COMPOSITIONS AND METHODS FOR ENHANCING VISUAL FUNCTION

The present disclosure provides a method of restoring or enhancing visual function in an individual, the method comprising administering to the individual a nucleic acid comprising a nucleotide sequence encoding one or more of a medium wavelength cone opsin (MW-opsin), a long wavelength cone opsin (LW-opsin), and a short wavelength cone opsin (SW-opsin). One or more of the MW-opsin, LW-opsin, and SW-opsin is expressed in a retinal cell in the individual, thereby restoring or enhancing visual function.

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Description
CROSS-REFERENCE

This application claims the benefit of U.S. Provisional Patent Application No. 62/585,237, filed Nov. 13, 2017, U.S. Provisional Patent Application No. 62/589,476, filed Nov. 21, 2017, and U.S. Provisional Patent Application No. 62/641,783, filed Mar. 12, 2018, each of which applications is incorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under EY018241 awarded by the National Institutes of Health. The government has certain rights in the invention.

INTRODUCTION

Inherited and age-related retinal degenerative diseases cause progressive loss of rod and cone photoreceptors, leading to complete blindness. Despite loss of the light-sensing cells required for vision, downstream neurons of the inner retina survive in a functional state, providing a target for optogenetic therapy. To date, optogenetic approaches have encountered certain limitations, including: a) very low light sensitivity in microbial opsins and chemically engineered mammalian receptors; b) very slow kinetics in retinal opsins; and c) a lack of the mechanisms of adaptation that provides natural vision with high sensitivity across a very wide range of ambient light levels.

There is a need in the art for improved optogenetic approaches to treating ocular disorders.

SUMMARY

The present disclosure provides a method of restoring or enhancing visual function in an individual, the method comprising administering to the individual a nucleic acid comprising a nucleotide sequence encoding one or more of a medium wavelength cone opsin (MW-opsin), a long wavelength cone opsin (LW-opsin), and a short wavelength cone opsin (SW-opsin). One or more of the MW-opsin, LW-opsin, and SW-opsin is expressed in a retinal cell in the individual, thereby restoring or enhancing visual function.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1C depict that activation by light of MW-opsin or rhodopsin turns on GIRK channels to generate an inward photocurrent at negative holding potentials in high external potassium.

FIG. 2A-2G depict protein expression and light responses in retina isolated from rd1 mice, whose rods and cones have degenerated. Expression of MW-opsin in retinal cells is shown (FIG. 2A-2D), and light-evoked responses that are mediated by MW-opsin are shown (FIG. 2E-2G).

FIG. 3A-3G depict light response timing, size and high sensitivity of MW-opsin or rhodopsin in cells of retinas isolated from blind rd1 mice.

FIG. 4A-4I depict behavioral tests demonstrating equal ability to distinguish light from dark mediated by MW-opsin and rhodopsin in retinal cells of rd1 mice (FIG. 4A-4C), but that only MW-opsin enables animals to distinguish between flashing and constant light (FIG. 4D-4E) or between different spatial light patterns (FIG. 4F-4G). MW-opsin also supports wt-level line differentiation between parallel lines at different spacing that are displayed as still images or in motion (FIG. 4H-4I).

FIG. 5A-5F depict MW-opsin mediated light adaptation in rd1 mice: in MEA recordings on isolated retina (FIG. 5A-5C) and visually-guided behavior (FIG. 5D-5F).

FIG. 6 depicts behavioral tests demonstrating restoration of the ability to distinguish between parallel lines at 1 versus 6 cm distance by MW-opsin, LW-opsin, and SW-opsin.

FIG. 7 depicts the threshold response of optogenetic systems in blind retinas compared to normal vision.

FIG. 8A-8E depict intensity dependent kinetic responses mediated by MW-opsin.

FIG. 9A-9G depict light avoidance and learned pattern discrimination behavior.

FIG. 10A-10G depict light adaptation of excised retina and behavioral mice.

FIG. 11 provides Table 1, which depicts statistical significance of light avoidance and learned visually-guided behavior.

FIG. 12A-12B provide an alignment of amino acid sequences of human SW-opsin (SEQ ID NO:5) and mouse SW-opsin (SEQ ID NO:6), and also provide an amino acid sequence of an example of a human/mouse SW-opsin chimera (SEQ ID NO:7). Transmembrane (TM) domains of human SW-opsin and chimeric human/mouse SW-opsin are underlined; intracellular domains of mouse SW-opsin and chimeric human/mouse SW-opsin are double underlined.

FIG. 13A-13L depict restoration of visually-guided exploratory behavior by MW-opsin.

FIG. 14A-14B depict MW-opsin expression in rd1 mouse retina.

FIG. 15A-15B depict rhodopsin expression in rd1 mouse retina.

FIG. 16A-16D depict transduction efficiency of MW-opsin in rd1 retina.

FIG. 17A-17D depict the characterization of slow component of light response in rd1 retina expressing MW-opsin.

FIG. 18A-18C depict contrast detection in an isolated retina of an MW-opsin expressing rd1 mouse.

FIG. 19A-19E depict the in vivo light response in V1 of a rd1 mouse expressing MW-opsin.

FIG. 20A-20B depict contrast detection in vivo in an MW-opsin expressing rd1 mouse.

FIG. 21A-21C depict temporal properties of in vivo V1 responses in rd1 mice expressing MW-opsin.

FIG. 22A-22B depict location preference in discrimination tasks.

 DEFINITIONS

The term “retinal cell” can refer herein to any of the cell types that comprise the retina, such as retinal ganglion cells; amacrine cells; horizontal cells; bipolar cells; and photoreceptor cells including rods and cones.

“Operatively linked” or “operably linked” refers to a juxtaposition of genetic elements, wherein the elements are in a relationship permitting them to operate in the expected manner. For instance, a promoter is operatively linked to a coding region if the promoter helps initiate transcription of the coding sequence. There may be intervening residues between the promoter and coding region so long as this functional relationship is maintained.

An “expression vector” is a vector comprising a region which encodes a polypeptide of interest, and is used for effecting the expression of the protein in an intended target cell. An expression vector also comprises control elements operatively linked to the encoding region to facilitate expression of the protein in the target. The combination of control elements and a gene or genes to which they are operably linked for expression is sometimes referred to as an “expression cassette,” a large number of which are known and available in the art or can be readily constructed from components that are available in the art.

As used herein, the terms “treatment,” “treating,” and the like, refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse affect attributable to the disease. “Treatment,” as used herein, covers any treatment of a disease in a mammal, particularly in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease or at risk of acquiring the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; (c) relieving the disease, i.e., causing regression of the disease; and (d) replacing a lost function that results from the disease.

The terms “individual,” “host,” “subject,” and “patient” are used interchangeably herein, and refer to a mammal, including, but not limited to, human and non-human primates, including simians and humans; mammalian sport animals (e.g., horses, camels, etc); mammalian farm animals (e.g., sheep, goats, cows, etc.); mammalian pets (dogs, cats, etc.); and rodents (e.g., mice, rats, etc.). In some cases, the individual is a human.

Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.

It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an MW-opsin polypeptide” includes a plurality of such polypeptides and reference to “the retinal” includes reference to one or more retinal cells and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to the invention are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present invention and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.

The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.

DETAILED DESCRIPTION

The present disclosure provides a method of restoring or enhancing visual function in an individual, the method comprising administering to the individual a nucleic acid comprising a nucleotide sequence encoding one or more of a medium wavelength cone opsin (MW-opsin), a long wavelength cone opsin (LW-opsin), and a short wavelength cone opsin (SW-opsin). One or more of the MW-opsin, LW-opsin, and SW-opsin is expressed in a retinal cell in the individual, thereby restoring or enhancing visual function.

An MW-opsin polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following human MW-opsin amino acid sequence:

(SEQ ID NO: 1) MAQQWSLQRL AGRHPQDSYE DSTQSSIFTY TNSNSTRGPF EGPNYHIAPR WVYHLTSVWM IFVVIASVFT NGLVLAATMK FKKLRHPLNW ILVNLAVADL AETVIASTIS VVNQVYGYFV LGHPMCVLEG YTVSLCGITG LWSLAIISWE RWMVVCKPFG NVRFDAKLAI VGIAFSWIWA AVWTAPPIFG WSRYWPHGLK TSCGPDVFSG SSYPGVQSYM IVLMVTCCIT PLSIIVLCYL QVWLAIRAVA KQQKESESTQ KAEKEVTRMV VVMVLAFCFC WGPYAFFACF AAANPGYPFH PLMAALPAFF AKSATIYNPV IYVFMNRQFR NCILQLFGKK VDDGSELSSA SKTEVSSVSS VSPA.

An MW-opsin polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following mouse MW-opsin amino acid sequence:

(SEQ ID NO: 8) MAQRLTGEQT LDHYEDSTHA SIFTYTNSNS TKGPFEGPNY HIAPRWVYHL TSTWMILVVV ASVFTNGLVL AATMRFKKLR HPLNWILVNL AVADLAETII ASTISVVNQI YGYFVLGHPL CVIEGYIVSL CGITGLWSLA IISWERWLVV CKPFGNVRFD AKLATVGIVF SWVWAAIWTA PPIFGWSRYW PYGLKTSCGP DVFSGTSYPG VQSYMMVLMV TCCIFPLSII VLCYLQVWLA IRAVAKQQKE SESTQKAEKE VTRMVVVMVF AYCLCWGPYT FFACFATAHP GYAFHPLVAS LPSYFAKSAT IYNPIIYVFM NRQFRNCILH LFGKKVDDSS ELSSTSKTEV SSVSSVSPA

A rhodopsin polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following rhodopsin amino acid sequence:

(SEQ ID NO: 2) MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA.

A channelrhodopsin polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following channelrhodopsin amino acid sequence:

(SEQ ID NO: 3) MDYGGALSAVGRELLFVTNPVVVNGSVLVPEDQCYCAGWIESRGTNGA QTASNVLQWLAAGFSILLLMFYAYQTWKSTCGWEEIYVCAIEMVKVIL EFFFEFKNPSMLYLATGHRVQWLRYAEWLLTCPVILIHLSNLTGLSND YSRRTMGLLVSDIGTIVWGATSAMATGYVKVIFFCLGLCYGANTFFHA AKAYIEGYHTVPKGRCRQVVTGMAWLFFVSWGMFPILFILGPEGFGVL SVYGSTVGHTIIDLMSKNCWGLLGHYLRVLIHEHILIHGDIRKTTKLN IGGTEIEVETLVEDEAEAGAVP.

An LW-opsin can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following human LW-opsin amino acid sequence:

(SEQ ID NO: 4) MAQQWSLQRL AGRHPQDSYE DSTQSSIFTY TNSNSTRGPF EGPNYHIAPR WVYHLTSVWM IFVVTASVFT NGLVLAATMK FKKLRHPLNW ILVNLAVADL AETVIASTIS IVNQVSGYFV LGHPMCVLEG YTVSLCGITG LWSLAIISWE RWMVVCKPFG NVRFDAKLAI VGIAFSWIWA AVWTAPPIFG WSRYWPHGLK TSCGPDVFSG SSYPGVQSYM IVLMVTCCII PLAIIMLCYL QVWLAIRAVA KQQKESESTQ KAEKEVTRMV VVMIFAYCVC WGPYTFFACF AAANPGYAFH PLMAALPAYF AKSATIYNPV IYVFMNRQFR NCILQLFGKK VDDGSELSSA SKTEVSSVSS VSPA.

An LW-opsin can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following mouse LW-opsin amino acid sequence:

(SEQ ID NO: 9) MNGTEGPNFY VPFSNVTGVV RSPFEQPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVVFT WIMALACAAP PLVGWSRYIP EGMQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIVIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIF FLICWLPYAS VAFYIFTHQG SNFGPIFMTL PAFFAKSSSI YNPVIYIMLN KQFRNCMLTT LCCGKNPLGD DDASATASKT ETSQVAPA.

An SW-opsin polypeptide can comprise an amino acid sequence having at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following human SW-opsin amino acid sequence:

(SEQ ID NO: 5) MRKMSEEEFY LFKNISSVGP WDGPQYHIAP VWAFYLQAAF MGTVFLIGFP LNAMVLVATL RYKKLRQPLN YILVNVSFGG FLLCIFSVFP VFVASCNGYF VFGRHVCALE GFLGTVAGLV TGWSLAFLAF ERYIVICKPF GNFRFSSKHA LTVVLATWTI GIGVSIPPFF GWSRFIPEGL QCSCGPDWYT VGTKYRSESY TWFLFIFCFI VPLSLICFSY TQLLRALKAV AAQQQESATT QKAEREVSRM VVVMVGSFCV CYVPYAAFAM YMVNNRNHGL DLRLVTIPSF FSKSACIYNP IIYCFMNKQF QACIMKMVCG KAMTDESDTC SSQKTEVSTV SSTQVGPN.

In some cases, an SW-opsin comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to human SW-opsin (SEQ ID NO:5) responds to light in the visible range, and exhibits excitatory activity.

An SW-opsin polypeptide can comprise an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following mouse SW-opsin amino acid sequence:

(SEQ ID NO: 6) MSGEDDFYLF QNISSVGPWD GPQYHLAPVW AFRLQAAFMG FVFFVGTPLN AIVLVATLHY KKLRQPLNYI LVNVSLGGFL FCIFSVFTVF IASCHGYFLF GRHVCALEAF LGSVAGLVTG WSLAFLAFER YVVICKPFGS IRFNSKHALM VVLATWIIGI GVSIPPFFGW SRFIPEGLQC SCGPDWYTVG TKYRSEYYTW FLFIFCFIIP LSLICFSYSQ LLRTLRAVAA QQQESATTQK AEREVSHMVV VMVGSFCLCY VPYAALAMYM VNNRNHGLDL RLVTIPAFFS KSSCVYNPII YCFMNKQFRA CILEMVCRKP MADESDVSGS QKTEVSTVSS SKVGPH.

In some cases, an SW-opsin comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to mouse SW-opsin (SEQ ID NO:6) responds to light in the ultraviolet range, and exhibits inhibitory activity.

In some cases, both a human SW-opsin and a mouse SW-opsin are produced in a retinal cell in an individual. In some cases, both a human SW-opsin and a mouse SW-opsin (but not an LW-opsin or an MW-opsin) are produced in a retinal cell in an individual. In some cases, both a human SW-opsin and a mouse SW-opsin, as well as an LW-opsin (but not an MW-opsin,) are produced in a retinal cell in an individual. In some cases, both a human SW-opsin and a mouse SW-opsin, as well as an MW-opsin (but not an LW-opsin), are produced in a retinal cell in an individual. In some cases, both a human SW-opsin and a mouse SW-opsin, as well as an LW-opsin an an MW-opsin, are produced in a retinal cell in an individual. For example, in some cases, a first recombinant expression vector comprising a nucleotide sequence encoding an SW-opsin polypeptide comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to human SW-opsin (SEQ ID NO:5); and a second first recombinant expression vector comprising a nucleotide sequence encoding an SW-opsin polypeptide comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to mouse SW-opsin (SEQ ID NO:6) are introduced into a retinal cell.

In some cases, both an MW-opsin and an LW-opsin (but not an SW-opsin) are produced in a retinal cell in an individual. In some cases, both an MW-opsin and an SW-opsin (but not an LW-opsin) are produced in a retinal cell in an individual. In some cases, an MW-opsin, an LW-opsin, and an SW-opsin are expressed in a retinal cell in an individual.

In some cases, a suitable opsin is a chimeric opsin, e.g., an opsin that includes an amino acid sequence(s) from a first species and an amino acid sequence(s) from a second species. For example, in some cases, a chimeric opsin comprises intracellular portions of mouse SW-opsin, and transmembrane portions of human SW-opsin. An example of a suitable chimeric SW-opsin is depicted in FIG. 12A-12B.

In some cases, a suitable chimeric SW-opsin comprises an amino acid sequence having at least at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the chimeric SW-opsin depicted in FIG. 12A-12B, which chimeric SW-opsin has the following amino acid sequence:

(SEQ ID NO: 7) EDDFYLFQNISSVGPWDGPQYHLAPVWAFYLQAAFMGTVFLIGFPLNA MVLVATLHYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFV FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYVVICKPFGSIRFNSKH ALTVVLATWTIGIGVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRS ESYTWFLFIFCFIVPLSLICFSYTQLLRALRAVAAQQQESATTQKAER EVSHMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSK SACIYNPIIYCFMNKQFRACILEMVCRKPMADESDVSGSQKTEVSTVS SSKVGPH.

An MW-opsin and/or an LW-opsin and/or an SW-opsin can be used in combination with a heterologous opsin, e.g., a non-mammalian opsin such as an algal opsin, an archaeal opsin, or a variant thereof. Suitable heterologous opsins include depolarizing opsins such as the channelrhodopsin ChR2 (Zhang et al. (2007) Nature 446:633; GenBank AB064386.1) derived from Chlamydomonas reinhardtii; a step function opsin (SFO) protein (Berndt et al. (2009) Nat. Neurosci. 12:229) or a stabilized step function opsin (SSFO) protein (WO 2010/056970; Yizhar et al. (2011) Nature 477:171); a cation channel derived from Volvox carteri (VChR1-NCBI Gene ID: 9619570; U.S. Pat. No. 9,249,200); a C1V1 chimeric protein derived from the VChR1 protein of Volvox carteri and the ChR1 protein from Chlamydomonas reinhardtii (U.S. Pat. No. 9,175,095); a C1C2 chimeric protein derived from the ChR1 and the ChR2 proteins from Chlamydomonas reinhardtii (Lin et al. (2009) Biophys. J. 96:1803); a red shifted variant of a depolarizing light-responsive polypeptide derived from Chlamydomonas reinhardtii, where such light-responsive polypeptides are referred to as “ReaChR” (Lin et al. (2013) Nat. Neurosci. 16:1499); CnChR2 (Genbank Accession No.: AHH02139), derived from Chlamydomonas noctigama; a CsChrimson chimeric protein derived from a CsChR (Genbank Accession No.: AHH02144; Klapoetke et al. (2014) Nature Methods 11:338) protein of Chloromonas subdivisa; ShChR1 (Genbank Accession No.: AHH02106), derived from Stigeoclonium helveticum; a “ChETA” opsin (Gunaydin et al. (2010 Nat. Neurosci. 13:387) a “SwiChR” protein (WO 2015/148974); a “bReaChes” protein (WO/2017/048808); and the like. Other suitable depolarizing opsins are known in the art; see, e.g., Zhang et al. (2011) Cell 147:1446; Deisseroth (2015) Nature Neurosci. 18:1213; Berndt and Deisseroth (2015) Science 349:590; and the like.

Expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for patterned vision and image recognition by the individual. Image recognition can be of a static image and/or of a moving image.

Expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition at a light intensity of from about 10−4 W/cm2 to about 10 W/cm2. For example, in some cases, expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition at a light intensity of from about 10−2 W/cm2 to about 10−4 W/cm2, from about 10−4 W/cm2 to about 1 W/cm2, from about 10−4 W/cm2 to about 10−1 W/cm2, or from about 10−4 W/cm2 to about 5×10−1 W/cm2. In some cases, expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition at a light intensity of from about 10−4 W/cm2 to about 10−3 W/cm2, from about 10−3 W/cm2 to about 10−2 W/cm2, from about 10−2 W/cm2 to about 10−1 W/cm2, or from about 10−1 W/cm2 to about 1 W/cm2. In some cases, expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition at a light intensity of up to 2 W/cm2 up to 3 W/cm2, up to 4 W/cm2, up to 5 W/cm2, or up to 10 W/cm2. Expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition at a light intensity of less than 5 W/cm2, less than 4 W/cm2, less than 3 W/cm2, or less than 2 W/cm2.

Expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition by the individual at a light intensity that is at least 10-fold lower than the light intensity required to provide for image recognition by an individual expressing a channelrhodopsin polypeptide (e.g., a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:3) in a retinal cell. For example, expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition by the individual at a light intensity that is at least 10-fold lower, at least 25-fold lower, at least 50-fold lower, at least 100-fold lower, at least 150-fold lower, at least 200-fold lower, at least 300-fold lower, at least 400-fold lower, or at least 500-fold lower, than the light intensity required to provide for image recognition by an individual expressing a channelrhodopsin polypeptide in a retinal cell.

Expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell provides for kinetics that are at least 2-fold faster than the kinetics conferred on a retinal cell by a rhodopsin polypeptide (e.g., a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2). For example, expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell provides for kinetics that are at least 2-fold, at least 5-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 50-fold, at least 100-fold, or more than 100-fold, faster than the kinetics conferred on a retinal cell by a rhodopsin polypeptide.

A method of the present disclosure comprises delivery to an eye of an individual a nucleic acid comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide. In some cases, the nucleotide sequence is operably linked to a transcriptional control element that is functional in a mammalian cell. In some cases, the nucleotide sequence is operably linked to a transcriptional control element that provides for expression in a retinal cell, e.g., that provides for selective expression in a retinal cell. In some cases, the nucleotide sequence is operably linked to a promoter that provides for expression in a retinal cell, e.g., that provides for selective expression in a retinal cell. In some cases, the nucleotide sequence is operably linked to a promoter that generally provides for expression in a eukaryotic or mammalian cell.

Suitable promoters include, but are not limited to, a CAG promoter (Miyazaki et al. (1989) Gene 79:269); a cytomegalovirus (CMV) promoter; a glutamate metabotropic receptor-6 (grm6) promoter (Cronin et al. (2014) EMBO Mol. Med. 6:1175); a Pleiades promoter (Portales-Casamar et al. (2010) Proc. Natl. Acad. Sci. USA 107:16589); a choline acetyltransferase (ChAT) promoter (Misawa et al. (1992) J. Biol. Chem. 267:20392); a vesicular glutamate transporter (V-glut) promoter (Zhang et al. (2011) Brain Res. 1377:1); a glutamic acid decarboxylase (GAD) promoter (Rasmussen et al. (2007) Brain Res. 1144:19; Ritter et al. (2016) J. Gene Med. 18:27); a cholecystokinin (CCK) promoter (Ritter et al. (2016) J. Gene Med. 18:27); a parvalbumin (PV) promoter; a somatostatin (SST) promoter; a neuropeptide Y (NPY) promoter; and a vasoactive intestinal peptide (VIP) promoter. Suitable promoters include, but are not limited to, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, and a GluR promoter (e.g., a GluR6 promoter; also referred to as grm6). Suitable promoters include, but are not limited to, a vitelliform macular dystrophy 2 (VMD2) gene promoter, and an interphotoreceptor retinoid-binding protein (IRBP) gene promoter. Also suitable for use is an L7 promoter (Oberdick et al. (1990) Science 248:223), a thy-1 promoter, a recoverin promoter (Wiechmann and Howard (2003) Curr. Eye Res. 26:25); a calbindin promoter; and a beta-actin promoter. Suitable promoters include synthetic (non-naturally occurring) promoter/enhancer combinations.

In some cases, a nucleic acid comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is in a recombinant expression vector. Suitable expression vectors include, but are not limited to, a lentivirus vector, a herpes simplex virus (HSV) vector, an adenovirus vector, a retroviral vector, an adenoassociated virus (AAV) vector, and the like. Thus, in some cases, a nucleic acid comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is a recombinant lentivirus vector, a recombinant HSV vector, a recombinant adenovirus vector, a recombinant retrovirus vector, or a recombinant AAV vector.

In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is complexed with a nanoparticle.

In some cases, a nucleic acid comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is recombinant AAV (rAAV) vector. In some cases, the rAAV vector comprises a nucleotide sequence encoding a variant AAV capsid protein, where the variant AAV capsid protein confers infectivity of a retinal cell and/or the ability to cross the inner limiting membrane (ILM) in the eye. See, e.g., Day et al. (2014) Adv. Exp. Med. Biol. 801:687; Boye et al. (2016) J. Virol. 90:4215; Vandenberghe and Auricchio (2012) Gene Therapy 19:162; Klimczak et al. (2009) PLoS One 4:e7467; U.S. Patent Publication No. 2012/0164106; and U.S. Patent Publication No. 2016/0017295.

Retinal cells include retinal ganglion cells; amacrine cells; horizontal cells; bipolar cells; and photoreceptor cells including rods and cones.

In some cases, a method of the present disclosure comprises administering to an individual in need thereof a pharmaceutical composition comprising: a) a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide; and b) a pharmaceutically acceptable excipient.

A pharmaceutical composition comprising a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide may be administered to a patient alone, or in combination with other supplementary active agents. The pharmaceutical compositions may be manufactured using any of a variety of processes, including, without limitation, conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, and lyophilizing. The pharmaceutical composition can take any of a variety of forms including, without limitation, a sterile solution, suspension, emulsion, lyophilisate, tablet, pill, pellet, capsule, powder, syrup, elixir or any other dosage form suitable for administration.

A pharmaceutical composition comprising a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide can optionally include a pharmaceutically acceptable carrier(s) that facilitate processing of an active ingredient into pharmaceutically acceptable compositions. As used herein, the term “pharmacologically acceptable carrier” refers to any carrier that has substantially no long-term or permanent detrimental effect when administered and encompasses terms such as “pharmacologically acceptable vehicle, stabilizer, diluent, auxiliary or excipient.” Such a carrier generally is mixed with an active compound (e.g., a nucleic acid of the present disclosure), or permitted to dilute or enclose the active compound and can be a solid, semi-solid, or liquid agent. It is understood that the active ingredients can be soluble or can be delivered as a suspension in the desired carrier or diluent. Any of a variety of pharmaceutically acceptable carriers can be used including, without limitation, aqueous media such as, e.g., distilled, deionized water, saline; solvents; dispersion media; coatings; antibacterial and antifungal agents; isotonic and absorption delaying agents; or any other inactive ingredient. Selection of a pharmacologically acceptable carrier can depend on the mode of administration. Except insofar as any pharmacologically acceptable carrier is incompatible with the active ingredient, its use in pharmaceutically acceptable compositions is contemplated. Non-limiting examples of specific uses of such pharmaceutical carriers can be found in “Pharmaceutical Dosage Forms and Drug Delivery Systems” (Howard C. Ansel et al., eds., Lippincott Williams & Wilkins Publishers, 7th ed. 1999); “Remington: The Science and Practice of Pharmacy” (Alfonso R. Gennaro ed., Lippincott, Williams & Wilkins, 20th 2000); “Goodman & Gilman's The Pharmacological Basis of Therapeutics” Joel G. Hardman et al., eds., McGraw-Hill Professional, 10.sup.th ed. 2001); and “Handbook of Pharmaceutical Excipients” (Raymond C. Rowe et al., APhA Publications, 4th edition 2003).

A pharmaceutical composition can optionally include, without limitation, other pharmaceutically acceptable components, including, without limitation, buffers, preservatives, tonicity adjusters, salts, antioxidants, physiological substances, pharmacological substances, bulking agents, emulsifying agents, wetting agents, sweetening or flavoring agents, and the like. Various buffers and means for adjusting pH can be used to prepare a pharmaceutical composition, provided that the resulting preparation is pharmaceutically acceptable. Such buffers include, without limitation, acetate buffers, citrate buffers, phosphate buffers, neutral buffered saline, phosphate buffered saline and borate buffers. It is understood that acids or bases can be used to adjust the pH of a composition as needed. Pharmaceutically acceptable antioxidants include, without limitation, sodium metabisulfite, sodium thiosulfate, acetylcysteine, butylated hydroxyanisole and butylated hydroxytoluene. Useful preservatives include, without limitation, benzalkonium chloride, chlorobutanol, thimerosal, phenylmercuric acetate, phenylmercuric nitrate and a stabilized oxy chloro composition, for example, PURITE™. Tonicity adjustors suitable for inclusion in a pharmaceutical composition include, without limitation, salts such as, e.g., sodium chloride, potassium chloride, mannitol or glycerin and other pharmaceutically acceptable tonicity adjustor. It is understood that these and other substances known in the art of pharmacology can be included in a pharmaceutical composition.

Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol, and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; and (22) other non-toxic compatible substances employed in pharmaceutical formulations.

In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is formulated with one or more biocompatible polymers. Suitable biocompatible polymers include, but are not limited to, polyamides, polycarbonates, polyalkylenes, polyalkylene glycols, polyalkylene oxides, polyalkylene terephthalates, polyvinyl alcohols, polyvinyl ethers, polyvinyl esters, polyvinyl halides, poly(vinylpyrrolidone), polyglycolides, polysiloxanes, polyurethanes and copolymers thereof, alkyl cellulose, hydroxyalkyl celluloses, cellulose ethers, cellulose esters, nitro celluloses, polymers of acrylic and methacrylic esters, methyl cellulose, ethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methyl cellulose, hydroxybutyl methyl cellulose, cellulose acetate, cellulose propionate, cellulose acetate butyrate, cellulose acetate phthalate, carboxylethyl cellulose, cellulose triacetate, cellulose sulfate sodium salt poly-methyl methacrylate), poly(ethyl methacrylate), poly(butyl methacrylate), poly(isobutyl methacrylate\poly(hexyl methacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), poly(octadecyl acrylate), polyethylene, polypropylene poly(ethylene glycol), poly(ethylene oxide), poly(ethylene terephthalate), poly(vinyl alcohols), polyvinyl acetate, polyvinyl chloride polystyrene, poly(vinyl pyrrolidone), polyhyaluronic acids, casein, gelatin, glutin, polyanhydrides, polyacrylic acid, alginate, chitosan, poly(methyl methacrylates), poly(ethyl methacrylates), poly(butyl methacrylate), poly(isobutyl methacrylate), poly(hexyl methacrylate) poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylatee), poly(isobutyl acrylate), poly(octadecyl acrylate) and combinations of any of the forgoing.

In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is formulated in a liposome. See, e.g., U.S. Patent Publication No. 2017/0119666. In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is formulated in a nanoparticle. Nanoparticles include, e.g., polyalkylcyanoacrylate nanoparticles, nanoparticles comprising poly(lactic acid), nanoparticles comprising poly(lactic-co-glycolic acid) (PLGA) nanoparticles, and the like. In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is formulated in a hydrogel. Suitable hydrogel components include, but are not limited to, silk (see, e.g., U.S. Patent Publication No. 2017/0173161), poly(lactic acid) (PLA), poly(glycolic acid) (PGA), poly(lactide-co-glycolide) (PLGA), polyesters, poly(ortho ester), poly(phosphazine), poly(phosphate ester), polycaprolactone, gelatin, collagen, cellulose, hyaluronan, poly(ethylene glycol) (PEG), triblock copolymers, polylysine, poly(ethylene oxide), poly(vinyl pyrrolidone), hyaluronic acid, acrylated hyaluronic acid, poly(N-isopropylacrylamide), and the like.

In some cases, a composition comprising a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is present in a buffered saline solution. In some cases, a composition comprising a recombinant viral expression vector comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is present in a buffered saline solution in an amount of from about 108 to about 1015 viral genomes (vg) in a volume of from about 50 μL to about 1000 μL. For instance, in some cases, a composition comprising a recombinant viral expression vector comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is present in a buffered saline solution in an amount of from about 108 vg to about 109 vg, from about 109 vg to about 1010 vg, from about 1010 vg to about 1011 vg, from about 1011 vg to about 1012 vg, from about 1012 vg to about 1013 vg, from about 1013 vg to about 1014 vg, or from about 1014 vg to about 1015 vg, in a volume of from about 50 μL to about 75 μL, from about 75 μL to about 100 μL, from about 100 μL to about 150 μL, from about 150 μL to about 200 μL, from about 200 μL to about 300 μL, from about 300 μL to about 400 μL, from about 400 μL to about 500 μL, from about 500 μL to about 600 μL, from about 600 μL to about 700 μL, from about 800 μL to 900 μL, or from about 900 μL to about 1000 μL. In some cases, a composition comprising a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is present in a buffered saline solution containing a non-ionic detergent in a concentration of about 0.001%. Suitable non-ionic detergents include, e.g., Pluronic F68®. In some cases, a composition comprising a recombinant viral expression vector comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is present in a buffered saline solution in an amount of from about 108 vg to about 109 vg, from about 109 vg to about 1010 vg, from about 1010 vg to about 1011 vg, from about 1011 vg to about 1012 vg, from about 1012 vg to about 1013 vg, from about 1013 vg to about 1014 vg, or from about 1014 vg to about 1015 vg, in a volume of from about 50 μL to about 75 μL, from about 75 μL to about 100 μL, from about 100 μL to about 150 μL, from about 150 μL to about 200 μL, from about 200 μL to about 300 μL, from about 300 μL to about 400 μL, from about 400 μL to about 500 μL, from about 500 μL to about 600 μL, from about 600 μL to about 700 μL, from about 800 μL to 900 μL, or from about 900 μL to about 1000 μL, where the buffered saline solution comprises a non-ionic detergent in a concentration of about 0.001%. A saline solution can comprise 0.9% NaCl.

A nucleic acid (e.g., a recombinant expression vector, such as a recombinant viral vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide can be administered to an individual in need thereof by any of a variety of routes of administration. Suitable routes of administration include, e.g., periocular, intraocular, intravitreal, subconjunctive, retrobulbar, into the sclera, and intercameral. In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is delivered by intravitreal injection. In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is delivered intraocularly. In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is delivered via sub-retinal injection.

In some cases, a method of the present disclosure comprises administering to an individual in need thereof a single administration (per eye) of a composition comprising a nucleic acid (e.g., a recombinant expression vector, such as a recombinant viral vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide.

In some cases, multiple doses of a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin are administered to an individual. The frequency of administration can vary depending on any of a variety of factors, e.g., severity of the symptoms, etc. For example, in some cases, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is administered once per month, twice per month, three times per month, every other week (qow), once per week (qw), twice per week (biw), three times per week (tiw), four times per week, five times per week, six times per week, every other day (qod), daily (qd), twice a day (qid), or three times a day (tid).

A nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide can be administered to an individual over a period of time of from about 1 day to about 1 year or more than 1 year. For example, a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide can be administered to an individual for a period of time of from 1 week to 2 weeks, from 2 weeks to 1 month, from 1 month to 4 months, from 4 months to 6 months, from 6 months to 1 year, or more than 1 year.

Where a nucleic acid comprising a nucleotide sequence is a recombinant viral expression vector comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide, the recombinant viral vector can be administered in an amount of from about 108 vg to about 109 vg, from about 109 vg to about 1010 vg, from about 1010 vg to about 1011 vg, from about 1011 vg to about 1012 vg, from about 1012 vg to about 1013 vg, from about 1013 vg to about 1014 vg, or from about 1014 vg to about 1015 vg, per dose.

A nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide is administered in an amount effective to increase visual function in an individual by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 2-fold, at least 5-fold, at least 10-fold, or more than 10-fold, compared with the visual function before administration of the nucleic acid. Tests for visual function are known in the art, and any known test can be applied to assess visual function.

Individuals suitable for treatment with a method of the present disclosure include individuals having reduced visual function due to loss of rod and cone photoreceptors. In some cases, the individual has an inherited retinal degenerative disease such as retinitis pigmentosa, retinoschisis, or Leber's Congenital Amaurosis. In some cases, the individual has an ocular disease (e.g., an inherited ocular disease) selected from retinitis pigmentosa, macular degeneration, age-related macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy. Individuals suitable for treatment with a method of the present disclosure include individuals having a retinal degeneration condition in which the natural light sensitivity is lost and vision is therefore compromised, but where neurons late in the retinal circuit (e.g. bipolar cells or amacrine interneurons or ganglion cells that output to the brain) are spared and can be made directly sensitive to light by introduction of the cone opsin(s).

Individuals suitable for treatment with a method of the present disclosure include individuals having retinal damage that is traumatic or acute, with no genetic or inherited basis. For example, in some cases, the individual has experienced retinal detachment resulting from blunt trauma, such as a blast injury (e.g., in a military battle), or resulting from an impact to the head, e.g., in the course of an auto accident or other accident resulting in impact to the head. In some instances, the photoreceptors are lost due to traumatic detachment of the retina from the underlying RPE, but the inner retinal neurons are intact. Individuals suitable for treatment with a method of the present disclosure include individuals having photoreceptor loss due to acute light damage, laser exposure, or chemical toxicity.

Compositions

The present disclosure provides compositions comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins. When the composition is administered to an individual in need thereof, the one or more nucleotide sequences encoding the one or more cone opsins are expressed in an eye of a subject in need thereof, such that the one or more cone opsins are produced in the eye of the subject, one or more beneficial clinical outcomes results. For example, when the composition is administered to an eye of an individual in need thereof, the one or more nucleotide sequences encoding the one or more cone opsins are expressed in an eye of a subject in need thereof, such that the one or more cone opsins are produced in the eye of the subject, one or more beneficial clinical outcomes results. When the one or more nucleotide sequences encoding the one or more cone opsins are expressed in an eye of a subject in need thereof, such that the one or more cone opsins are produced in the eye of the subject, one or more beneficial clinical outcomes results. Beneficial clinical outcomes include: 1) the subject can distinguish between an image comprising a vertical line and an image comprising a horizontal line in a spatial pattern discrimination assay; 2) the subject can distinguish between an image comprising a static line and an image comprising a moving line in a spatial pattern discrimination assay; 3) the subject can distinguish between flashing light and constant light in a temporal light pattern assay; 4) the subject can recognize an image at a light intensity of from about 10−4 W/cm2 to about 10 W/cm2 in an image recognition assay; and 5) subject can distinguish between an area with white light and an area without white light in a light avoidance assay.

Whether a composition provides one or more of the above-noted beneficial clinical outcomes can be determined using tests that are known in the art. See e.g., Leinonen and Tanila (2017) Behavioural Brain Research pii: S0166-4328(17)30870-7; Caporale et al. (2011). Molecular Therapy 19, 1212-9; Gaub et al. (2014) Proc. Natl. Acad. Sci. USA 111, E5574-83; Gaub et al. (2015) Molecular Therapy 23:1562; and Berry et al. (2017) Nat. Commun. 8:1862.

The present disclosure composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when: i) the composition is administered to an individual in need thereof; or ii) the composition is administered to an eye of an individual in need thereof, such that the one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between an image comprising a vertical line and an image comprising a horizontal line in a spatial pattern discrimination assay. The present disclosure composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when the one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between an image comprising a vertical line and an image comprising a horizontal line in a spatial pattern discrimination assay.

The present disclosure composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when: i) the composition is administered to an individual in need thereof; or ii) the composition is administered to an eye of an individual in need thereof, such that the one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between an image comprising a static line and an image comprising a moving line in a spatial pattern discrimination assay. The present disclosure provides a composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between an image comprising a static line and an image comprising a moving line in a spatial pattern discrimination assay.

The present disclosure composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when: i) the composition is administered to an individual in need thereof; or ii) the composition is administered to an eye of an individual in need thereof, such that the one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between flashing light and constant light in a temporal light pattern assay. The present disclosure provides a composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between flashing light and constant light in a temporal light pattern assay.

The present disclosure composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when: i) the composition is administered to an individual in need thereof; or ii) the composition is administered to an eye of an individual in need thereof, such that the one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can recognize an image at a light intensity of from about 10−4 W/cm2 to about 10 W/cm2 in an image recognition assay. The present disclosure provides a composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can recognize an image at a light intensity of from about 10−4 W/cm2 to about 10 W/cm2 (e.g., a light intensity of from about 10−4 W/cm2 to about 10−3 W/cm2, from about 10−3 W/cm2 to about 10−2 W/cm2, from about 10−2 W/cm2 to about 10−1 W/cm2, or from about 10−1 W/cm2 to about 1 W/cm2. In some cases, expression of an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide in a retinal cell in an individual provides for image recognition at a light intensity of up to 2 W/cm2 up to 3 W/cm2, up to 4 W/cm2, up to 5 W/cm2, or up to 10 W/cm2) in an image recognition assay.

The present disclosure composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when: i) the composition is administered to an individual in need thereof; or ii) the composition is administered to an eye of an individual in need thereof, such that the one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between an area with white light and an area without white light in a light avoidance assay. The present disclosure provides a composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof (such that the one or more opsins is produced in the eye of the subject), the subject can distinguish between an area with white light and an area without white light in a light avoidance assay.

Cone opsins that can be encoded by the one or more recombinant nucleic acids present in a composition of the present disclosure are described above, and include, e.g., an MW-opsin, an LW-opsin, an SW-opsin, a chimeric opsin, and the like.

In some cases, the one or more cone opsins encoded by the one or more recombinant nucleic acids present in a composition of the present disclosure is selected from the group consisting of:

a) an MW-opsin comprising an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1;

b) an LW-opsin comprising an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4;

c) an SW-opsin comprising an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5; and

d) a chimeric SW-opsin comprising: i) intracellular portions of a mouse SW-opsin comprising an amino acid sequence having at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:6; and ii) transmembrane portions of a human SW-opsin comprising an amino acid sequence having at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

In some cases, a composition of the present disclosure comprises a recombinant nucleic acid comprising a nucleotide sequence that encodes a single cone opsin. In some cases, the one or more recombinant nucleic acid vectors present in a composition of the present disclosure comprises one or more nucleotide sequences encoding 2 different cone opsins. For example, in some cases, the one or more recombinant nucleic acid vectors present in a composition of the present disclosure comprises one or more nucleotide sequences encoding an MW-opsin and an LW-opsin. As another example, in some cases, the one or more recombinant nucleic acid vectors present in a composition of the present disclosure comprises one or more nucleotide sequences encoding an MW-opsin and an SW-opsin. As another example, in some cases, the one or more recombinant nucleic acid vectors present in a composition of the present disclosure comprises one or more nucleotide sequences encoding an LW-opsin and an SW-opsin. The 2 different cone opsins can be encoded on a single recombinant nucleic acid. The 2 different cone opsins can be encoded on 2 separate recombinant nucleic acids.

In some cases, the one or more recombinant nucleic acid vectors present in a composition of the present disclosure comprises one or more nucleotide sequences encoding 3 different cone opsins. For example, in some cases, the one or more recombinant nucleic acid vectors present in a composition of the present disclosure comprises one or more nucleotide sequences encoding an MW-opsin, an SW-opsin, and an LW-opsin. The 3 different cone opsins can be encoded on a single recombinant nucleic acid. The 3 different cone opsins can be encoded on 3 separate recombinant nucleic acids.

Suitable recombinant nucleic acid vectors include a recombinant adeno-associated viral vector, a recombinant lentiviral vector, a recombinant herpes simplex virus vector, and a recombinant retroviral vector. In some cases, the one or more recombinant nucleic acid vectors is/are recombinant adeno-associated virus vectors. In some instances, the recombinant AAV vector comprises a nucleotide sequence encoding a variant capsid polypeptide that confers increased infectivity of a retinal cell and/or confers increased ability to cross the inner limiting membrane, compared to a wild-type AAV capsid.

A nucleotide sequence encoding a cone opsin can be operably linked to one or more transcriptional control elements. For example, a nucleotide sequence encoding a cone opsin can be operably linked to a promoter. Examples of suitable promoters include, but are not limited to, a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, and an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

A composition of the present disclosure is administered to an individual in need thereof. In some instances, the composition is administered directly to or into an eye of the individual, e.g., an eye that is affected by a vision disorder. In some cases, the subject has an ocular disease selected from retinitis pigmentosa, macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy. In some cases, the subject has experienced retinal detachment or photoreceptor loss due to trauma or head injury. In some cases, the subject has a retinal degeneration condition in which the natural light sensitivity is lost and vision is therefore compromised, but where neurons late in the retinal circuit (e.g. bipolar cells or amacrine interneurons or ganglion cells that output to the brain) are spared and can be made directly sensitive to light by introduction of the cone opsin(s).

A composition of the present disclosure can include, in addition to the one or more recombinant nucleic acids, a pharmaceutically acceptable excipient. Suitable pharmaceutically acceptable excipients are known in the art, and are described elsewhere herein. In some cases, a composition of the present disclosure is suitable for administration to a human subject; e.g., in some cases, the composition is sterile and is free of pyrogens, contaminants, and the like.

Recombinant Viral Vector

The present disclosure provides a recombinant viral vector comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin and/or an SW-opsin polypeptide. Suitable viral expression vectors include, but are not limited to, a lentivirus vector, a herpes simplex virus (HSV) vector, an adenovirus vector, a retroviral vector, an adenoassociated virus (AAV) vector, and the like. Thus, in some cases, a recombinant viral vector comprising a nucleotide sequence encoding an MW-opsin polypeptide and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is a recombinant lentivirus vector, a recombinant HSV vector, a recombinant adenovirus vector, a recombinant retrovirus vector, or a recombinant AAV vector.

In some cases, the nucleotide sequence encoding the MW-opsin and/or the LW-opsin, and/or the SW-opsin is operably linked to a promoter that provides for expression in a retinal cell. In some cases, the nucleotide sequence is operably linked to a promoter that generally provides for expression in a eukaryotic or mammalian cell.

Suitable promoters include, but are not limited to, a CAG promoter (Miyazaki et al. (1989) Gene 79:269); a cytomegalovirus (CMV) promoter; a glutamate metabotropic receptor-6 (grm6) promoter (Cronin et al. (2014) EMBO Mol. Med. 6:1175); a Pleiades promoter (Portales-Casamar et al. (2010) Proc. Natl. Acad. Sci. USA 107:16589); a choline acetyltransferase (ChAT) promoter (Misawa et al. (1992) J. Biol. Chem. 267:20392); a vesicular glutamate transporter (V-glut) promoter (Zhang et al. (2011) Brain Res. 1377:1); a glutamic acid decarboxylase (GAD) promoter (Rasmussen et al. (2007) Brain Res. 1144:19; Ritter et al. (2016) J. Gene Med. 18:27); a cholecystokinin (CCK) promoter (Ritter et al. (2016) J. Gene Med. 18:27); a parvalbumin (PV) promoter; a somatostatin (SST) promoter; a neuropeptide Y (NPY) promoter; and a vasoactive intestinal peptide (VIP) promoter. Suitable promoters include, but are not limited to, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, and a GluR promoter (e.g., a GluR6 promoter). Suitable promoters include, but are not limited to, a vitelliform macular dystrophy 2 (VMD2) gene promoter, and an interphotoreceptor retinoid-binding protein (IRBP) gene promoter. Also suitable for use is an L7 promoter (Oberdick et al. (1990) Science 248:223), a thy-1 promoter, a recoverin promoter (Wiechmann and Howard (2003) Curr. Eye Res. 26:25); a calbindin promoter; and a beta-actin promoter.

In some cases, a recombinant viral vector of the present disclosure comprises nucleotide sequences encoding an MW-opsin, an LW-opsin, and an SW-opsin. In some cases, the nucleotide sequences encoding an MW-opsin, an LW-opsin, and an SW-opsin are operably linked to a single promoter. In some cases, a recombinant viral vector comprises an internal ribosome entry site (IRES) between the nucleotide sequences encoding the MW-opsin and the LW-opsin, and between the nucleotide sequences encoding the LW-opsin and the SW-opsin.

In some cases, a recombinant viral vector comprising a nucleotide sequence encoding an MW-opsin and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide is recombinant AAV (rAAV) vector. In some cases, the rAAV vector comprises: i) a nucleotide sequence encoding an MW-opsin and/or an LW-opsin polypeptide and/or an SW-opsin polypeptide; and ii) a nucleotide sequence encoding a variant AAV capsid protein, where the variant AAV capsid protein confers infectivity of a retinal cell and/or increased ability to cross the inner limiting membrane (ILM) in the eye, compared to a parental wild-type AAV. See, e.g., Day et al. (2014) Adv. Exp. Med. Biol. 801:687; Boye et al. (2016) J. Virol. 90:4215; Vandenberghe and Auricchio (2012) Gene Therapy 19:162; Klimczak et al. (2009) PLoS One 4:e7467; U.S. Patent Publication No. 2012/0164106; and U.S. Patent Publication No. 2016/0017295.

For example, a variant AAV capsid protein can comprise an amino acid substitution at amino acid 451 of an AAV6 capsid, or the corresponding position in another AAV serotype. In some cases, the amino acid substitution at amino acid 451 of an AAV6 capsid, or the corresponding position in another AAV serotype, is an asparagine to aspartic acid substitution. As another example, a variant AAV capsid protein can comprise an amino acid substitution at amino acid 532 of an AAV6 capsid, or the corresponding position in another AAV serotype. In some cases, the amino acid substitution at amino acid 532 of an AAV6 capsid, or the corresponding position in another AAV serotype, is an aspartic acid to asparagine substitution.

The AAV6 capsid can have the following amino acid sequence:

(SEQ ID NO: 10) MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLP GYKYLGPFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHA DAEFQERLQEDTSFGGNLGRAVFQAKKRVLEPFGLVEEGAKTAPGKKR PVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSESVPDPQPLGEPP ATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVI TTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRF HCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANN LTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNG SQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLD RLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLP GPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHK DDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATER FGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPH TDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFIT QYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGL YTEPRPIGTRYLTRPL, where Asn-451 and Asp-532 are bolded and underlined.

In some cases, the AAV capsid protein comprises the following amino acid sequence:

(SEQ ID NO: 11) MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLP GYKYLGPFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHA DAEFQERLQEDTSFGGNLGRAVFQAKKRVLEPFGLVEEGAKTAPGKKR PVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSESVPDPQPLGEPP ATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVI TTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRF HCHFSPRDWQRLINNNWGFRPKRLNFKLFNVQVKEVTTNDGVTTIANN LTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNG SQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLD RLMNPLIDQYLYYLNRTQDQSGSAQNKDLLFSRGSPAGMSVQPKNWLP GPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHK DDKNKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATER FGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPH TDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFIT QYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGL YTEPRPIGTRYLTRPL.

The present disclosure provides a method of delivering an MW-opsin and/or an LW-opsin and/or an SW-opsin to a retinal cell, the method comprising administering a recombinant viral vector of the present disclosure (or a viral particle comprising the recombinant viral vector) to the eye of an individual. Following administration of the recombinant viral vector (or viral particle comprising the recombinant viral vector), the MW-opsin is produced in the retinal cell.

The present disclosure provides a method of enhancing or restoring visual function in an individual, the method comprising administering a recombinant viral vector of the present disclosure (or a viral particle comprising the recombinant viral vector) to the eye of an individual. Following administration of the recombinant viral vector (or viral particle comprising the recombinant viral vector), the MW-opsin and/or an LW-opsin and/or an SW-opsin is produced in the retinal cell. Production of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for enhanced or restored visual function in the individual.

The present disclosure provides a pharmaceutical composition comprising: a) a recombinant viral vector of the present disclosure, or a viral particle comprising the recombinant viral vector; and b) a pharmaceutically acceptable excipient. Suitable pharmaceutically acceptable excipients are described above.

The present disclosure provides a method of delivering an MW-opsin and/or an LW-opsin and/or an SW-opsin to a retinal cell, the method comprising administering a pharmaceutical composition comprising a recombinant viral vector (or a viral particle comprising the recombinant viral vector) to the eye of an individual. Following administration of the recombinant viral vector (or viral particle comprising the recombinant viral vector), the MW-opsin and/or an LW-opsin and/or an SW-opsin is produced in the retinal cell.

The present disclosure provides a method of enhancing or restoring visual function in an individual, the method comprising administering a pharmaceutical composition comprising a recombinant viral vector of the present disclosure (or a viral particle comprising the recombinant viral vector) to the eye of an individual. Following administration of the recombinant viral vector (or viral particle comprising the recombinant viral vector), the MW-opsin and/or an LW-opsin and/or an SW-opsin is produced in the retinal cell. Production of the MW-opsin and/or an LW-opsin and/or an SW-opsin in the retinal cell provides for enhanced or restored visual function in the individual.

A recombinant expression vector of the present disclosure (or a viral particle comprising the recombinant viral vector) can be administered to an individual in need thereof by any of a variety of routes of administration. Suitable routes of administration include, e.g., periocular, intraocular, intravitreal, subconjunctive, retrobulbar, into the sclera, and intercameral. In some cases, recombinant expression vector of the present disclosure (or a viral particle comprising the recombinant viral vector) is delivered by intravitreal injection. In some cases, a recombinant expression vector of the present disclosure (or a viral particle comprising the recombinant viral vector) is delivered intraocularly. In some cases, recombinant expression vector of the present disclosure (or a viral particle comprising the recombinant viral vector) is delivered via sub-retinal injection.

Individuals suitable for treatment with a method of the present disclosure include individuals having reduced visual function due to loss of rod and cone photoreceptors. In some cases, the individual has an inherited retinal degenerative disease. In some cases, the individual has an ocular disease selected from retinitis pigmentosa, macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy. In some cases, the individual has an age-related retinal degenerative disease. In some cases, the individual has age-related macular degeneration.

Examples of Non-Limiting Aspects of the Disclosure

Aspects, including embodiments, of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting aspects of the disclosure numbered 1-54 are provided below. As will be apparent to those of skill in the art upon reading this disclosure, each of the individually numbered aspects may be used or combined with any of the preceding or following individually numbered aspects. This is intended to provide support for all such combinations of aspects and is not limited to combinations of aspects explicitly provided below:

Aspect 1. A method of restoring or enhancing visual function in an individual, the method comprising administering to the individual a nucleic acid comprising a nucleotide sequence encoding a medium wavelength opsin (MW-opsin) and/or a long wavelength opsin (LW-opsin) and/or a short wavelength opsin (SW-opsin), wherein said administering provides for expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in a retinal cell in the individual and restoration or enhancement of visual function.

Aspect 2. The method of aspect 1, wherein the MW-opsin comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1; wherein the LW-opsin comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4, and wherein the SW-opsin comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

Aspect 3. The method of aspect 1, wherein the SW-opsin comprises an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the human SW-opsin amino acid sequence set forth in SEQ ID NO:5 or having at least 87% amino acid sequence identity to the mouse SW-opsin amino acid sequence set forth in SEQ ID NO:6.

Aspect 4. The method of aspect 1, comprising administering to the individual: i) a first nucleic acid comprising a nucleotide sequence encoding an SW-opsin comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the human SW-opsin amino acid sequence set forth in SEQ ID NO:5; and ii) a second nucleic acid comprising a nucleotide sequence encoding an SW-opsin comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the mouse SW-opsin amino acid sequence set forth in SEQ ID NO:6.

Aspect 5. The method of aspect 1, wherein the SW-opsin is a chimeric SW-opsin comprising mouse SW-opsin intracellular domains and human SW-opsin transmembrane domains.

Aspect 6. The method of aspect 5, wherein the chimeric SW-opsin comprises an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the chimeric SW-opsin amino acid sequence set forth in SEQ ID NO:7.

Aspect 7. The method of any one of aspects 1-6, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for patterned vision and image recognition by the individual.

Aspect 8. The method of aspect 7, wherein the image recognition is of a static image or a pattern.

Aspect 9. The method of aspect 7, wherein the image recognition is of a moving image or a pattern.

Aspect 10. The method of any one of aspects 1-9, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for image recognition at a light intensity of from about 10−4 W/cm2 to about 1 W/cm2.

Aspect 11. The method of any one of aspects 1-9, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for image recognition at a light intensity that is at least 10-fold lower than the light intensity required to provide for image recognition by an individual expressing a channelrhodopsin polypeptide in a retinal cell.

Aspect 12. The method of any one of aspects 1-9, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for kinetics that are at least 2-fold faster than the kinetics conferred on a retinal cell by a rhodopsin polypeptide.

Aspect 13. The method of any one of aspects 1-12, wherein the nucleic acid is a recombinant expression vector.

Aspect 14. The method of aspect 13, wherein the recombinant expression vector is a recombinant viral vector.

Aspect 15. The method of aspect 14, wherein the recombinant viral vector is an adeno-associated viral vector, a lentiviral vector, a herpes simplex virus vector, or a retroviral vector.

Aspect 16. The method of any one of aspects 1-15, wherein the nucleotide sequence is operably linked to a transcriptional control element that is functional in a retinal cell.

Aspect 17. The method of aspect 16, wherein the transcriptional control element is a retinal cell-specific promoter.

Aspect 18. The method of aspect 17, wherein the promoter is a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, or an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

Aspect 19. The method of any one of aspects 1-18, wherein said administering is via intraocular injection.

Aspect 20. The method of any one of aspects 1-18, wherein said administering is via intravitreal injection.

Aspect 21. The method of any one of aspects 1-18, wherein said administering is via subretinal injection.

Aspect 22. The method of any one of aspects 1-21, wherein the individual has an ocular disease selected from retinitis pigmentosa, macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy.

Aspect 23. The method of any one of aspects 1-21, wherein the individual has experienced retinal detachment or photoreceptor loss due to trauma or head injury.

Aspect 24. The method of any one of aspects 1-23, wherein the nucleic acid is complexed with a nanoparticle.

Aspect 25. A recombinant viral vector comprising a nucleotide sequence encoding a medium wavelength opsin (MW-opsin) and/or a long wavelength opsin (LW-opsin) and/or a short wavelength opsin (SW-opsin).

Aspect 26. The recombinant viral vector of aspect 25, wherein the viral vector is an adenoassociated viral vector.

Aspect 27. The recombinant viral vector of aspect 25 or aspect 26, wherein the MW-opsin comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1; wherein the LW-opsin comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4, and wherein the SW-opsin comprises an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in one of SEQ ID NOs:5-7.

Aspect 28. The recombinant viral vector of any one of aspects 25-27, wherein the nucleotide sequence is operably linked to a promoter.

Aspect 29. The recombinant viral vector of aspect 28, wherein the promoter is a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, or an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

Aspect 30. The recombinant viral vector of any one of aspects 25-29, wherein the recombinant viral vector is a recombinant AAV vector, wherein the recombinant AAV vector comprises a nucleotide sequence encoding a variant capsid polypeptide that confers increased infectivity of a retinal cell and/or confers increased ability to cross the inner limiting membrane, compared to a wild-type AAV capsid.

Aspect 31. A pharmaceutical composition comprising:

a) the recombinant viral vector of any one of aspects 25-30; and

b) a pharmaceutically acceptable excipient.

Aspect 32. A method of restoring or enhancing visual function in an individual, the method comprising administering to the individual the recombinant viral vector of any one of aspects 25-30, or the pharmaceutical composition of aspect 31, wherein said administering provides for expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in a retinal cell in the individual and restoration or enhancement of visual function.

Aspect 33. A chimeric SW-opsin comprising intracellular portions of a mouse SW-opsin comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:6, and comprising transmembrane portions of a human SW-opsin comprising an amino acid sequence having at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

Aspect 34. The chimeric SW-opsin of aspect 33, comprising an amino acid sequence having at least 90% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:7.

Aspect 35. A recombinant expression vector comprising a nucleotide sequence encoding the chimeric SW-opsin of aspect 33 or aspect 34.

Aspect 36. A composition comprising:

a) the recombinant expression vector of aspect 35; and

b) a pharmaceutically acceptable excipient.

Aspect 37. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between an image comprising a vertical line and an image comprising a horizontal line in a spatial pattern discrimination assay.

Aspect 38. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between an image comprising a static line and an image comprising a moving line in a spatial pattern discrimination assay.

Aspect 39. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between flashing light and constant light in a temporal light pattern assay.

Aspect 40. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can recognize an image at a light intensity of from about 10−4 W/cm2 to about 10 W/cm2 in an image recognition assay.

Aspect 41. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between an area with white light and an area without white light in a light avoidance assay.

Aspect 42. The composition of any one of aspects 37-41, wherein the one or more cone opsins is selected from the group consisting of: a) an MW-opsin comprising an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1; b) an LW-opsin comprising an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4; c) an SW-opsin comprising an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5; and d) a chimeric SW-opsin comprising: i) intracellular portions of a mouse SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:6; and ii) transmembrane portions of a human SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

Aspect 43. The composition of any one of aspects 37-41, wherein the one or more recombinant nucleic acid vectors comprise one or more nucleotide sequences encoding 2 different cone opsins.

Aspect 44. The composition of any one of aspects 37-41, wherein the one or more recombinant nucleic acid vectors comprise one or more nucleotide sequences encoding 3 different cone opsins.

Aspect 45. The composition of any one of aspects 37-44, wherein the one or more recombinant nucleic acid vectors are an adeno-associated viral vector, a lentiviral vector, a herpes simplex virus vector, or a retroviral vector.

Aspect 46. The composition of any one of aspects 37-44, wherein the one or more recombinant nucleic acid vectors are recombinant adeno-associated virus vectors.

Aspect 47. The composition of aspect 46, wherein the recombinant AAV vector comprises a nucleotide sequence encoding a variant capsid polypeptide that confers increased infectivity of a retinal cell and/or confers increased ability to cross the inner limiting membrane, compared to a wild-type AAV capsid.

Aspect 48. The composition of any one of aspects 37-47, wherein the one or more nucleotide sequences are operably linked to a promoter.

Aspect 49. The composition of aspect 48, wherein the promoter is a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, or an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

Aspect 50. The composition of any one of aspects 37-49, wherein the subject has an ocular disease selected from retinitis pigmentosa, macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy.

Aspect 51. The composition of any one of aspects 37-49, wherein the subject has experienced retinal detachment or photoreceptor loss due to trauma or head injury.

Aspect 52. The composition of any one of aspects 37-51, wherein the composition comprises a pharmaceutically acceptable excipient.

Aspect 53. The composition of aspect 52, wherein the pharmaceutically acceptable excipient comprises saline.

Aspect 54. The composition of any one of aspects 37-53, wherein the composition is sterile.

EXAMPLES

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like.

Example 1: Effect of Expression of MW-Opsin in Retinal Cells In Vitro and In Vivo

Inherited and age-related retinal degenerative diseases cause progressive loss of rod and cone photoreceptors, leading to complete blindness. Despite loss of the light-sensing cells required for vision, downstream neurons of the inner retina survive in a functional state, providing a target for optogenetic therapy. To date, optogenetic approaches have encountered two major limitations: very low light sensitivity in microbial opsins and very slow kinetics in retinal opsins. The data presented below show that the vertebrate medium wavelength cone opsin (MW-opsin) overcomes these limitations and supports patterned vision under low light. Expression of MW-opsin in retinal ganglion cells (RGCs) of blind rd1 mice introduces an ON transient light response that is highly sensitive to light with fast kinetics. MW-opsin restores photo-avoidance with similar light sensitivity to that seen in wildtype animals, three orders of magnitude below level required for microbial opsins, and on par with rhodopsin. MW-opsin enables rd1 animals to discriminate both between different temporal light patterns and between different spatial light patterns, even when the spatial patterns are in motion. In contrast, rd1 animals with rhodopsin in RGCs are incapable of both temporal and spatial discrimination. Strikingly, the MW-opsin light response adapts to ambient light over an ˜1,000-fold range. Thus, MW-opsin combines speed, sensitivity and adaptation to restore adjustable patterned vision under realistic light intensities. LW-opsin and SW-opsin also support vision discrimination between static visual patterns, suggesting that the cone opsins can individually restore natural monochromatic vision and that, in combination, they may restore color vision.

Materials and Methods Animals and AAVs

Mouse experiments were conducted under the express approval of the University of California Animal Care and Use Committee. wt mice (C57BL/6J) and rd1 mice (C3H) were purchased from the Jackson Laboratory and housed on a 12-h light/dark cycle with food and water ad libitum. cDNA encoding vertebrate medium wave cone opsin or rhodopsin was linked with yellow florescent protein (YFP) gene on the c-terminus and inserted in an established viral cassette under control of the human synapsin promoter (hsyn-1). Gene and promoter was flanked by inverted terminal repeat domains, stabilized by a polyadenylation signal sequence (polyA) with a woodchuck hepatitis post-transcriptional regulatory element (WPRE) and packaged in the AAV 2/2-4YF capsid. The titer of AAVs was determined via qPCR relative to inverted repeat domains standard and reported to contain 1010-1012 viral genomes. AAVs were produced as previously described15. Vector was delivered in a 2 μl volume to the vitreous of the rd1 mouse eye via microinjection using a blunt 32-gauge Hamilton syringe though an incision made posterior of the ora serrata using a sharp 30-gauge needle. rAAV injections were at p30-p60 and in vivo and in vitro experiments at p90-p160. Mice were anesthetized with IP ketamine (72 mg/kg) and xylazine (64 mg/kg). Eyes were anesthetized with proparacaine (0.5%) and pupils were dilated with phenylephrine (2.5%) and tropicamide (1%).

Electrophysiology and Light Stimulation

HEK cell recordings were performed as previously described15,51,52 Briefly, cells were clamped in whole cell mode in a high external potassium solution (50 mM), and held at VH=−80 mV, to provide an inward driving force for potassium. 5-10 s pulses of light were given at low intensity (1 mW cm−2) at 535 nm (for MW-opsin) or 500 nm (for rhodopsin).

MEA recordings were performed on wt (C57BL/6J) mice, and untreated and treated rd1 mice at >p90 6-10 wks following AAV injection experimental retina were excised from the eye under dim red light, mounted on 4 μm cell membranes and placed in an incubator (35° C.) for 30 min and perfused with exogenous chromophore 9-cis retinal. Retinal tissue was placed ganglion cell side down53 in the recording chamber (pMEA 100/30iR-Tpr; Multi Channel Systems) of a 60-channel MEA system with a constant perfusion of Ames recording media (32° C.). A Multi Channel Systems harp weight (Scientific Instruments—Slice grids) was placed on the retina to prevent movement and vacuum was applied to the retina using a pump (perforated MEA1060 system with CVP; Multi Channel Systems), improving electrode-to-tissue contact and to provide consistent signal-to-noise ratios across retinas. Additionally, a dry crystal of exogenous chromophore 9-cis retinal was dissolved in μl 100% ethanol under dark conditions. Dissolved retinal was then added to 100 μl matrigel on ice and added to the top of the harp, just above the retina, in order to supply a continues supply of chromophore. Additionally, 9-cis retinal was dissolved in the recording solution and perfused consistently into the recording chamber. Further detail regarding MEA methods are previously detailed in Gaub. et al. (2015)15. Illumination in vitro was by a 300-W mercury arc lamp (DG-4; Sutter Instruments) with a 535/50 nm bandpass filter for MW-opsin or a 510/89 nm bandpass filter for Rhodopsin. Light intensity was controlled by modifying the light source duty cycle or by using neutral density filters and ranged from 0.038 μW cm−2 to 38.2 mW/cm2. Relative comparisons with natural light intensities were obtained in various environments using direct light measurement with a power meter (Thorlabs). Spectral component of white light measured using a CCD Spectrometer with Fourier Transform Optical Spectrum Analyzer software (Thorlabs).

MEA Data Acquisition & Analysis

Retinal activity on the MEA was sampled at 25 kHz filtered between 100 and 2,000 Hz and recorded using MC_rack software (Multi Channel Systems). Voltage traces were converted to spike trains offline and the spikes recorded at each electrode were sorted into single units, which are defined as “cells,” via principal component analysis using Offline Sorter (Plexon-64 bit) with each electrode commonly identifying 1-3 cells. Single-unit spike clusters were exported to MATLAB (MathWorks) and were analyzed and graphed with custom software. All firing rates were extracted from traces averaged over 3-10 light response cycles unless otherwise specified, details of which are denoted in figure legends. Responses across cells and across retina were normalized using the Light Response Index (LRI) adopted from Tochitsky, I., et al. (2014)37 and Gaub et al. (2014)47 (LRI=(peak firing rate in the light−average firing rate in dark)/peak firing rate in the light+average firing rate in dark). Under experiments where conditions were changed within retina (light sensitivity, light and dark adaption sensitivity, and dependence of response on flash duration) the responses were normalized to the peak of the greatest response from baseline and channels were tracked across all recording parameters. All curve fitting and kinetic analysis was performed in Clampfit 10.6 (Molecular Devices). Cells were defined as “responders” if the LRI satisfied the condition LRI >0.1 or LRI <−0.1. The width of response at half maximum of peak from baseline was determined with custom MATLAB (MathWorks) analysis software, which interpolated the traces of individual cells and applied smoothing before identifying FWHM. Intensity-response relations were fit with a single Boltzmann and normalized to the fit between 0 and 1.

Comparing Light Sensitivity of Optogenetic Probes

The natural sensitivity of human vision covers a wide range, from scotopic (dim 10−4-1011 photons cm−2 s−1) to photopic (bright 1010-1017 photons cm−2 s−1), allowing perception under dynamic lighting conditions. To relate the sensitivity of MW-opsin to that of other optogenetic systems and of normal vision, experiments were performed that measured natural light intensities under various outdoor and indoor conditions using a portable power meter (Thorlabs), compared them to experimental paradigms and to light sensitivity thresholds (lowest measurable light responses) reported in the literature using monochromatic wavelengths of light at or near peak functional maxima in retinal explants isolated from rd1 mice to which the optogenetic probe was delivered via AAV transfection (FIG. 7).

Electrophysiology and Light Stimulation for In Vivo Brain Recordings

In vivo recordings were performed as previously described by Veit et. al. (2017)58. Mice were anesthetized with isoflurane (2.5% vapor concentration). The scalp was removed, the fascia retracted, and the skull lightly etched with a 27 gauge needle. Following application of Vetbond to the skull surface, a custom stainless steel headplate was fixed to the skull with dental cement (Metabond). Mice were allowed to recover from surgery for at least 2 days. Then mice were habituated for 2-5 days to head-fixation on a free-spinning circular treadmill. On the day of recording, mice were briefly anesthetized with isoflurane (2%), the skull over V1 was thinned, and a small (<250 μm) craniotomy was opened over the primary visual cortex with a fine needle. A 16-channel linear electrode array with 25 micron spacing (NeuroNexus, A1x16-5 mm-25-177-A16) was guided into the brain using a micromanipulator (Sensapex) and a stereomicroscope (Leica). Electrical activity was amplified and digitized at 30 kHz (Spike Gadgets), and stored on a computer hard drive. The cortical depth of each electrical contact was determined by zeroing the bottom contact to the surface of the brain. The electrode was inserted close to perpendicular to the brain surface.

Visual stimuli were generated with Psychophysics Toolbox59 running on an Apple Mac Mini and were presented on a gamma corrected 23-inch Eizo FORIS FS2333 LCD display with a 60-Hz refresh rate. The monitor was centered 15 cm from the right eye of the mouse covering roughly 108 by 61 degrees of visual angle. Mice were dark adapted for 7-10 minutes before every block of recordings. Two different stimulation paradigms were used: 1) Contrast: Mice were presented with 500 ms full screen flashes at 0.5 Hz of four different luminance levels (15, 25, 50 and 100% of maximal luminance) that were repeated 10 times in different random orders. 2) Flicker: Mice were presented with 20 500 ms full screen flashes (maximum luminance 116 μW cm−2) at 0.0167 Hz (one per minute) or 100 flashes at 0.5, 1, 2 and 4 Hz in separate blocks.

In Vivo Cortical Recording Data, Acquisition and Analysis

Spiking activity was extracted by filtering the raw signal between 800 and 7000 Hz. Spike detection was performed using the UltraMega Sort package60. Detected spike waveforms were sorted using the MClust package (http://redishlab.neuroscience.umn.edu/MClust/MClust.html). Waveforms were first clustered automatically using KlustaKwik and then manually corrected to meet criteria for further analysis. Units with more than 2% of their individual waveforms violating a refractory period of 2 ms were classified as multi-units. The depth of each unit was assigned based on the calculated depth of the electrode on the array that exhibited its largest amplitude sorted waveform. Firing rates were computed by counting spikes in a two second window starting 250 ms after the onset of the visual stimulus for FIG. 20b and in a 5 s window starting directly after stimulus onset for FIG. 21c. Traces for Peri-stimulus time histograms (PSTH)s were generated by binning the spiking response into either 20 ms (FIG. 19) 50 ms (FIG. 20) or 25 ms (FIG. 21) bins and smoothing the resulting traces with a moving average filter. For FIG. 21, modulation amplitude was calculated on trial averaged spiking responses binned at 25 ms in a 2, 1, 0.5 or 0.25s window for 0.5, 1, 2 and 4 Hz flicker respectively. Corresponding baseline modulation amplitudes were generated from trial averaging the same number of same-length windows from before the onset of the first visual stimulus (during the dark adaptation period). Local field potentials were extracted by low pass filtering the raw signal, sampled at 30 kHz, below 200 Hz and subsequent down-sampling to 1 kHz.

Statistics

To assess statistical significance of MEA recordings, nonparametric two-tailed Mann-Whitney U tests where applied. For learned dark avoidance behavior and the learned pattern discrimination behaviors significance was determined in two ways. (1) Significance for behavioral performance was calculated using two-tailed unpaired student's t-tests with Bonferroni correction when applicable. Significance was also determined by computing the proportion of successful performances (2). A success was defined as greater than the sum of the control group average and one S.D, and a failure was any value that did not achieve this criteria. Success ratios were then calculated for each condition. To determine significance in differences between conditions a pairwise contingency table was then constructed, and a Two-Sided Pearson's Chi-Square Test was initially conducted. To correct for conditions with a small n, a One-Sided Fisher's Exact Test was also conducted. FIG. 11 (Table 1).

Tissue Preparation and Immunohistochemistry

Mice >4-6 wks post-AAV2/2-hsyn-MW-coneopsin-YFP treatment were sacrificed, eyes were fixed in 4% paraformaldehyde (Ted Pella) (30 min), retinas were removed and washed thoroughly using PBS and flat mounted on slides using Vectashield (Vector Laboratories) medium impregnated with DAPI (cell nuclei stain—blue). For retinal sections, whole mounts were embedded in agarose (Sigma) and sectioned transverse using a vibratome (Leica Microsystems) at medium speed, maximum vibration, and 180-μm thickness. Retinal tissues used for immunohistochemistry on retinal cryosections or whole mounts were processed and examined by confocal microscopy (Leica TCS SP5; Leica Microsystems).

Passive Avoidance—Open Field Test

The open field test was performed as described previously16,47. Briefly, a two-compartment (light & dark) shuttle box (Colbourn Instruments) allows the mouse to move freely through a small opening that connects the two compartments. The light compartment was illuminated by a LCD panel over the compartment. White light as well as wavelengths of 535 nm and 460 nm were used at light intensity of ˜100 μW cm−2 (white light) & 0.5-25 μW cm−2 (blue and green light) was homogeneously distributed throughout the floor. Day 1—mice were transferred into the testing box, and allowed to habituate to the new environment with their littermates for 45 min. Mice were then retuned in to their home cage and then tested individually. Day 2—Mice were placed in the light compartment and were given a maximum of 3 min to discover that there is a second compartment. A 15-min trial began when they crossed into the dark compartment, and time spent in the light was recorded. Mice that crossed the opening only once and stayed in the dark compartment for entire time were disqualified. For adaptation experiments mice were pre-exposed to 1 hr of white light (1 mW cm−2) or dark exposure conditions then immediately performed the open field test Animals movements were tracked using IR sensors on the shuttle box. Time spent on either side was collected and analyzed using the Graphic State, and Graphic State RT programs (Colbourn Instruments).

Visually Cued Fear-Conditioning Paradigm

Fear conditioning experiments were performed using Colbourn shock chambers-Colbourn Habitest chamber with test cage (Coulbourn Instruments, PA) with an LED screen mounted to the ceiling. On day 1—animals were brought into the testing room in their home cages and then individually acclimated to clean Colbourn shock chambers for 30 minutes. On day 2-3 animals were subjected to paired or unpaired light cued fear conditioning, consisting of 5 minutes habituation to the chamber (dark) followed by three shock trials at 0.7 mA over a span of 15 min. For paired trials, the transition from either static or flashing (2 Hz) on the LCD coincided with a brief foot shock at a 2 seconds intershock-interval (for 10 sec). For unpaired trials, animals also received shocks but were independent of the stimulus transition. These brief, low current shocks provided the minimal aversive stimuli to create a fearful memory associated with patterned light. On day 4 the flooring of box was replaced with plastic instead of shock grating. Mice were habituated to the chamber for 5 minutes and subjected to the same light stimulation protocol as on day 2 & 3 but without shock. Freezing behavior in anticipation of the shock was recorded by Colbourn's FreezeFrame software and normalized to movement behavior gathered before the stimulation. The performance was then compared between paired and unpaired cohorts in order to determine if a fear response was conditioned to the stimulus transition.

Modified Active Avoidance Protocol

Avoidance protocols were done using Colbourn shuttle box (H10-11M-SC) Colbourn Habitest Isolation Cubicle (H10-24), and the Graphic State and Graphic State RT software (Colbourn Instruments, PA). On Day 1—animals were acclimated to darkened procedure room for 30 minutes in their home cages, followed by individual acclimation to darkened shuttle box until animals were non-fearful and spending approximately equal amounts of time on each side of shuttle box (exploratory behavior). On day 2-3 iPad screens were mounted in shuttle cage wall and displayed two distinct images of equal shape, size, light intensity. Each run began when the animal moved to the other side of shuttle box from where it was placed. Each run was 15 minutes long. The aversive image side was paired with a foot shock of 0.7 mA at intervals of 5 seconds until the animal returned to the “safe” side. Any animal remaining on the aversive side for more than 60 seconds was removed from cage and that run was discarded. On Day 4 the light patterns were reversed (so the aversive screen is on what was formerly the “safe” side) to avoid a bias for location rather than pattern. Additionally, the flooring of the cage is replaced with plastic instead of shock grating. This ensures that the only related association with training day is the light stimuli. Again, animals were run for 15 minutes and time spent on each side was recorded. For light adaptation experiments, the same protocol was followed except that on day 4, the recall phase was preceded with either a light (65 W white bulb) or dark adaptation phase for one hour. iPad screens were dimmed or brightened to test adaptation to the different light intensities. Visual discrimination optical angle calculations were performed using the parameters of the behavioral shuttle cage (15.24×36 cm), the distance from the decision point (divider), the central position of the LCD panel (18.85 cm), and the parameters of the stimulus pattern (1-6 cm distance between the parallel lines) using the optical (physical) angle equation. Visual angle=V=2 tan−1((D/2)/(L))=18 degrees=0.33-0.49 radians. Cycles per degree=1/V˜0.056 cpd. This is ˜9-fold lower than performance in visually intact wt mice (˜0.3-0.5 cpd) reported in other studies39,54,55,56.

For exploratory behavior analysis, two objects were placed in a 50 cm×50 cm open field box Animals were positioned in the empty box and allowed to explore freely over the course of 10 minutes. The following day, two novel objects were placed in the box and animals were again positioned along the wall of the box and allowed to explore freely for 10 minutes while the arena was filmed continuously. Using Noldus Technology Ethosvision XT v13.5, videos were analyzed for the latency to arrive at and explore each object, the velocity of travel (cm/s) and distance travelled (cm).

Results Characterization of MW-Opsin in HEK293 Cells

Recent studies have established that vertebrate rhodopsin, found in rod outer segments, may be used ectopically to control Gi/o signaling in cultured cells, under low light intensities25, but runs down with repeated stimulation and has slow deactivation24,26. The slow kinetics are also seen when rhodopsin is expressed in ON-bipolar cells of the blind retina14,15, raising concern that it may not support vision of natural scenes because of movement of the observer and surrounding objects. The question was asked whether another vertebrate opsin would have the high sensitivity of rhodopsin, but faster kinetics. Melanopsin and extra-retinal opsins have each been measured outside of photoreceptor cells, in a variety of cell types, including in non-photoreceptor cells of the retina, and all found to be as slow or slower than rhodopsin14-16,27-29. Opsins from mammalian cone photoreceptor cells were chosen because these deactivate more rapidly in cones than does rhodopsin in rods30. Among the cone opsins, MW-opsin, which operates in the center of the visible spectrum, was chosen. Either MW-opsin or rhodopsin was expressed in HEK293T cells with GIRK1(F137S), a version of the G protein-coupled inward-rectifier potassium channel that forms a homotetramer, which is activated by Gβγ following activation of a Gαi coupled receptor31 (FIG. 1). In the presence of 9-cis-retinal (a functionally stable analog of the natural chromophore 11-cis-retinal), both MW-opsin and rhodopsin expressing cells displayed large inward photocurrents at negative holding potentials in high external potassium, which were triggered by low intensity (1 mW cm−2) flashes of light at 535 nm (for MW-opsin) or 500 nm (for rhodopsin) (FIG. 1 a,b). Following illumination, the current elicited by MW-opsin decayed ˜8× more rapidly than that elicited by rhodopsin, and recovered more completely, providing reproducible responses over repeated bouts of illumination (FIG. 1a,c), as shown earlier in heterologous cells for the short and long wave cone opsins24. This suggested that higher speed may be intrinsic to MW-opsin signaling, rather than a specialization of cones. MW-opsin was then tested in non-photoreceptor retinal neurons.

FIGS. 1a-1c. MW-opsin and rhodopsin activation of GIRK channels in HEK293 cells. (a,b) Representative traces of activation of homotetramer GIRK(F137S) channels by photo-stimulation of rhodopsin (a) or MW-opsin (b) measured in whole cell patch in 50 mM [K+]ext at VH=−80 mV in response to low intensity (1 mW cm−2) pulses of light at 535 nm (for MW-opsin) or 500 nm (for rhodopsin). (c) Decay of photo-response (Tau OFF) for Rhodopsin (blue) and MW-opsin (green). Values are mean±SEM; n=6 (Rho), 8 (MW-opsin) cells.

MW-Opsin Restores Fast and Sensitive Light Responses to Blind Retina

MW-opsin was tested in the retina of the rd1 mouse, which has a mutation in the PDE-6-β gene, resulting in progressive loss of rod and cone photoreceptor cells. MW-opsin under control of the human synapsin promoter (hSyn-1), with a yellow fluorescent (YFP)C-terminal tag for tracking expression, was packaged in AAV2/2(4YF) and injected intravitreally at postnatal day 45 (FIG. 2a,b). Retinas were isolated 4-8 weeks weeks later. Expression was found to be pan-retinal with a transfection rate of 45%±19% (SD), restricted to the RGC layer, and localized to the soma and dendrites of both ON- and OFF-RGCs (FIG. 2c,d and 14), a well-defined expression profile consistent with previously shown targeting32 and similar to expression of rhodopsin under identical parameters (FIG. 15). Retinas were mounted on a multi-electrode array (MEA), with the RGC layer in contact with the electrodes, to test for light-evoked activity. Due to complete photoreceptor degeneration in animals ≥3 months old33, no light-evoked response was detected in the retina of control rd1 littermates (FIG. 2e), with the exception of a few RGCs which displayed slow responses characteristic of intrinsically photosensitive RGCs57. In contrast, retinas from animals injected with the MW-opsin encoding AAV displayed robust light-evoked increases in action potential firing, consisting of a large fast, transient component and a small (˜30% in size) slow component (FIGS. 2f, g, 3a, 16, and 17). The light responses ran down with repeated bouts of light stimulation, as expected following removal of the retinal pigment epithelium, a source of 11-cis. The run down was reduced by the addition of 9-cis-retinal (a stable analog of 11-cis retinal) to the recording solution (FIG. 2g).

FIGS. 2a-2g. Expression and function of MW-opsin in RGCs of rd1 mouse retina. (a) Viral DNA expression cassette. MW-opsin with YFP (green) under control of hSyn-1 promoter, flanked by inverted terminal repeat (ITR) domains, stabilized by a polyadenylation signal sequence (polyA) and a woodchuck hepatitis posttranscriptional regulatory element (WPRE). (b) Schematic of a degenerated rd1 mouse retina with targeted RGCs highlighted (green). ONL: outer nuclear layer. IPL: inner plexiform layer. Photoreceptor degeneration denoted in light gray. (c,d) En face view of flat mount (c) and transverse slice (d) confocal images of MW-opsin expression of rd1 mouse retina 4 wks after intravitreal injection of AAV2/2-hSyn-MW-opsin-YFP. Images of YFP fused to C terminal end of MW-opsin (green) show pan-retinal distribution (c) in RGC layer in relation to DAPI staining of nuclei (d, blue). Scales 60 μm (c) and 20 μm (d). (e,f) MEA recordings from uninjected control (e) and MW-opsin expressing (f) rd1 mouse retinas. (Top) Raster plot with spikes for each RGC (e: n=75 cells; g: n=84 units). (Bottom) Peristimulus time histogram (PSTH). Light stimulation protocol: 4 pulses of light of 1 s duration (λ=535 nm, green bars) separated by 30 s dark intervals. (g) Normalized Light response Index (LRI) for rd1 retina without (gray) and with MW-opsin expression (green) (gray: N=3 retinas, n=190 cells; green: N=6 retinas, n=273 cells). LRI for 1st and 5th light flash without (light green; N=3 retinas, n=106 cells) and with (dark green; N=3 retinas, n=167 cells) 9-cis retinal. Light intensity 3.38 mW cm−2. Wavelength: =535 nm (MW-O), Values are mean±SEM. All cells refer to sorted units. Statistical significance assessed using Mann-Whitney U test (*p≤0.001).

FIGS. 14a-14b. MW-opsin expresses in rd1 mouse retina. Flat mount (a) and slice (b) confocal images of MW-opsin-YFP in RGCs of rd1 mouse retina 4-6 wks after intravitreal injection of AA V2/2-hSyn-MW-opsin-YFP. YFP fluorescence (green) and DAPI stain of nuclei (blue). INL=Inner nuclear layer, RGC=Retinal ganglion cell layer. Scale 40 μm (a) and 20 μm (b).

FIGS. 15a-15b. Rhodopsin expresses in rd1 mouse retina. Flat mount (a) and slice (b) confocal images of rhodopsin-YFP in RGCs of rd1 mouse retina 4-6 wks after intravitreal injection of AA V2/2-hSyn-rhodopsin-YFP. YFP fluorescence (green) and DAPI stain of nuclei (blue). INL=Inner nuclear layer, RGC=Retinal ganglion cell layer. Scale 40 μm (a) and 20 μm (b).

FIGS. 16a-16d. Transduction efficiency of MW-opsin in rd1 retina. (a) Average percent of channels identified in retina of rd1 mouse expressing MW-opsin that display light responsiveness in MEA recordings. Light responsiveness defined as Light Responsive Index (LRI) >0.1, parameters established in Tochitsky et al. (2014)37, Gaub. et al (2014)47 and Berry et al. (2017)62. (LRI=peak firing rate in light−average firing rate in dark/peak firing rate in light+average firing rate in dark). (b) Average normalized response across retinas). (a,b) N=8 rd1 retinas, N=5 wt retinas. (c) Average cross-correlation values in MW-opsin rd1 (n=370 cells, N=3 retinas) and in wildtype (n=237 cells, N=3 retinas). Cross-correlation of all light-sensitive units in a period 1 s before to 2 s after the light pulse. (d) Correlative value distributions for light sensitive units within the same retina for MW-opsin (n=370 cells, N=3 retinas) and wt retina (n=237 cells, N=3 retinas).

FIGS. 17a-17d. Characterization of slow component of light response in rd1 retina expressing MW-opsin. (a) Representative trace of average RGC population response for rd1 expressing MW-opsin (λ=510 nm; pulse duration 1 sec; 5 flashes averaged at 30 sec interval) shows fast transient component and slow component of the light response (SEM in gray). (b) Comparison of LRI of fast transient (green) and slow (steel-gray) components of light response and their ratio (black) fast/slow) (n=122 channels, N=3 retinas). (c) Kinetics of slow component: time to peak (T.—peak) and time-constant of decay (tau decay). (d) LRI of fast (green) and slow (steel-gray) components under dark (left) and light (right) adapted conditions.

One potential advantage of retinal opsins is their high sensitivity to light in their normal cellular environments. Rhodopsin and melanopsin remain very sensitive when expressed ectopically25, including in the retina as shown for rhodopsin in ON-BCs and RGCs and melanopsin in RGCs14-17. Consistent with this, MW-opsin in RGCs in the rd1 mouse retina was highly sensitive to light, to a degree that is indistinguishable from rhodopsin (FIG. 3b,c). This sensitivity is approximately 1000-fold higher than that of channelrhodopsin8,13 or halorhodopsin11,12 and within the range of normal indoor light intensities. FIG. 7. While similar in sensitivity to rhodopsin, MW-opsin had showed kinetics: ˜3.5-fold faster rise and ˜4-fold shorter time to peak at the start of the light pulse, and ˜7-fold faster decay after the end of the light pulse (FIG. 3d,e), resulting in an impulse response that was 270±21 ms in duration at half amplitude, ˜10-fold shorter than the 2.61±0.21 s duration at half-amplitude of the rhodopsin impulse response. Tau ON, time to peak, and tau OFF changed modestly with decreasing light intensities, maintaining the advantage in speed over rhodopsin (FIG. 8a-c)14,15. The rise and decay kinetics of the response in RGCs of rd1 retina expressing MW-opsin resembled those of the RGC transient ON-response seen in wt retina, except that the former had a longer latency (FIGS. 3e & 8d,e). The fast response kinetics and sensitivity of MW-opsin suggested that it would respond to brief flashes of light. Indeed, illumination pulses as short as 25 ms still triggered responses that reached ˜60% of the maximal peak response (FIG. 3f,g), similar to what is seen in wt retina34.

Contrast sensitivity in the excised retina and in primary visual cortex was examined in vivo by measuring responses to full-field gray scale steps. In the excised rd1 retina expressing MW-opsin, RGC activity changed in response to changes in brightness of as little as 25% (FIG. 18a,b), approaching but not equivalent to the contrast sensitivity of the wild type retina (FIG. 18c). In complementary in vivo experiments on rd1 animals expressing MW-opsin in RGCs, the experiments involved measuring single unit responses and visually evoked potentials across the layers of primary visual cortex in awake, free running animals (FIG. 19) and observing similar contrast sensitivity using a standard computer monitor (FIG. 20). The cortical responses followed flash frequencies up to at least 4 Hz (FIG. 21). The sensitivity and kinetics of the light responses imparted by MW-opsin in RGCs suggested that it may support visually-guided behavior.

FIGS. 3a-3g. Light response in isolated rd1 mouse retina with MW-Opsin in RGCs. (a) (Top) Average response to 1 sec light flash of RGC population expressing MW-opsin (green) or rhodopsin (blue) in RGCs of rd1 mouse retina. (Bottom) Raster plot of average response of rd1 mouse retina RGCs to 5 flashes of 1 s duration light at 535 nm for MW-opsin (n=88 cells) and 510 nm for rhodopsin (n=54 cells) expressing in RGCs. (b,c) Light sensitivity for MW-opsin (N=2 retinas, n=127 cells) and Rhodopsin (N=2 retinas, n=95 cells) in RGCs of rd1 mouse retina. Peak firing rate normalized to maximum at highest intensity. (d,e) Time-course of light response. Population average traces with time from light onset to max excitation (time to peak: 355±21 ms), exponential fits for excitatory phase (Tau ON: 112±25 ms) and decay (Tau OFF: 260±31 ms) and full width at half max (FWHM: 183±85 ms) (e) for MW-opsin (d; e, green; N=3 retinas, n=95 cells) and rhodopsin (e, blue; N=2 retinas, n=67 cells). (f,g) Dependence of MW-opsin light response on flash duration. (f) Representative retina light response (n=117 cells): population average firing rate (top) and raster plot of unit responses (bottom). (h) Normalized peak responses for different stimulation durations (N=2 retina, n=183 cells). Light intensity 3.82×10−1 mW cm−2 unless specified, Wavelength: λ=535 nm (MW-opsin) or 510 nm (rhodopsin). N=# of retina, n=# of cells/units. All cells refer to sorted units. Values are mean±SEM. Statistical significance assessed using Mann-Whitney U test (*p≤0.001).

FIG. 7. Threshold response of optogenetic systems in blind retinas compared to normal vision. Comparison of threshold sensitivity of natural vision (top) to that of various optogenetic systems introduced to a defined set of surviving neurons in a retina following degeneration of photoreceptor cells (bottom). Mammalian MW-opsin (green), rhodopsin (blue) and melanopsin (cyan) are ˜1000× more sensitive than microbial Channelrhodopsin2 and Halorodopsin. Threshold for alternative optogenetic approaches from Bi et al. (2006)8, Zhang et al (2009)12, Sengupta et al. (2016)13, Doroudchi et al. (2011)45, Gaub et al. (2014)47, Cronin et al (2014)65, Berry et al. (2017)66 De Silva et al. (2017)17. (8) Bi et al. (2006) Channelrhodopsin expressed with AAV2-CAG promoter stimulated at 460 nm in rd1 mouse with sensitivity limit in RGCs=2.2×1015 photons cm−2 s−1˜1 mW cm−2. (12) Zhang et al (2009) Halorhodopsin expressed with AAV2-CMV promoter stimulated at 555-575 nm band pass in rd1 mouse with a sensitivity limit in RGCs=5.8×1016 photons cm−2 s−1˜20 mW cm−2. (13) Sengupta et al. (2016) Red-shifted channelrhodopsin expressed with AAV2-hSyn promoter stimulated at 595 nm in rd1 mouse with a sensitivity limit in RGCs=2.5×1015 photons cm−2 s−1−1 mW cm−2. (45) Doroudchi et al. (2011) Channelrhodopsin expressed with AAV8-Y733F & SV-40 promoter stimulated at 450-490 nm band pass in rd10 mouse with a sensitivity limit in ON-BCs=4×1016 photons cm−2 s−1˜17 mW cm−2. (47) Gaub et al. (2014) LiGluR-MAG460 expressed with AAV2-hSyn and AAV2-4xGrm6 promoter stimulated at 445/20 nm in rd1 mouse with a sensitivity limit in RGCs & ON-BCs=7.1×1014 photons cm−2 s−1˜0.3 mW cm−2. (65) Cronin et al (2014) Channelrhodopsin expressed with AAV2/8BP2 & 4xGRM6 promoter stimulated in rd1 mouse with a sensitivity limit in ON-BCs=1×1016 photons cm−2 s−1˜5 mW cm−2. (66) Berry et al. (2017) SNAG-MGluR2 expressed with AAV2-hSyn promoter stimulated at 445/50 nm in rd1 mouse with a sensitivity limit in RGCs=1×1014 photons cm−2 s−1˜0.5 mW cm−2.

(17) De Silva et al. (2017) expressed with AAV2/8(Y733F) & CMV enhancer/CBA promoter stimulated at 480/20 nm in rd1 mouse with a Melanopsin sensitivity limit in RGCs=1.20×1012 photons cm−2 s−1˜0.5 μW cm−2.

FIGS. 8a-8e. Intensity-dependent kinetics of MW-opsin light response. (a-c) Dependence of light intensity (in seconds) of Tau ON (a), Tau OFF (b), and Time to peak (T-peak) (c) in rd1 retina expressing MW-opsin n=111 cells, N=3 retina. All cells refer to sorted units. Values are mean, error bars are SEM. Wavelength: λ=535 nm. (d,e) Average response of RGC population with SEM in gray (top) and averaged raster plot over 5 light flashes of 1 sec duration (bottom) for rd1 expressing MW-opsin (d; λ=510 nm; n=117 cells) and wt (e, white light; n=50 cells).

FIGS. 18a-18c. Contrast detection in isolated retina of MW-opsin expressing rd1 mouse. MEA recording of responses to steps from dark to full-field gray scale of different intensities in example isolated retina from MW-opsin expressing rd1 mouse (average of 14 channels) (a). (b,c) Normalized change in RGC firing rate in response to changes in contrast for rd1 mice expressing MW-opsin (N=2 retinas) (b) and wt mice (N=2 retinas) (c). 100% light=25 μW cm−2.

FIGS. 19a-19e. In vivo light responses in V1 of rd1 mouse expressing MW-opsin. (a) Schematic of head-fixed mouse on a running wheel. Stimuli displayed on a standard computer monitor positioned within the visual field of one eye. (b) Responses to 500 ms light pulse. Top, representative visually evoked potential from layer 4 of V1 (average of 20 responses, shaded area represents mean±SEM). Bottom, heat map of responses of individual units from all 16 electrodes of the linear electrode array across the depth of the visual cortex (average of 20 responses). (c) Scatter plot of light-evoked versus baseline firing rate for 39 units across 3 rd1 mice expressing MW-opsin. (d) PSTH (binned at 50 ms) of a representative unit in response to a light flash. (e) Plot of percent change of neuronal firing following stimulation in 39 units across 3 mice.

FIGS. 20a-20d. Contrast detection in vivo in MW-opsin expressing rd1 mouse. (a) Illustration of visual cortex recordings in awake free running rd1 mouse expressing MW-opsin. Randomized contrast changes presented on a computer monitor placed within the animals' visual field. (b) Average firing rate in response to full field contrast steps (500 ms duration) recorded in layer 4 of V1. Inset shows PSTHs binned at 20 ms. 100% light=115 μW cm−2.

FIGS. 21a-21c. Temporal properties of in vivo V1 responses in rd1 mice expressing MW-opsin. (a-c) Changes in neuronal firing in the visual cortex induced by full field flickering stimuli of 1, 2 and 4 Hz across 100 cycles.

MW-Opsin Restores Innate Light Avoidance

Having observed that MW-opsin produces large light responses at low intensities in the isolated rd1 retina, the intact animal was used to assess the ability of MW-opsin to support visual behavior. Sighted mice innately avoid illuminated areas, a survival mechanism associated with evading capture35. This behavior is lost following photoreceptor degeneration in the rd1 mouse model9,16. To determine if this behavior could be restored, rd1 mice with MW-opsin in RGCs were tested in a behavior box consisting of adjoining light and dark compartments (FIG. 4a). The fraction of time spent in each compartment was recorded and compared to rd1 mice that were not treated and to wt mice (FIG. 4, FIG. 9a-c, FIG. 11), as was the proportion of successful avoidance for each cohort (FIG. 9a-c; and FIG. 11, Table 1). The light compartment was illuminated with low intensity white light, equivalent to indoor office lighting (100 μW cm−2). While untreated rd1 animals cannot distinguish by sight between the compartments, they spent about 40-50% of the time in the dark compartment, consistent with an established bias in favor of the light compartment due to familiarity with release location (see Methods) (FIG. 4b). In contrast, rd1 mice expressing either rhodopsin or MW-opsin showed a strong preference for the dark compartment, similar to normally sighted wt animals (FIG. 4b & FIG. 9a). Next, using the same behavioral paradigm, the white light was replaced with blue (460±22 nm) or green (534±25 nm) light and the intensity that was reduced to the lower end of the isolated retina intensity-response curves for MW-opsin and rhodopsin (1 μW cm−2; FIG. 3b). Under green light both MW-opsin and rhodopsin expressing animals showed light avoidance (FIG. 4c, left & FIG. 9b), however, under blue light, only rhodopsin animals showed light-avoidance (FIG. 4c, right & FIG. 9c). This display of monochromatic sensitivity is consistent with the action spectrum of MW-opsin36.

FIGS. 9a-9g. Light avoidance and learned pattern discrimination behaviors. (a-c) Proportion of successful avoidance of the light compartment (proportion of successful avoidance trials) for rd1 expressing rhodopsin in RGCs (blue; n=6 mice) or MW-opsin (green; n=5), and wt mice (white; n=5 mice) when illuminated with either (a) white light (100 μW cm−2), (b) 25 μW cm−2 green light (535 nm) or (c) 25 μW cm−2 blue light (470 nm). Statistical significance assessed using Two-Sided Pearson's Chi-Square Test and One-Sided Fisher's Exact Test when applicable (FIG. 11). Success defined as avoidance greater than mean+S.D. of rd1 untreated control mice (See Methods). (d) Schematic of pattern discrimination experiment. Mice habituated at day 1, exposed to electric shock in association with specific pattern of light (stimulus A/B) paired randomly in either chamber on days 2 and 3 and tested (time spent in each chamber) on day 4, in absence of shock with light patterns reversed to avoid location bias. (e-g) Proportion of successful discrimination of the pattern paired with shock (proportion of successful avoidance trials) compared to rd1 untreated controls. (e) Horizontal vs. vertical parallel bars. Discrimination of parallel static (f) or moving (g) bars at distances of 1 vs. 6 cm. Respectively for e,f and g: rd1 rhodopsin (blue; n=8(e), 6(f) mice), rd1 MW-opsin (n=17(e), 11(f), 6(g) mice) and wt (n=5(e), 6(f), 9(g) mice). (25 μW cm−2). Statistical significance assessed using Two-Sided Pearson's Chi-Square Test and One-Sided Fisher's Exact Test when applicable (FIG. 11). Success defined as avoidance greater than mean+S.D. of rd1 untreated control mice.

MW-Opsin Supports Detection of Temporal Light Patterns

Having observed that MW-opsin triggers faster light responses than does rhodopsin in the isolated rd1 retina, it was asked whether this would translate into a superior ability to discriminate between different temporal patterns of light. A visually cued fear-conditioning paradigm was used to test the ability of animals to differentiate flashing from constant light. Wt mice, or rd1 mice expressing either MW-opsin or rhodopsin in RGCs, were placed in a behavioral apparatus consisting of a single compartment in which a low intensity (100 μW cm−2) LCD screen switched between constant light and flashing light (2 Hz). In each animal, either constant light or flashing light was consistently paired with a mild foot shock. This was done for 1 trial per day for 2 days (FIG. 4d) and animals were tested on day 3 with light cues presented in the absence of foot shock, with freezing time used to measure fear association, as done earlier15,27,37. Freezing time was measuredover a period of 10 seconds following the switch of temporal light pattern. The measurements from animals in which the visual cue and shock were paired (paired group) were compared to measurements from a cohort of animals in which the training shocks were randomized (i.e. not paired consistently with one of the stimuli) (unpaired group). Freezing times in untreated rd1 mice did not differ between paired and unpaired conditions, consistent with the expected inability of the animals to see the visual cues (FIG. 4e, gray). In contrast, rd1 mice expressing MW-opsin in RGCs showed more freezing in the paired condition, as observed in wt animals (FIG. 4e, green and white). Strikingly, rd1 mice expressing rhodopsin in RGCs did not differ between paired and unpaired conditions (FIG. 4e, blue). This suggests that, unlike blind mice expressing MW-cone opsin, rhodopsin mice cannot discriminate light flashing at 2-Hz from constant light, consistent with the slow light response kinetics observed in MEA (FIG. 3e).

MW-Opsin Restores Spatial Pattern Discrimination

It was next determined if MW-opsin in RGCs would enable rd1 mice to detect spatial patterns of light. A behavioral chamber with two adjoining compartments (FIG. 4f), each with a low intensity LCD tablet (iPad) mounted on a wall, was used. Each tablet displayed a pair of parallel lines. In one case, the lines were oriented vertically (II) and in the other horizontally (=). For MW-opsin the wavelength was centered at 535 nm (520-560) and for rhodopsin at 497 nm (480-520) (FIG. 9d). Initially, mice were given time to habituate to the compartments with the visual displays turned off (day 1). During a 2-day training period, an aversive foot shock was paired with either the vertically or horizontally oriented lines. The aversive cue was assigned randomly and maintained consistently for that animal. On day 4 the locations of the stimuli were switched to avoid location bias and conditioned avoidance was tested (FIG. 9d). It was found that rd1 animals with MW-opsin in RGCs showed avoidance of the aversive visual cue that was significantly greater than that seen in untreated rd1 control animals, and similar to that seen in wt mice (FIG. 4g and FIG. 9e). In contrast, rd1 animals with rhodopsin in RGCs did not differ from the untreated rd1 control animals and displayed a slight preference for the adverse stimulus, a clear example of location bias seen in blind animals. These observations indicate that MW-opsin restores the ability to recognize spatial light patterns, but that rhodopsin does not.

Having observed that MW-opsin supports spatial pattern recognition, the question was asked if mice could discriminate differences between lines of identical orientation but different spacing, a visual task adopted from tests of visual acuity in humans and animals38,39 Parallel vertical lines were separated by distances of either 1 or 6 cm. As above, an aversive foot shock was randomly paired with one of the stimuli during the training period on days 2 and 3, and recall was tested on day 4 as a measure of avoidance. It was found that rd1 mice expressing MW-opsin are able to distinguish between the two patterns with a performance preference for the non-aversive stimuli that was similar to that seen in wt mice, whereas rhodopsin expressing animals are similar to untreated rd1 mice (FIG. 4h, FIG. 9f, and FIG. 22). MW-opsin also supported line differentiation when the parallel lines were in motion (1 cm/sec) (FIGS. 4i and 9g).

The question was asked if the “refresh” rate of MW-opsin is fast enough to support recognition of line pattern when the pattern is in motion. To test this, the same close line differentiation task was performed, but now with the parallel lines moving at 5 cm per sec. It was found that rd1 mice expressing MW-opsin displayed a preference for the moving pattern that was paired with the non-aversive stimulus, and performed as well as did wt mice (FIG. 4i & FIG. 9g). These results indicate that MW-opsin in RGCs supports recognition of both static and moving spatial patterns at the low indoor light intensity of an LCD screen.

FIGS. 4a-4i. Light avoidance and learned visually-guided behavior in rd1 mice expressing MW-opsin or rhodopsin in RGCs. (a) Schematic of light/dark box for light avoidance test. (b, c) Proportion of time spent in the dark compartment (proportion of avoidance) for rd1 control (gray; n=4 mice), rd1 expressing rhodopsin in RGCs (blue; n=6 mice) or MW-opsin (green; n=5), and wt mice (white; n=5 mice) when illuminated with either (b) white light (100 μW cm−2), (c) 25 μW cm−2 blue light (470 nm) (right) or green light (535 nm) (left). (d) Schematic of freezing response fear conditioning experiment. (e) Quantification of fear response for discrimination of temporally patterned stimulation. Time freezing above baseline is shown for when illumination transitions from static to 2 Hz frequency stimulation (100 μW cm−2) was paired or unpaired with a electric shock for control rd1, rhodopsin, MW-opsin, and wt mice (n=4,6,12,10 paired, n=7,8,7,12 unpaired). (f) Schematic of pattern discrimination experiment. Mice habituated at day 1, then exposed to electric shock in association with specific pattern of light projected to ipads and paired randomly in either chamber (conditioning days 2 and 3). On day 4 recall tested (time spent in each chamber), in absence of shock with light patterns reversed to avoid location bias (See FIG. 8d). (g-i) Learned pattern discrimination. Time spent avoiding pattern paired with shock. (g) Horizontal vs. vertical parallel bars. (h) Discrimination of parallel static (h) or moving (i) bars at distances of 1 vs. 6 cm. Respectively for g,h and i: rd1 control (n=8, 5, 16 mice), rd1 rhodopsin (blue; n=8 mice), rd1 MW-opsin (n=17, 11, 6 mice) and wt (n=5, 6, 9 mice). (25 μW cm−2). (Note, proportion of success for these experiments shown in FIG. 9a-c). Light intensity=25-100 μW cm−2; Wavelength: =535 nm (MW-opsin), 510 nm (rhodopsin) or white light (MW-opsin). n=# of mice. Statistical significance assessed using Student's two-tailed t-test with Bonferroni correction: *p<0.01.

FIGS. 22a-22b. Location preference in discrimination task. (a) Illustration of arena used in discrimination tasks, showing a virtual divider separating each compartment in half in order to determine the proportion of time spent near the central divider between the two chambers versus near the screen. (b) Ratio of time spent in the zone close to central divider versus zone closest to the screen for the aversive and non-aversive sides reveals preference for zone closest to the central divider. Values are mean; error bars are SEM.

MW-Opsin Undergoes Light Adaptation

A fundamental characteristic of vision is the ability to distinguish objects across a wide range of ambient light intensities. This adaptation is mediated by several different mechanisms in photoreceptor cells. The question was asked whether some aspect of adaptation would transfer to RGCs with MW-opsin. Retinas expressing MW-opsin in RGCs were excised, mounted on the MEA and perfused with 9 cis-retinal. The retina was first kept in complete darkness for 15 min (dark-adapted); then, a series of brief (1 s) flashes of green light (535±25 nm) at long intervals (60 sec) and over a range of intensities was tested. The light was then adapted for 10 minutes to a moderate indoor light level (light-adapted; white light at 100 μW cm−2) and the light pulse series was repeated.

The kinetics of the light responses was examined. The light response decayed rapidly, as shown above, for both the light and dark-adapted retina, except in one case: the response to a bright flash in the dark-adapted retina decayed ˜12× more slowly (3.14±0.63 s, n=171, N=3) than the same retinas under light adapted conditions (FIG. 5a & FIG. 10a,b). Light responses driven by intact photoreceptors show similar behavior and this is believed to play a role in desensitization to subsequent stimulation40,41 and to underlie the “afterimage” in humans following a bright flash that transiently obscures vision42. Because of its unusual properties, this response of the dark-adapted retina to the brightest light flash was excluded from the intensity-response analysis.

The intensity-response curve showed that the dark-adapted retinas had a high light sensitivity, responding at ˜0.5 μW cm−2, whereas the light-adapted retinas were far less sensitive, requiring ˜100 μW cm−2 to respond (FIGS. 5b,c and 10c,d). This adaptation shifted the intensity curve by ˜3 orders of magnitude (780±82), N=3) (FIG. 5b,c). A striking feature of the adaptation was that the maximal light response was similar in the dark-adapted and light-adapted retina (FIG. 5c), as shown earlier in native cone photoreceptors43,44.

Having observed that the light response mediated by MW-opsin in RGCs undergoes light adaptation in the isolated retina, the question was asked if this would translate into visually useful light adaptation in the behaving animal. The MW-opsin-mediated light response in RGCs was examined in the context of light avoidance behavior. Prior to testing, rd1 mice expressing MW-opsin in RGCs were held for 1 hour either in complete darkness (dark adapted) or under indoor illumination (white light, 1 mW cm−2/535 nm light component, 50 μW cm−2) (FIG. 5d). They were then tested immediately in the two-chamber light-dark box for light avoidance behavior where the light box had green (535 nm) illumination at either 1 μW cm−2 (indoor light) or 100 μW cm−2 (outdoor light). The light adapted MW-opsin expressing rd1 mice showed strong light avoidance when the test light was brighter (535 nm, 100 μW cm−2) than the light level to which they were light-adapted (FIG. 5e). The light avoidance was reduced when the test light was the dimmer (535 nm, 1 μW cm−2) than light level to which they were light-adapted (FIG. 5e & FIG. 10e). In contrast, the dim test light of 1 μW cm−2 produced a high level of light avoidance in the dark-adapted animals, indicating behaviorally relevant light adaptation.

The question was asked if the effect of light adaptation on light avoidance behavior would also operate for pattern recognition in a learned visual image discrimination task. As above (FIG. 4), mice were conditioned over a 3-day training period by pairing mild foot shock with one of two displays of parallel lines at differing spacing presented on LCD screens in two adjoining chambers (FIGS. 4h and 9d). Once again, mice were tested with only the visual stimulus on day 4, but this time, immediately before testing, they underwent 1 hour of either dark adaptation (no light) or light adaptation (white light) for 4 or 8 hrs. The intensity of the line patterns during the recall was either 0.25 μW cm−2 or 10 μW cm−2 following light adaptation. It was found that rd1 mice expressing MW-opsin in RGCs that had been dark-adapted were able to discriminate between the line patterns and avoid the aversive cue whether it was presented at the low (0.25 μW cm−2) or moderate (10 μW cm−2) indoor intensity (FIG. 5f & FIG. 10f). In contrast, light-adapted animals only succeeded with the brighter test line patterns and were identical in performance between the groups that were light adapted for 1, 4, and 8 hours (FIGS. 5f and 10g). The results show that spatial pattern recognition mediated by MW-opsin is adaptive over a range of natural light intensities.

MW-Opsin Restores Novel Object Exploration

The experiments above show that MW-opsin enables pattern recognition across a wide range of light intensities using illuminated displays. A question was how it would operate in a natural environment, where ambient, incidental light illuminates three-dimensional objects. To address this, experiments employed an open field arena that is commonly used to test novel object recognition and exploratory behavior62,63. Mice naturally avoid open spaces and maintain proximity to walls of their environment. Exploratory excursions from these places of safety can be motivated by novel stimuli. Although mice employ multiple sensory modalities during exploration, vision has been shown to be critical for spatial navigation64. The arena consisted of a cube containing two distinct novel objects. The mouse was placed against the arena wall, far enough from the objects, which themselves were far enough apart, so that the chance of an accidental encounter was low whether the animal walked along the wall or explored the other object. rd1 untreated, rd1-sham injected, rd1 expressing rhodopsin or rd1 expressing MW-opsin mice, as well as wt animals, were filmed. Their movements were tracked for 10 minutes the first time that they were placed into the arena (FIG. 13a-d). It was found that wt animals travel 1.57-fold farther and moved at an average velocity 1.55-fold faster than blind rd1 animals, consistent with the known visual component of exploratory behavior. Strikingly, like wt animals, rd1 animals expressing MW-opsin traveled farther (by 1.39-fold) and faster (by 1.37-fold) than their untreated rd1 littermates (FIG. 13e,f), suggesting that MW-opsin supports normal novel object exploration. To analyze this further, experiments focused on aspects of exploratory behavior that most likely depend on vision at a distance; the latency to exploration of the novel objects and the velocity and distance traveled on the excursions to the objects. Sham injected and rhodopsin expressing rd1 mice performed similarly to untreated rd1 animals, but MW-opsin mice reached the first and second objects in 3.88-fold and 3.62-fold shorter times, respectively (FIG. 13g,h), moved at velocities that were 2.1-fold and 1.83-fold faster to the first and second objects, respectively (FIG. 13i,j), and took shorter pathways that were 0.69-fold and 0.64-fold the distance to the first and second objects, respectively (FIG. 13k,l), as compared to untreated rd1 mice. In each of these measures, MW-opsin expressing rd1 mice reached levels that were similar to those of wt animals (FIG. 13e-g). These results suggest that MW-opsin in RGCs provides previously blind animals with naturalistic vision of objects under ambient light.

FIGS. 5a-5f. Light adaptation in RGC activity and visually-guided behavior mediated by MW-opsin. (a-c) MEA recordings in isolated retina of RGC light response mediated by MW-opsin in RGCs of rd1 mouse retina show sensitivity difference with retina adapted to dark versus light. (a) Light response decay (Tau OFF) as a function of flash intensity in dark versus light adapted condition (N=3 retinas, n=171 cells). (b) Example intensity-response curve for representative retina first dark adapted (filled symbols) then light adapted (open symbols) (n=57 cells). White light adaptation. ChR2 minimum value from Bi et al. (2006)8 & Sengupta et al. (2016)13. (c) Average (error bars are SEM) normalized Light response Index (LRI) at 3 flash intensities in same retina, first dark adapted and then light adapted (N=3 retinas, n=171 cells). (d-f) Behavior shows light adaptation in visually-guided tasks. (d) Schematic of adaptation to dark or light prior to testing of innate avoidance behavior or learned pattern discrimination behavior. (e) Proportion of time spent in the dark compartment (proportion of avoidance) under outdoor light (100 μW cm−2) or indoor light (1 μW cm−2) following 1 hr. of adaptation to dark (n=11 mice) or adaptation to light (white light; 1 mW cm−2/535 nm spectral component; 50 μW cm−2; n=12,13 mice). (f) Learned pattern discrimination of parallel bars spaced at distances of 1 versus 6 cm displayed at low (0.25 μW cm−2) or indoor (10 μW cm−2) light levels following 1 hr. of adaptation to dark (n=8,8 mice) or light (white light; 1 mW cm−2/535 nm spectral component; 50 μW cm−2; n=7,7 mice). Dotted line denotes average performance of untreated rd1 control mice. Light intensity 3.82×101 mW cm−2, Wavelength: =535 nm. All cells refer to sorted units. Values are mean±SEM. Statistical significance assessed using Mann-Whitney U test (*p≤0.01). Student's two-tailed t-test with Bonferroni correction: *p<0.05.

FIGS. 10a-10g. Light adaptation in excised retina and mouse visual behavior. (a-d) Representative trace of average RGC population response in retina expressing MW-opsin (n=57). Response to 500 ms light flashes of 3.82×101 mW cm−2 (a,b) or 3.82×103 mW cm−2 (c,d) following adaptation to dark (a,c) or light (b,d). (e) Avoidance of the light compartment (proportion of successful avoidance trials) under indoor light (1 μW cm−2) following 1 hr. of adaptation to dark (n=11 mice) compared with proportion of successful avoidance mice under indoor light (1 μW cm−2; n=12 mice) and outdoor light (100 μW cm−2; n=13 mice) following 1 hr. of adaptation to light (white light; 1 mW cm−2/535 nm spectral component; 50 μW cm−2). (f) Proportion of successful discrimination of the parallel bars spaced at distances of 1 versus 6 cm displayed at low (0.25 μW cm−2) or indoor (10 μW cm−2) light levels following 1 hr. of adaptation to dark (n=8 mice at 0.25 μW cm−2, 8 mice at 10 μW cm−2) or light (n=7 mice at 0.25 μW cm−2, 7 mice at 10 μW cm−2). (g) Learned pattern discrimination of parallel bars spaced at distances of 1 versus 6 cm displayed at indoor (10 μW cm−2) light levels following 1, 4 or 8 hrs. of light adaptation (n=7,4,4) compared to unadapted rd1 controls.

FIG. 11 (Table 1). Statistical significance of light avoidance and learned visually-guided behavior. Success ratios were calculated for avoidance performance of condition behaviors (FIG. 4,5 & FIG. 9, 10). To determine significance in differences between conditions a pairwise contingency table was then constructed, and a Two-Sided Pearson's Chi-Square Test was initially conducted. To correct for conditions with a small n, a One-Sided Fisher's Exact Test was also conducted.

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While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

Claims

1. A method of restoring or enhancing visual function in an individual, the method comprising administering to the individual a nucleic acid comprising a nucleotide sequence encoding a medium wavelength opsin (MW-opsin) and/or a long wavelength opsin (LW-opsin) and/or a short wavelength opsin (SW-opsin), wherein said administering provides for expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in a retinal cell in the individual and restoration or enhancement of visual function.

2. The method of claim 1, wherein the MW-opsin comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1; wherein the LW-opsin comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4, and wherein the SW-opsin comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

3. The method of claim 1, wherein the SW-opsin comprises an amino acid sequence having at least 87% amino acid sequence identity to the human SW-opsin amino acid sequence set forth in SEQ ID NO:5 or having at least 87% amino acid sequence identity to the mouse SW-opsin amino acid sequence set forth in SEQ ID NO:6.

4. The method of claim 1, comprising administering to the individual: i) a first nucleic acid comprising a nucleotide sequence encoding an SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the human SW-opsin amino acid sequence set forth in SEQ ID NO:5; and ii) a second nucleic acid comprising a nucleotide sequence encoding an SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the mouse SW-opsin amino acid sequence set forth in SEQ ID NO:6.

5. The method of claim 1, wherein the SW-opsin is a chimeric SW-opsin comprising mouse SW-opsin intracellular domains and human SW-opsin transmembrane domains.

6. The method of claim 5, wherein the chimeric SW-opsin comprises an amino acid sequence having at least 90% amino acid sequence identity to the chimeric SW-opsin amino acid sequence set forth in SEQ ID NO:7.

7. The method of any one of claims 1-6, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for patterned vision and image recognition by the individual.

8. The method of claim 7, wherein the image recognition is of a static image or a pattern.

9. The method of claim 7, wherein the image recognition is of a moving image or a pattern.

10. The method of any one of claims 1-9, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for image recognition at a light intensity of from about 10−4 W/cm2 to about 1 W/cm2.

11. The method of any one of claims 1-9, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for image recognition at a light intensity that is at least 10-fold lower than the light intensity required to provide for image recognition by an individual expressing a channelrhodopsin polypeptide in a retinal cell.

12. The method of any one of claims 1-9, wherein expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in the retinal cell provides for kinetics that are at least 2-fold faster than the kinetics conferred on a retinal cell by a rhodopsin polypeptide.

13. The method of any one of claims 1-12, wherein the nucleic acid is a recombinant expression vector.

14. The method of claim 13, wherein the recombinant expression vector is a recombinant viral vector.

15. The method of claim 14, wherein the recombinant viral vector is an adeno-associated viral vector, a lentiviral vector, a herpes simplex virus vector, or a retroviral vector.

16. The method of any one of claims 1-15, wherein the nucleotide sequence is operably linked to a transcriptional control element that is functional in a retinal cell.

17. The method of claim 16, wherein the transcriptional control element is a retinal cell-specific promoter.

18. The method of claim 17, wherein the promoter is a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, or an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

19. The method of any one of claims 1-18, wherein said administering is via intraocular injection.

20. The method of any one of claims 1-18, wherein said administering is via intravitreal injection.

21. The method of any one of claims 1-18, wherein said administering is via subretinal injection.

22. The method of any one of claims 1-21, wherein the individual has an ocular disease selected from retinitis pigmentosa, macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy.

23. The method of any one of claims 1-21, wherein the individual has experienced retinal detachment or photoreceptor loss due to trauma or head injury.

24. The method of any one of claims 1-23, wherein the nucleic acid is complexed with a nanoparticle.

25. A recombinant viral vector comprising a nucleotide sequence encoding a medium wavelength opsin (MW-opsin) and/or a long wavelength opsin (LW-opsin) and/or a short wavelength opsin (SW-opsin).

26. The recombinant viral vector of claim 25, wherein the viral vector is an adenoassociated viral vector.

27. The recombinant viral vector of claim 25 or claim 26, wherein the MW-opsin comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1; wherein the LW-opsin comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4, and wherein the SW-opsin comprises an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in one of SEQ ID NOs:5-7.

28. The recombinant viral vector of any one of claims 25-27, wherein the nucleotide sequence is operably linked to a promoter.

29. The recombinant viral vector of claim 28, wherein the promoter is a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, or an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

30. The recombinant viral vector of any one of claims 25-29, wherein the recombinant viral vector is a recombinant AAV vector, wherein the recombinant AAV vector comprises a nucleotide sequence encoding a variant capsid polypeptide that confers increased infectivity of a retinal cell and/or confers increased ability to cross the inner limiting membrane, compared to a wild-type AAV capsid.

31. A pharmaceutical composition comprising:

a) the recombinant viral vector of any one of claims 25-30; and
b) a pharmaceutically acceptable excipient.

32. A method of restoring or enhancing visual function in an individual, the method comprising administering to the individual the recombinant viral vector of any one of claims 25-30, or the pharmaceutical composition of claim 31, wherein said administering provides for expression of the MW-opsin and/or the LW-opsin and/or the SW-opsin in a retinal cell in the individual and restoration or enhancement of visual function.

33. A chimeric SW-opsin comprising intracellular portions of a mouse SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:6, and comprising transmembrane portions of a human SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

34. The chimeric SW-opsin of claim 33, comprising an amino acid sequence having at least 90% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:7.

35. A recombinant expression vector comprising a nucleotide sequence encoding the chimeric SW-opsin of claim 33 or claim 34.

36. A composition comprising:

a) the recombinant expression vector of claim 35; and
b) a pharmaceutically acceptable excipient.

37. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between an image comprising a vertical line and an image comprising a horizontal line in a spatial pattern discrimination assay.

38. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between an image comprising a static line and an image comprising a moving line in a spatial pattern discrimination assay.

39. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between flashing light and constant light in a temporal light pattern assay.

40. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can recognize an image at a light intensity of from about 10−4 W/cm2 to about 10 W/cm2 in an image recognition assay.

41. A composition comprising one or more recombinant nucleic acid vectors comprising one or more nucleotide sequences encoding one or more cone opsins, wherein, when said one or more nucleotide sequences is expressed in an eye of a subject in need thereof, said subject can distinguish between an area with white light and an area without white light in a light avoidance assay.

42. The composition of any one of claims 37-41, wherein the one or more cone opsins is selected from the group consisting of:

a) an MW-opsin comprising an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:1;
b) an LW-opsin comprising an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:4;
c) an SW-opsin comprising an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5; and
d) a chimeric SW-opsin comprising: i) intracellular portions of a mouse SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:6; and ii) transmembrane portions of a human SW-opsin comprising an amino acid sequence having at least 87% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:5.

43. The composition of any one of claims 37-41, wherein the one or more recombinant nucleic acid vectors comprise one or more nucleotide sequences encoding 2 different cone opsins.

44. The composition of any one of claims 37-41, wherein the one or more recombinant nucleic acid vectors comprise one or more nucleotide sequences encoding 3 different cone opsins.

45. The composition of any one of claims 37-44, wherein the one or more recombinant nucleic acid vectors are an adeno-associated viral vector, a lentiviral vector, a herpes simplex virus vector, or a retroviral vector.

46. The composition of any one of claims 37-44, wherein the one or more recombinant nucleic acid vectors are recombinant adeno-associated virus vectors.

47. The composition of claim 46, wherein the recombinant AAV vector comprises a nucleotide sequence encoding a variant capsid polypeptide that confers increased infectivity of a retinal cell and/or confers increased ability to cross the inner limiting membrane, compared to a wild-type AAV capsid.

48. The composition of any one of claims 37-47, wherein the one or more nucleotide sequences are operably linked to a promoter.

49. The composition of claim 48, wherein the promoter is a synapsin promoter, a CAG promoter, a CMV promoter, a grm6 promoter, a Pleiades promoter, a ChAT promoter, a V-glut promoter, a GAD promoter, a PV promoter, a somatostatin (SST) promoter, a neuropeptide Y (NPY) promoter, a VIP promoter, a red cone opsin promoter, rhodopsin promoter, a rhodopsin kinase promoter, vitelliform macular dystrophy 2 (VMD2) gene promoter, or an interphotoreceptor retinoid-binding protein (IRBP) gene promoter.

50. The composition of any one of claims 37-49, wherein the subject has an ocular disease selected from retinitis pigmentosa, macular degeneration, retinoschisis, and Leber's Congenital Amaurosis, and diabetic retinopathy.

51. The composition of any one of claims 37-49, wherein the subject has experienced retinal detachment or photoreceptor loss due to trauma or head injury.

52. The composition of any one of claims 37-51, wherein the composition comprises a pharmaceutically acceptable excipient.

53. The composition of claim 52, wherein the pharmaceutically acceptable excipient comprises saline.

54. The composition of any one of claims 37-53, wherein the composition is sterile.

Patent History
Publication number: 20200339641
Type: Application
Filed: Jul 6, 2020
Publication Date: Oct 29, 2020
Inventors: Ehud Y. Isacoff (Berkeley, CA), Michael H. Berry (Berkeley, CA), Amy Holt (Berkeley, CA), Meike Visel (El Cerrito, CA), Autoosa Salari (Berkeley, CA), John G. Flannery (Berkeley, CA), Benjamin M. Gaub (Berkeley, CA)
Application Number: 16/921,783
Classifications
International Classification: C07K 14/47 (20060101); A61P 27/04 (20060101); C12N 15/85 (20060101); A61K 48/00 (20060101); A61K 9/00 (20060101); A61K 9/51 (20060101);