). Starting from highly confluent adherent iPS cell cultures and in the absence of fibroblast growth factor 2 (FGF2), self-forming retinal organoids can be identified after 2 weeks. At this point the organoids were mechanically isolated and cultured in 3D conditions for up to 43 days. FGF2 was supplemented to the medium in 3 conditions for 7 days after the mechanical isolation of the organoids to promote their growth. The retinal organoids were infected at day 28 of differentiation at a dose of 5xl0¹⁰ vg/organoid with AAV2-7m8 vectors carrying the GFP gene under the control of pR1.7 promoter. 10 μΜ DAPT (Selleck) was added to the medium for a week from day 28 on to promote cell cycle arrest of the existent cell populations. Fluorescence intensity was observed for the first time 5 days after infection and continued to increase up to day 43.

Human post-mortem retinal explants

Human retinal explants were prepared using a previously described protocol (38). Briefly, eyes were dissected in C02-independent-medium (Thermo Fischer Scientific). The anterior parts were removed, retina was isolated and cut into small pieces. These explants were placed photoreceptor side-up on a Transwell cell culture insert (Corning), and 2mL of Neurobasal medium (Thermo Fischer Scientific) supplemented with B27 (Thermo Fischer Scientific) were added to each well below each explant. The following day, each explant was infected with a single 0,5 drop of AAV-pRl .7-GFP containing 10¹⁰ viral particles. Vector- infected explants were incubated for 10-15 days to allow GFP expression, which was checked using an epifiuorescence macroscope.

Histology, immunohistochemistry and microscopy

Mouse eyes were enucleated and immediately fixed in 10% formalin - 4% formaldehyde for 2 hours for cryosections. Macaque retinas were fixed after dissection in 4% formaldehyde for 3 hours. Retinal organoids and human retinal explants were rinsed in PBS at the end of their culture periods and fixed in 4% paraformaldehyde for 10 minutes. For cryosections, mouse and macaque retinas, retinal organoids and human retinal explants were immersed in PBS-30% sucrose overnight at 4°C. Mouse eyecups, human retinal explants, macaque retinas were embedded in OCT medium and frozen in liquid nitrogen, while retinal organoids were embedded in gelatin- sucrose and frozen in dry ice-cold isopentane. 10 μιη- thick vertical sections were cut with a Microm cryostat. After incubation in the blocking buffer, sections were incubated with primary antibodies overnight at 4°C: human Cone Arrestin antibody (gift from Cheryl Craft); M/L opsin antibody (Millipore AB5405), mouse Cone Arrestin antibody (Millipore, AB 15282). After multiple washes of the sections, the secondary antibodies (Alexa Fluor 488, 594 or 647, ThermoFisher) were added, followed by several washes. Retinal flatmounts or cryosections were mounted in Vectashield mounting medium (Vector Laboratories) for fluorescence microscopy. Retinal sections were visualized using an Olympus Upright confocal microscope.

In silico identification of potential regulatory elements and transcriptomic analysis TF binding site analysis was performed on red opsin gene promoter sequence -pR2.1 and pR1.7 sequences- and the cone arrestin 3 genomic region. The TRANSFAC database 8.3 (http://alggen.lsi.upc.es/) was used for TF binding site prediction. Each TF from the predicted list was analyzed using the Knowledge Base for Sensory System (KBASS, http://kbass.institut-vision.org/KBaSS/transcriptomics/index.php) to select those expressed in human retina using the transcriptomic experiment RNG209 (51). A filter was used to retain TFs with a signal intensity value superior to 40 units in the sample prepared from the experiment RNG209 after normalization by Robust Multi-array Average (RMA) as previously described (52). In this experiment, human retinal specimens used as controls were post-mortem specimens collected within 12 hours following death of patients with no past medical history of eye disease or diabetes. Nineteen samples were collected from 19 eyes representing 17 patients. Sex ratio was 12 men / 7 women with a mean age of 61 years (range 25-78 years).

Statistics

Data were analyzed using a one-way Anova test in Graphpad Prism (multiple comparison, Tukey correction). Error bars on the graphs show the Standard Error of the Mean (SEM). p values are expressed as the following *p<0,033, ns: non significant.

Study approval

For animals, the experiments were realized in accordance with the National Institutes of Health Guide for Care and Use of Laboratory Animals. The protocols were approved by the Local Animal Ethics Committees and conducted in accordance with Directive 2010/63/EU of the European Parliament. Postmortem human ocular globes from donors were acquired from the School of Surgery (Ecole de Chirugie, Assitance Publique Hopitaux de Paris). The protocol was approved by the institutional review boards of the School of Surgery and the Quinze-Vingts National Ophtalmology Hospital. All experiments on postmortem human retinal explants were performed according to the local regulations as well as the guidelines of the Declaration of Helsinki.

Results:

Selection of a strong and specific cone-cell specific promoter in murine models In order to find vector-promoter combinations suitable for strong and specific cone targeting away from the injection site, we compared several AAVs after intravitreal and subretinal delivery in mouse retinas. To enable efficient cone photoreceptor targeting, we used an engineered AAV variant called AAV2-7m8, which has been shown to target photoreceptors efficiently via both administration routes (16, 17). Specific targeting of cone cells has never been attempted using vitreally administered AAV. In order to find suitable promoter sequences for restricted gene expression in cones applicable in the clinic, we focused on promoters that have previously been validated in either non-human primate (NHP) (18) or human tissue (4). We generated AAV2-7m8 vectors encoding GFP under the control of mCAR (mouse Cone Arrestin), PR2.1 and PR1.7 promoters (synthetic promoters based on the human red opsin gene enhancer and promoter sequences) and injected them at equal titers into eyes of six weeks old wild-type mice. Three weeks after subretinal injections, retinal cross-sections were stained with cone arrestin and GFP expression was examined (data not shown). We found high GFP expression in both rod and cone photoreceptors with mCAR promoter while PR2.1 and PR1.7 lead to strong expression mostly in cones, as reported previously (18, 19). Using the same vectors, we obtained strikingly different expression patterns after intravitreal delivery (Figure 1). mCAR promoter lead to GFP expression in some cones, but was leaky towards rods as well as cells of the inner nuclear layer (INL) and ganglion cell layer (GCL) (Figure 1). Both PR2.1 and PR 1.7 promoters lead to more cone labeling than mCAR promoter (Figure 1). PR2.1 transduced more cones than PR1.7 but, it also produced non-specific GFP expression in the INL and GCL. Only the PR1.7 promoter showed GFP expression in cones with minimal expression in rods and was not leaky towards the inner retina (data not shown). Finally, as retinal disease state can influence AAV-mediated gene delivery and transgene expression patterns (20, 21) we validated AAV2-7m8-PR1.7 vector-promoter combination in a mouse model of retinal degeneration. We injected AAV2- 7m8-PR1.7-GFP intravitreally in the rdlO mouse model of retinitis pigmentosa. Two months after injection, GFP expression was restricted to cones (Figure 2) supporting the suitability of this vector for cone-directed gene therapy via both intravitreal and subretinal injections.

Bioinformatic analysis of mCAR, pR1.7 and pR2.1 promoter sequences

Before moving onto further studies in other species, we aimed to better understand the reasons behind the divergent expression patterns obtained with the three promoters. To do so, we analyzed transcription factor (TF) binding sites within each promoter sequence using bioinformatics (data not shown). The present analysis aimed to answer the following questions: (i) why is pR1.7 more efficient than PR2.1 in cones (18)? (ii) why do pR2.1 and mCAR promoters lead to off-target expression after intravitreal administration? We hypothesized that the differential expression patterns observed between PR1.7 and PR2.1 are due to additional TF binding sites found in the 337 bp sequence located in the 5' region of PR2.1 promoter but not in PR1.7 promoter (data not shown). Interestingly, we found a COUP-TFI binding site within this 337 bp sequence (data not shown). COUP-TFI has been shown to suppress green opsin gene (Opnlmw) expression in the mouse retina (22) and might thus be accountable for lower expression with PR2.1 promoter in macaque cones when AAV is delivered subretinally as previously shown (18). Within the same specific 337bp region we also found multiple binding sites for generic, ubiquitous activator TFs (data not shown), such as CEBPB and GTF2I. These additional binding sites of TFs that enhance binding and basal transcriptional machinery assembly and that are not specifically expressed in cones might be responsible for some of the off-target expression observed with PR2.1 compared to PR1.7 (data not shown). We also analyzed TF binding sites in the genomic mCAR promoter sequence to explain the lack of specificity using the short version of this promoter used in the AAV constructs. The short sequence consists of a 521bp portion of the genomic proximal CAR promoter (data not shown) presenting a TATA-box, a TATA-like box, as well as binding sites for CRX (Cone-rod homeobox protein) and SP (Specificity Protein) TFs (23) (data not shown). However, the 'Reg' sequence modulating CAR promoter activity (23) located directly upstream of the 521bp region is excluded from the short sequence (data not shown). Based on the interactome of the TFs binding mCAR promoter obtained from the STRING database (24), CRX and SP TFs interact with each other and with RARA (Retinoic Acid Receptor Alpha), RXRA (Retinoid X Receptor Alpha) and THRB (Thyroid Hormone Receptor Beta) TFs (data not shown). These three nuclear receptors (NR) are involved in cell- type specific regulation of gene expression via MEDl (25) (Mediator Complex Subunit 1) by forming a cell-specific transcription co-activator complex (26, 27) (data not shown). CRX and SP binding sites are located on the 521bp region, while RXRA, RARA and THRB binding sites are positioned on the Reg region (data not shown). Moreover, the Reg region contains five binding sites for THR 2, an important nuclear receptor expressed in cones (28) (data not shown). For all of these reasons, removal of the Reg region is likely responsible for the off- target expression observed with the short mCAR promoter.

Safe gene delivery to macaque foveal cones via intravitreal administration of AAV Others and we have shown transduction of macaque cones using AAV variants with ubiquitous promoters (16, 29-31), but achieving cone transduction by vitreally administered AAV has only been possible at high doses leading to inflammation (16, 29). We reasoned that foveal cone targeting could be achieved if we use a strong cone-specific promoter at lower intravitreally injected AAV doses compatible with safety (29, 32). To test if such "dose sparing" is possible, we injected two macaque eyes with AAV2-7m8-PRl .7-GFP and two other eyes with AAV2-7m8-CMV-GFP at a dose of 10¹¹ viral genome (vg). Using in vivo eye fundus imaging, we observed GFP expression as early as two weeks post-injection with CMV (Figure 3). GFP fluorescence was predominantly in the periphery and in the parafoveal region. GFP expression with PRl .7 became detectable 6 to 8 weeks after administration and was restricted to the fovea (Figure 3). There was no detectable damage to the fovea as assessed by Optical Coherence Tomography (OCT) (data not shown). After sacrifice, flatmounts of the maculas were prepared (Figure 3) and retinal cryosections at the level of the fovea (data not shown) and imaged GFP fluorescence using confocal microscopy, with equal acquisition settings for each eye. These images corroborated the in vivo findings and show specific and robust cone transduction from the vitreous, at a dose of 10¹¹ particles, using AAV2-7m8-PR1.7. Using a similar dose, it is not possible to transduce cones with CMV.

Therapeutic gene delivery to foveal cones for vision restoration using ontogenetics

We next aimed to evaluate the possibility of using this promoter for therapeutic gene delivery. There is no existing blind macaque or primate model of retinal degeneration to test functional outcomes after gene replacement (i.e. CNGB3 for treatment of achromatopsia). However, it is possible to evaluate vision restoration in wild-type macaques using optogenetic strategies since we can distinguish between optogenetic-mediated light responses versus endogenous cone opsin-mediated responses (4). We evaluated the potential of optogenetic vision restoration by expression of Jaws, a hyperpolarizing microbial opsin (15), in foveal cones. We injected one macaque with 10¹¹ vg of AAV2-7m8-PR1.7-Jaws-GFP in the vitreous to evaluate its therapeutic potential for reactivation of dormant cones in mid-stage retinitis pigmentosa as described previously in mice (4,15). We found high-level Jaws-GFP expression restricted to the foveal cones in the injected eyes (Figure 4) similar to GFP expression alone (Figure 3). The animal was then sacrificed two months post injection and half of the retina was processed for histology. Retinal flat-mounts showed typical anatomy of cones in the foveola, the region of the fovea that contains densely packed cones responsible our high acuity vision. Immunostaining for cone arrestin was used to quantify transduced cones (data not shown). About 50 percent of the cone arrestin positive cells were found to express detectable levels of Jaws-GFP in this foveola.

The other half of the retina was conserved as explants (33) for characterization of optogenetic light responses arising from the hyperpolarizing pump Jaws (data not shown). Electrophysiological recordings were performed on transduced cones expressing Jaws and in control cones without GFP expression (data not shown). Whole-cell patch-clamp recordings in GFP positive Jaws-cones exhibited robust light responses to orange light flashes (n=4) (data not shown), while control cones never responded to the same light stimuli (data not shown). Action spectrum of recorded cells showed that highest light responses were obtained using orange light between 575 and 600nm (data not shown) as previously shown for Jaws (15). Cones recorded in current-clamp configuration displayed light-elicited hyperpolarizations followed by short depolarizations (data not shown).

Finally, we injected intravitreally another macaque eye with 10¹⁰ particles of AAV2- 7m8-pR1.7-Jaws-GFP to evaluate feasibility of foveal transduction at even lower doses. We obtained detectable foveal Jaws expression even with this lower dose (data not shown), although expression levels were lower. Altogether, all three macaque eyes injected with AAV2-7m8-pPvl .7-GFP (n=2) or Jaws-GFP (n=2) show reproducibility and strength of intravitreal approach compatible with optogenetic reactivation of cones.

PRl.7 promoter drives strong and highly specific gene expression in human cones

Altogether our data in non-human primates show for the first time non-invasive, specific and high-level primate foveal cone transduction compatible with optogenetic applications for vision restoration. However as promoter activity shows important variations across species (29, 35, 36) we deemed it necessary to validate PRl .7 in human cells and tissues. Due to the lack of a good human photoreceptor cell line or other model that could be used to test efficiency of cone promoter activity, we used 3D retinal organoids derived from human induced Pluripotent Stem (iPS) cells (37). We generated photoreceptor-enriched retinal organoids and infected them with AAV2-7m8 vectors encoding GFP under the control of PRl .7 promoter (Figure 5). GFP expression was observed as early as 5 days post infection and continued to increase until the experiment was terminated for analysis on day 43. GFP expression in these organoids colocalized with human Cone Arrestin (data not shown). Lastly, as human retinal organoids do not represent all features of mature human retina, we validated the efficacy and specificity of PRl .7 promoter in post-mortem human retinal explants. Human retinal explants were cultured as described previously (38) and infected with a single drop of AAV2-7m8-pR1.7-GFP (Figure 5). Ten days after infection, GFP expression was analyzed on cryosections. The expression was restricted to the ONL (data not shown) and co-localized with M/L-opsin, a cone cell marker (data not shown). These data collectively point towards high efficiency and specificity of PRl .7 in leading to restricted gene expression in human cones. Discussion:

The fovea accounts for less than 1% of the retinal surface area in primates yet it provides the input to about 50% of the cells in the primary visual cortex (1). The high concentration of cones in the fovea, the thinnest and most delicate part of the retina allows for high acuity vision and it is of utmost importance to preserve the unique functions (39) and architecture (40) of the cones in this area during therapeutic interventions. Foveal cones can be targeted via different administration routes, using either subretinal or intravitreal injections (35, 41, 42) but detaching the fovea might lead to mechanical damage, especially in the degenerating retina (43). For all of these reasons, ways to deliver therapeutics to the fovea, without detaching this region are needed. Intravitreal injections are a surgically simple way to deliver therapeutics without retinal detachment. Gene therapy vectors can target the outer retina via intravitreal injections in rodents without damage to the photoreceptors (17, 35). However, safe and efficient gene delivery to primate cones via intravitreal injection had not been achieved so far, likely due to the substantial dilution of the vector in the vitreous and resulting loss of efficacy. The use of cell-type specific promoters that provide high-level gene expression with a lower local concentration is critical to overcome this challenge (29, 44).

In this study, we sought to first achieve strong and exclusive transduction of cones via non-invasive, intravitreal injection using various promoters in combination with AAV2-7m8 capsid. We selected three previously described promoters in view of their utility in driving gene expression in primate cones (4, 18, 19, 45, 46) and tested them for specificity and strength of cone transduction side-by-side. All promoters tested in vivo in mouse retinas lead to transgene expression in the photoreceptor layer when delivered subretinally. mCAR promoter led to expression in rods and cones. Surprisingly after intravitreal delivery; only PR1.7 maintained its specificity towards cones, while PR2.1 and mCAR gave rise to non- specific gene expression in inner retinal neurons. mCAR and PR2.1 gave rise to non-specific expression in inner retinal cells, making them unsuitable for optogenetic applications where any expression in downstream neurons would cancel out the response from the photoreceptors. Subsequent in silico analysis of TF binding sites within each promoter sequence proposed basis for more specific transduction with PR1.7 and the observed the lack of specificity with mCAR promoter. Next, to study the ability of AAV2-7m8 equipped with PR1.7 promoter to transduce foveal cones, we conducted gene delivery studies in macaque eyes. Complete restriction of gene expression to primate cones was achieved using AAV2- 7m8-PR1.7 in the fovea via intravitreal administration. One shortcoming with intravitreal injection route is the higher susceptibility of AAVs administered into this compartment to interactions with the immune system compared to subretinal administration (32). It has been shown that antibody neutralization poses a barrier to intravitreal AAV vector mediated gene delivery in non-human primates and this will likely pose a challenge for human application. We thus aimed to develop another gene delivery approach for patients who have neutralizing antibodies towards AAV2. To this aim we tested gene delivery to foveal cones by subretinal administration of AAV9-7m8 at a distal site. We demonstrated that robust light responses could be obtained with this new delivery approach, thanks to the vector's ability to diffuse laterally and mediate expression outside of the bleb. Using the same optogenetic cone reactivation strategy, we showed that this approach also affords robust light responses mediated by Jaws but in a higher percentage of cones compared to intravitreal route (4, 15).

Our in vivo findings collectively point to three important considerations in retinal gene delivery. First, enhanced AAV vectors, whether obtained via directed evolution (AAV2-7m8 (35)) or rational design (AAV9-7m8 (17)), can achieve therapeutic objectives where parental serotypes fail to provide sufficient gene delivery. Indeed AAV2 and AAV9 cannot perform efficient non-invasive foveal targeting (30, 31) while 7m8 modified vectors bridge this gap. Second, strong cell-type specific promoters allow dose sparing important for the safety of gene therapy (i.e avoiding immune response). Third, our study shows the non-negligible impact of vector administration route on transgene expression patterns. Finally, to complement our in vivo results in animals, we performed a battery of ex vivo tests in human tissues; that in combination with in vivo experiments constitute a versatile platform for validating gene therapy for clinical application. The vector-promoter combinations described here will find utility in all retinal diseases where cone targeting is desired. Each administration route and vector can be considered based on the serological state of the patient and natural history of the targeted disease (see Table 1). The combination of PR1.7 and AAV2-7m8 is ideal for therapeutic gene expression in human foveal cones when delivered into the vitreous and can be an ideal way to reanimate remaining dormant cones with optogenetics in retinitis pigmentosa (4). Since cones subsist in both the center and the periphery in achromatopsia, gene delivery in the periphery, using AAV9-7m8-PR1.7 can be more efficacious, as it would deliver the therapeutic gene into both the foveal and peripheral cones.

Table 1: AAV vector administration strategies for cone-directed gene therapy. Injection Peripheral SR Central SR Peripheral SR (near Intravitreal route macula)

Therapeutic Peripheral Central (macula- Peripheral and central Central

gene fovea)

expression

Potential AAV2-3YF(18, 47) AAV2 in clinical AAV9-7m8 as used in AAV2-7m8 as capsids AAV9(18, 30, 47) trials(8, 9, 48) this study used in this study

Advantages Immune privilege Immune privilege Immune privilege Non invasive

High level High level therapeutic High level therapeutic Potential high therapeutic gene gene expression gene expression acuity vision expression Foveal transduction Larger expression area Controlled area of

High acuity vision that includes the fovea expression pattern

Not invasive to the

fovea

Disadvantages Invasive No Invasive, risk of Presence of NAbs foveal adverse effects such in the vitreous (use transduction as macular of

Low acuity vision thinning(l 1) glucocorticoids^ 9) could prevent anti- vector immune response if patient is seropositive for AAV2)

Lower gene expression than SR

Potential Retinitis Pigmentosa: optogenetic vision restoration (Jaws) (4, 15)

target Achromatopsia: CNGA3 or CNGB3(47)

diseases and

applications

SEQUENCES:

SEQ ID NO: 1: VP1 capsid of the recombinant AAV2-derived vector

MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYK YLGPFNGLDKGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKE DTSFGGNLGRAVFQAKKRVLEPLGLVEEPVKTAPGK RPVEHSPVEPDSSSGTGKAG QQPARKRLNFGQTGDADSVPDPQPLGQPPAAPSGLGTNTMATGSGAPMAD NEGAD GVGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGY STPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTI A NLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTL NGSQAVG RSSFYCLEYFPSQMLRTG NFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLS RTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSAD NNSEYSWT GATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMIT DEEEIRTTNPVATEQYGSVSTNLQRGLALGETTRPARQAATADVNTQGVLPGMVW QDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIK TPVPANPSTTFS AA KFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYS EPRPIGTRYLTR SEQ ID NO:2: PR1.7 promoter

ggaggctgaggggtggggaaagggcatgggtgtttcatgaggacagagcttccgtttcatgcaatgaaaagagtttggaga cggatggtggtgactggactatacacttacacacggtagcgatggtacactttgtattatgtatattttaccacgatctttttaaagtgtcaaa ggcaaatggccaaatggttccttgtcctatagctgtagcagccatcggctgttagtgacaaagcccctgagtcaagatgacagcagccc ccataactcctaatcggctctcccgcgtggagtcatttaggagtagtcgcattagagacaagtccaacatctaatcttccaccctggccag ggccccagctggcagcgagggtgggagactccgggcagagcagagggcgctgacattggggcccggcctggcttgggtccctct ggcctttccccaggggccctctttccttggggctttcttgggccgccactgctcccgctcctctccccccatcccaccccctcaccccctc gttcttcatatccttctctagtgctccctccactttcatccacccttctgcaagagtgtgggaccacaaatgagttttcacctggcctgggga cacacgtgcccccacaggtgctgagtgactttctaggacagtaatctgctttaggctaaaatgggacttgatcttctgttagccctaatcat caattagcagagccggtgaaggtgcagaacctaccgcctttccaggcctcctcccacctctgccacctccactctccttcctgggatgtg ggggctggcacacgtgtggcccagggcattggtgggattgcactgagctgggtcattagcgtaatcctggacaagggcagacaggg cgagcggagggccagctccggggctcaggcaaggctgggggcttcccccagacaccccactcctcctctgctggacccccacttca tagggcacttcgtgttctcaaagggcttccaaatagcatggtggccttggatgcccagggaagcctcagagttgcttatctccctctagac agaaggggaatctcggtcaagagggagaggtcgccctgttcaaggccacccagccagctcatggcggtaatgggacaaggctggc cagccatcccaccctcagaagggacccggtggggcaggtgatctcagaggaggctcacttctgggtctcacattcttggatccggttc caggcctcggccctaaatagtctccctgggctttcaagagaaccacatgagaaaggaggattcgggctctgagcagtttcaccaccca ccccccagtctgcaaatcctgacccgtgggtccacctgccccaaaggcggacgcaggacagtagaagggaacagagaacacataa acacagagagggccacagcggctcccacagtcaccgccaccttcctggcggggatgggtggggcgtctgagtttggttcccagcaa atccctctgagccgcccttgcgggctcgcctcaggagcaggggagcaagaggtgggaggaggaggtctaagtcccaggcccaatta agagatcaggtagtgtagggtttgggagcttttaaggtgaagaggcccgggctgatcccacaggccagtataaagcgccgtgaccctc aggtgatgcgccagggccggctgccgtcggggacagggctttccatagcc

SEQ ID NO:3 : Jaws-GFP= Halo57 +2 mutations + KGC + GFP + ER2

MTAVSTTATTVLQATQSDVLQEIQSNFLLNSSIWVNIALAGVVILLFVAMGRD LESPRAKLIWVATMLVPLVSISSYAGLASGLTVGFLQMPPGHALAGQEVLSPWGRYL TWTFSTPMILLALGLLADTDIASLFTAITMDIGMCVTGLAAALITSSHLLRWVFYGISC AFFVAVLYVLLVQWPADAEAAGTSEIFGTLRILTVVLWLGYPILFALGSEGVALLSVG VTSWGYSGLDILAKYVFAFLLLRWVAANEGTVSGSGMGIGSGGAAPADDRPVVKSR ITSEGEYIPLDQIDINVAPAGAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDA TYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQ ERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYI MADKQK GIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSK DPNEKRDHMVLLEFVTAAGITLGMDELYKVAFCYENEV SEQ ID NO: 4: Jaws = Halo57 + 2 mutations + KGC + ER2

MTAVSTTATTVLQATQSDVLQEIQSNFLLNSSIWVNIALAGVVILLFVAMGRD LESPRAKLIWVATMLVPLVSISSYAGLASGLTVGFLQMPPGHALAGQEVLSPWGRYL TWTFSTPMILLALGLLADTDIASLFTAITMDIGMCVTGLAAALITSSHLLRWVFYGISC AFFVAVLYVLLVQWPADAEAAGTSEIFGTLRILTVVLWLGYPILFALGSEGVALLSVG VTSWGYSGLDILAKYVFAFLLLRWVAANEGTVSGSGMGIGSGGAAPADDRPVVKSR ITSEGEYIPLDQIDINVAPAGAVAFCYENEV SEQ ID NO: 5: Halo57 + 2 mutations + KGC

MTAVSTTATTVLQATQSDVLQEIQSNFLLNSSIWVNIALAGVVILLFVAMGRD LESPRAKLIWVATMLVPLVSISSYAGLASGLTVGFLQMPPGHALAGQEVLSPWGRYL TWTFSTPMILLALGLLADTDIASLFTAITMDIGMCVTGLAAALITSSHLLRWVFYGISC AFFVAVLYVLLVQWPADAEAAGTSEIFGTLRILTVVLWLGYPILFALGSEGVALLSVG VTS WGYSGLDILAKYVFAFLLLRWVAANEGTVSGSGMGIGSGGAAPADDRPVVKSR ITSEGEYIPLDQIDINV

REFERENCES:

Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.

1. Wassle H, Grunert U, Rohrenbeck J, Boycott BB. Cortical magnification factor and the ganglion cell density of the primate retina. Nature 1989;341(6243):643-646.

2. Kolb H, Zhang L, Dekorver L, Cuenca N. A new look at calretinin-immunoreactive amacrine cell types in the monkey retina.. J. Comp. Neurol. 2002;453(2): 168-84.

3. Wikler KC, Williams RW, Rakic P. Photoreceptor mosaic: Number and distribution of rods and cones in the rhesus monkey retina. J. Comp. Neurol. 1990;297(4):499-508.

4. Busskamp V et al. Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. [Internet]. Science 2010;329(5990):413-7.

5. Byrne LC et al. Viral-mediated RdCVF and RdCVFL expression protects cone and rod photoreceptors in retinal degeneration. [Internet]. J. Clin. Invest. 2015; 125(1): 105-16.

6. Komaromy AM et al. Gene therapy rescues cone function in congenital achromatopsia. Hum. Mol. Genet. 2010;19:2581-2593. 7. Maguire AM et al. Safety and Efficacy of Gene Transfer for Leber's Congenital Amaurosis. N. Engl. J. Med. 2008;358(21):2240-2248.

8. Bainbridge JWB et al. Effect of gene therapy on visual function in Leber's congenital amaurosis.. N. Engl. J. Med. 2008;358(21):2231-9.

9. Cideciyan A V et al. Human gene therapy for RPE65 isomerase deficiency activates the retinoid cycle of vision but with slow rod kinetics.. Proc. Natl. Acad. Sci. U. S. A. 2008;105(39): 15112-7.

10. Bainbridge JWB et al. Long-Term Effect of Gene Therapy on Leber's Congenital Amaurosis. N. Engl. J. Med. 2015;150504083137004.

11. Jacobson SG et al. Improvement and Decline in Vision with Gene Therapy in

Childhood Blindness. N. Engl. J. Med. 2015;150503141523009.

12. Jacobson SG et al. Gene therapy for leber congenital amaurosis caused by RPE65 mutations: safety and efficacy in 15 children and adults followed up to 3 years.. Arch. Ophthalmol. 2012;130(l):9-24.

13. MacLaren RE et al. Retinal gene therapy in patients with choroideremia: Initial fi ndings from a phase 1/2 clinical trial. Lancet 2014;383(9923): 1129-1137.

14. Duncan JL. Visual Consequences of Delivering Therapies to the Subretinal Space. JAMA Ophthalmol. 2017;135(3):242-243. doi: 10.100 l/jamaophthalmol.2016.5659.

15. Chuong AS et al. Noninvasive optical inhibition with a red-shifted microbial rhodopsin [Internet]. Nat N euro sci 2014;17(8): 1123-1129.

16. Dalkara D et al. In Vivo-Directed Evolution of a New Adeno-Associated Virus for Therapeutic Outer Retinal Gene Delivery from the Vitreous. Sci. Transl. Med. 2013;5(189): 189ra76-189ra76.

17. Khabou H et al. Insight into the mechanisms of enhanced retinal transduction by the engineered AAV2 capsid variant -7m8.. Biotechnol. Bioeng. [published online ahead of print: June 2016]; doi:10.1002/bit.26031

18. Ye G-J et al. Cone-Specific Promoters for Gene Therapy of Achromatopsia and Other Retinal Diseases. Hum. Gene Ther. 2016;27(l):72-82.

19. Ye G et al. Safety and Biodistribution Evaluation in CNGB3 -Deficient Mice of rAAV2tYF-PRl . 7-hCNGB3 , a Recombinant AAV Vector for Treatment of

Achromatopsia2016;27(l):27-37.

20. Kolstad KD et al. Changes in adeno-associated virus-mediated gene delivery in retinal degeneration.. Hum. Gene Ther. 2010;21(5):571-578. 21. Vacca O et al. AAV-mediated gene delivery in Dp71-null mouse model with compromised barriers. [Internet]. Glia 2014;62(3):468-76.

22. Satoh S et al. The spatial patterning of mouse cone opsin expression is regulated by bone morphogenetic protein signaling through downstream effector COUP-TF nuclear receptors.. J. Neurosci. 2009;29(40): 12401-11.

23. Pickrell SW, Zhu X, Wang X, Craft CM. Deciphering the contribution of known cis-elements in the mouse cone arrestin gene to its cone-specific expression. Investig. Ophthalmol. Vis. Sci. 2004;45(11):3877-3884.

24. von Mering C et al. STRING 7 - Recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007;35(SUPPL. 1):358— 362.

25. Blazek E, Mittler G, Meisterernst M. The mediator of RNA polymerase II. Chwmosoma 2005;113(8):399-408.

26. Regulators LT. Letter to the Editor A Unified Nomenclature for Protein Subunits of Mediator Complexes. Mol. Cell 2004;14:553-557.

27. Boyd JM, Verma S, Uhlmann E. 14584 Corrections. Annu. Rev. Microbiol.

1998;95:2-3.

28. Viets K, Eldred KC, Jr RJJ. Mechanisms of Photoreceptor Patterning in Vertebrates and Invertebrates. Trends Genet. 2016;32(10):638-659.

29. Ramachandran PS et al. Evaluation of Dose and Safety of AAV7m8 and AAV8BP2 in the Non-Human Primate Retina.. Hum. Gene Ther. [published online ahead of print: October 2016]; doi: 10.1089/hum.2016.111

30. Vandenberghe LH et al. AAV9 targets cone photoreceptors in the nonhuman primate retina.. PLoS One 2013;8(l):e53463.

31. Vandenberghe LH et al. Dosage thresholds for AAV2 and AAV8 photoreceptor gene therapy in monkey.. Sci. Transl. Med. 201 l;3(88):88ra54.

32. Kotterman M a et al. Antibody neutralization poses a barrier to intravitreal adeno- associated viral vector gene delivery to non-human primates.. Gene Ther. 2014;(August): l- 11.

33. Sengupta A et al. Red-shifted channelrhodopsin stimulation restores light responses in blind mice , macaque retina , and human retina. EMBO Mol Med 2016; 1-17.

34. Bell CL, Gurda BL, Van Vliet K, Agbandje-McKenna M, Wilson JM. Identification of the Galactose Binding Domain of the Adeno-Associated Virus Serotype 9 Capsid. J. Virol. 2012;86(13):7326-7333. 35. Dalkara D et al. In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. [Internet]. Sci. Transl. Med. 2013;5: 189ra76.

36. Yin L et al. Intravitreal injection of AAV2 transduces macaque inner retina.. Invest. Ophthalmol. Vis. Sci. 2011;52(5):2775-83.

37. Reichman S, Terray A, Slembrouck A, Nanteau C, Orieux G. From confluent human iPS cells to self-forming neural retina and retinal pigmented epithelium[published online ahead of print: 2014]; doi: 10.1073/pnas.1324212111

38. Fradot M, Busskamp V, Bennett J. Gene Therapy in Ophthalmology : Validation on Cultured201 l;593(May):587-593.

39. Sinha R et al. Cellular and Circuit Mechanisms Shaping the Perceptual Properties of the Primate Fovea. Cell 2017;168(3):413-426.el2.

40. Anderson DH, Fisher SK. The relationship of primate foveal cones to the pigment epithelium.. J. Ultrastruct. Res. 1979;67(l):23-32.

41. Allocca M et al. Novel adeno-associated virus serotypes efficiently transduce murine photoreceptors.. J. Virol. 2007;81(20):11372-80.

42. Kay CN et al. Targeting photoreceptors via intravitreal delivery using novel, capsid-mutated AAV vectors.. PLoS One 2013;8(4):e62097.

43. Jacobson SG et al. Gene Therapy for Leber Congenital Amaurosis caused by RPE65 mutations: Safety and Efficacy in Fifteen Children and Adults Followed up to Three

Years. Arch. Ophthalmol. 2012;130(l):9-24.

44. Tenenbaum L, Lehtonen E, Monahan PE. Evaluation of risks related to the use of adeno-associated virus-based vectors.. Curr. Gene Ther. 2003;3(6):545-65.

45. Boyd RF et al. Photoreceptor-targeted gene delivery using intravitreally administered AAV vectors in dogs. Gene Ther. 2016;23(2):223-230.

46. Ye G-J et al. Safety and Biodistribution Evaluation in Cynomolgus Macaques of rAAV2tYF-PR1.7-hCNGB3, a Recombinant AAV Vector for Treatment of Achromatopsia. Hum. Gene Ther. Clin. Dev. 2016;27(l):hum.2015.164.

47. Maguire AM et al. Safety and efficacy of gene transfer for Leber's congenital amaurosis.. N. Engl. J. Med. 2008;358(21):2240-8.

48. Gernoux G, Wilson JM, Mueller C. Regulatory and Exhausted T Cell Responses to AAV Capsid. Hum. Gene Ther. 2017;28(4):338-349.

49. Choi VW, Asokan A, Haberman R a, Samulski RJ. Production of recombinant adeno-associated viral vectors.. Curr. Protoc. Hum. Genet. 2007;Chapter 12:Unit 12.9. 50. Aurnhammer C et al. Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences.. Hum. Gene Ther. Methods 2012;23(l): 18-28.

51. Delyfer M-N et al. Transcriptomic Analysis of Human Retinal Detachment Reveals Both Inflammatory Response and Photoreceptor Death. PLoS One

2011;6(12):e28791.

52. Reichman S et al. The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina.. Hum. Mol. Genet. 2010;19(2):250-61.

Claims

CLAIMS:

1. A method of expressing a polynucleotide of interest in the cone photoreceptors of a subject comprising the intravitreal delivery of a therapeutically effective amount of a recombinant AAV2-derived vector comprising a VP1 capsid protein as set forth in SEQ ID NO: l and the polynucleotide of interest under the control of the PR1.7 promoter as set forth in SEQ ID NO: 2.

2. The method of claim 1 wherein the subject is affected or likely to be affected with a retinal disease affecting cone photoreceptors.

3. The method of claim 1 wherein the subject suffers from a retinal disease selected from the group consisting of age-related macular degeneration, Bassen-kornzweig syndrome, choroideremia, gyrate atrophy, Refsum syndrome, Usher syndrome, color blindness, blue cone monochromacy, achromatopsia, incomplete achromatopsia, oligocone trichromacy, retinitis pigmentosa (RP), macular degeneration, Stargardt's Disease, Bardet-Biedl syndrome, Bornholm eye disease, Best's Disease and Leber's congenital amaurosis.

4. The method of claim 1 wherein the polynucleotide of interest encodes for retinitis pigmentosa GTPase regulator (RPGRORF15), CNGB3 (beta subunit of the cone cyclic nucleotide-gated cation channel), CNGA3 (alpha subunit of the cone cyclic nucleotide-gated cation channel) or GNAT2.

5. The method of claim 1 wherein the polynucleotide of interest encodes for a neurotrophic factor.

6. The method of claim 1 wherein the polynucleotide of interest encodes for RdCVF, RdCVF2, RdCVFL or RdCVFL2.

7. The method of claim 1 wherein the polynucleotide of interest encodes for an opsin such as rhodopsin like halorhodopsin or cruxhalorhodopsin, photopsin, L/M wavelength (red/green) cone-opsin, or short wavelength (S) cone-opsin (blue).

8. The method of claim 7 wherein the polynucleotide of interest encodes for an opsin consisting of an amino acid sequence as set forth in SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5.

9. The method of claim 1 wherein the polynucleotide of interest encodes for a site- specific endonuclease that provides for site-specific knock-down of gene function selected from the group consisting of zinc finger nucleases (ZFNs); transcription activator-like effector nucleases (TALENs), and CRISPR-associated endonucleases.

10. The method of claim 1 wherein the polynucleotide of interest encodes for Cas9 nuclease.

11. The method of claim 1 wherein the polynucleotide of interest encodes for an interfering RNA (RNAi), in particular a siRNA.

12. The method of claim 1 wherein the polynucleotide of interest encode for an antisense oligonucleotide.

13. A recombinant AAV2-derived vector comprising a VP1 capsid protein as set forth in SEQ ID NO: l and a polynucleotide of interest under the control of the PR1.7 promoter as set forth in SEQ ID NO:2.

14. The recombinant AAV2-derived vector of claim 13 for use in a method for the treatment of a retinal disease affecting cone photoreceptors.