Patent Application
20250108133
The present disclosure provides vectors and compositions for treating or preventing CRB1-related diseases and disorders.
The contents of the electronic sequence listing titled COLUM_40990_601.xml (Size: 17,497 bytes; and Date of Creation: Jun. 15, 2023) is herein incorporated by reference in its entirety.
The Crumbs complex (CRB) is crucial for cell polarity and epithelial tissue function, having an essential role during retinogenesis. Disruption of the CRB complex will interrupt the precise orchestration of spatiotemporal process during retinal development, such as cell fate choice, division, migration, and differentiation. This can cause retinal degeneration leading to impairment of retinal function and thus vision.
Mutations in the Crumbs homologue-1 (CRB1) gene cause progressive and disabling autosomal recessive retinal dystrophies. Approximately 80,000 patients are affected worldwide, with a prevalence in the United States of 1 in 86,500. CRB1 mutations exhibit high phenotypic variability, with approximately 310 pathogenic variants reported. According to a meta-analysis, CRB1 gene mutations account for 2.7% and 10.1% of autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) cases, respectively, as well as an increasing number of juvenile macular dystrophy cases. LCA is a group of severe, infantile-onset retinal dystrophies that constitute more than 5% of all retinal dystrophies and is the most common cause of inherited blindness in childhood. Despite its prevalence and severity, the pathogenesis of CRB1 LCA remains unclear, and there is no treatment available to date.
Despite the large number of pathogenic CRB1 mutations identified, there is still no clear genotype-phenotype correlation. This may be due to the existence of multiple isoforms of CRB1 with cell type-specific roles.
There is an urgent need in the art for compositions and methods that can be used to treat a subject that has or is at risk of developing a disease characterized by Crumbs homologue 1 (CRB1) mutations.
The disclosure provides compositions consisting, comprising, or consisting essentially of one or more transgenes encoding more than one isoform of Crumbs homologue-1 (CRB1), for example, CRB1-A, CRB1-B, and CRB1-C. In some embodiments, the composition consists, comprises, or consists essentially of a transgene encoding CRB1-A and a transgene encoding CRB1-B.
In some embodiments, at least one or all of the more than one isoform of CRB1 is operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, the tissue-specific or cell type-specific control or regulatory element comprises a mini promoter. In some embodiments, at least one of the more than one isoform of CRB1 is operably linked to constitutive or ubiquitous promoter.
In some embodiments, CRB1-A is operably linked to a promoter which induces expression in Müller glial cells. In some embodiments, the promoter which induces expression in Müller glial cells is selected from the group consisting of RLBP1, GfaABC1D, GFAP, ProB2 and PROC17. In some embodiments, CRB1-A is operably linked to a mini promoter which induces expression in Müller glial cells. In some embodiments, the promoter which induces expression in Müller glial cells is a GFAP mini promoter. In some embodiments, the GFAP mini promoter comprises SEQ ID NO: 10.
In some embodiments, the CRB1-B is operably linked to a promoter which induces expression in photoreceptor cells. In some embodiments, the promoter which induces expression in photoreceptor cells is selected from the group consisting of IRBP, CAR, RHO, PR1.7, ProA1, ProA6, ProC1, ProA14, ProA36 and GRK1. In some embodiments, CRB1-B is operably linked to a mini promoter which induces expression in photoreceptor cells. In some embodiments, the promoter which induces expression in photoreceptor cells is a GRK1 mini promoter. In some embodiments, the GRK1 mini promoter comprises SEQ ID NO: 11.
In some embodiments, CRB1-A is operably linked to a promoter which induces expression in Müller glial cells and CRB1-B is operably linked to a promoter which induces expression in photoreceptor cells. In some embodiments, CRB1-A is operably linked to a GFAP mini promoter and CRB1-B is operably linked to a GRK1 mini promoter. In some embodiments, CRB1-A is operably linked to a GFAP mini promoter of SEQ ID NO: 10 and CRB1-B is operably linked to a GRK1 mini promoter of SEQ ID NO: 12.
In some embodiments, the one or more transgenes encoding more than one isoform of CRB1 are provided on a single vector. In some embodiments, the single vector is a viral vector. In some embodiments, the viral vector is derived from a virus selected from the group consisting of adeno-associated virus (AAV), adenovirus, lentivirus, retrovirus, poxvirus, baculovirus, herpes simplex virus, vaccinia virus, and a synthetic virus. In some embodiments, the viral vector is derived from lentivirus. In some embodiments, the transgenes encoding more than one isoform of CRB1 are operably linked to the same or different promoter.
In some embodiments, the one or more transgenes encoding more than one isoform of CRB1 are provided on two or more vectors. In some embodiments, the two or more vectors are each individually derived from a virus selected from the group consisting of adeno-associated virus (AAV), adenovirus, lentivirus, retrovirus, poxvirus, baculovirus, herpes simplex virus, vaccinia virus, and a synthetic virus. In some embodiments, at least one or both of the two or more vectors are derived from adeno-associated virus. In some embodiments, the transgenes encoding more than one isoform of CRB1 are operably linked to the same or different type promoter.
The disclosure further provides a nucleic acid encoding more than one isoform of CRB1. In some embodiments, the more than one isoform of CRB1 comprises CRB1-A and CRB1-B.
In some embodiments, at least one or all of the more than one isoform of CRB1 is operably linked to a tissue-specific or cell type-specific control or regulatory element comprising a mini promoter. In some embodiments, each of the more than one isoform is operably linked to a single tissue-specific or cell type-specific control or regulatory element. In some embodiments, each of the more than one isoform is operably linked to a different tissue-specific or cell type-specific control or regulatory element.
In some embodiments, CRB1-A is operably linked to a promoter which induces expression in Müller glial cells. In some embodiments, the promoter which induces expression in Müller glial cells is selected from the group consisting of RLBP1, GfaABC1D, GFAP, ProB2 and PROC17. In some embodiments, CRB1-A is operably linked to a mini promoter which induces expression in Müller glial cells. In some embodiments, the promoter which induces expression in Müller glial cells is a GFAP mini promoter. In some embodiments, the GFAP mini promoter comprises SEQ ID NO: 10.
In some embodiments, the CRB1-B is operably linked to a promoter which induces expression in photoreceptor cells. In some embodiments, the promoter which induces expression in photoreceptor cells is selected from the group consisting of IRBP, CAR, RHO, PR1.7, ProA1, ProA6, ProC1, ProA14, ProA36 and GRK1. In some embodiments, CRB1-B is operably linked to a mini promoter which induces expression in photoreceptor cells. In some embodiments, the promoter which induces expression in photoreceptor cells is a GRK1 mini promoter. In some embodiments, the GRK1 mini promoter comprises SEQ ID NO: 11.
In some embodiments, CRB1-A is operably linked to a promoter which induces expression in Müller glial cells and CRB1-B is operably linked to a promoter which induces expression in photoreceptor cells. In some embodiments, CRB1-A is operably linked to a GFAP mini promoter and CRB1-B is operably linked to a GRK1 mini promoter. In some embodiments, CRB1-A is operably linked to a GFAP mini promoter of SEQ ID NO: 10 and CRB1-B is operably linked to a GRK1 mini promoter of SEQ ID NO: 12.
In some embodiments, the nucleic acid is a viral vector. In some embodiments, the viral vector is derived from a virus selected from the group consisting of adeno-associated virus (AAV), adenovirus, lentivirus, retrovirus, poxvirus, baculovirus, herpes simplex virus, vaccinia virus, and a synthetic virus. In some embodiments, the viral vector is derived from lentivirus.
Thus, the disclosure also provides a recombinant viral vector comprising one or more transgenes encoding more than one isoform of CRB1. In some embodiments, the more than one isoform of CRB1 comprises CRB1-A and CRB1-B. In some embodiments, viral vector is derived from a virus selected from the group consisting of adeno-associated virus (AAV), adenovirus, lentivirus, retrovirus, poxvirus, baculovirus, herpes simplex virus, vaccinia virus, and a synthetic virus. In some embodiments, the viral vector is derived from a lentivirus.
In some embodiments, the vector further comprises a polyadenylation sequence (e.g., SV40, bGHpolyA and spA), a post-transcriptional regulatory element (e.g., WPRE, WPRE3 and HPRE), or combinations thereof.
Also provided are compositions comprising the nucleic acid or recombinant vector.
In some embodiments, the compositions disclosed herein may further comprise a pharmaceutical carrier or vehicle. In some embodiments, the compositions are suitable for subretinal injection or intravitreal injection.
The present disclosure additionally provides methods that can be used to treat a subject (e.g., a mammalian subject, such as a human subject) that has or is at risk of developing a disease characterized by Crumbs homologue 1 (CRB1) mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA).
Using the compositions of the disclosure, a subject (e.g., a mammalian subject, such as a human subject) that has or is at risk of developing a disease characterized by Crumbs homologue 1 (CRB1) mutations may be administered a composition, nucleic acid, or vector as described herein. Thus, in some embodiments, the method includes administering to the subject a therapeutically effective amount of a composition, nucleic acid, or vector as described herein.
In some embodiments, the method includes administering to the subject a therapeutically effective amount of a composition containing, comprising, or consisting essentially of transgenes encoding more than one isoform of CRB1 (e.g., CRB1-A, CRB1-B, CRB1-C), as described herein. In some embodiments, the composition contains, comprises, or consists essentially of a transgene encoding CRB1-A and a transgene encoding CRB1-B.
In an additional embodiment, the disclosure features a method of alleviating one or more symptoms associated with a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) in a subject in need thereof. The method includes administering to the subject a therapeutically effective amount of a composition containing, comprising, or consisting essentially of transgenes encoding more than one isoform of CRB1 (e.g., CRB1-A, CRB1-B, CRB1-C), as described herein. In some embodiments, the composition contains, comprises, or consists essentially of a transgene encoding CRB1-A and a transgene encoding CRB1-B.
In certain embodiments, the route of administration is subretinal injection or intravitreal injection.
Other aspects and embodiments of the disclosure will be apparent in light of the following detailed description.
For the purpose of illustrating the invention, there are depicted in drawings certain embodiments of the invention. However, the invention is not limited to the precise arrangements of the embodiments depicted in the drawings.
Crumbs (Crb) is a large transmembrane protein initially discovered at the apical membrane of Drosophila epithelial cells (Tepass et al., 1990). The human CRB1 gene is mapped to chromosome 1q31.3, and contains 12 exons, has 12 identified transcript variants so far, three CRB family members, and over 210 kb genomic DNA (Den Hollander et al., 1999). Canonical CRB1 (CRB1-A) is a large transmembrane protein consisting of multiple epidermal growth factor (EGF) and laminin-globular like domains in its extracellular N-terminus. The intracellular C-terminal domain contains a FERM and a conserved glutamic acid-arginine-leucine-isoleucine (ERLI) PDZ binding motives. An alternative transcript of CRB1, CRB1-B, was recently described and suggested to have significant extracellular domain overlap with canonical CRB1 while bearing unique 5′ and 3′ domains (Ray et al., 2020). In mammals, CRB1 is a member of the Crumbs family together with CRB2 and CRB3.
CRB is localized in the retina. The current disclosure is based upon the finding that CRB1-A is predominantly expressed in Müller glial cells and CRB1-B in photoreceptor cells as well as the fact that approximately 70% of novel CRB1 patient mutations affect both CRB1-A and CRB1-B. Sec
These findings indicate that diseases characterized by CRB1 mutations may be treated, prevented and/or cured via gene therapy by delivery of nucleic acids encoding more than one isoform of CRB1 (e.g., in one viral vector-denoted CRB1 Isoform Dual Expression Vector herein) or composition comprising one or more nucleic acids encoding more than one isoform of CRB1.
The terms used in this specification generally have their ordinary meanings in the art, within the context of this invention and the specific context where each term is used. Certain terms are discussed below, or elsewhere in the specification, to provide additional guidance to the practitioner in describing the methods of the invention and how to use them. Moreover, it will be appreciated that the same thing can be said in more than one way. Consequently, alternative language and synonyms may be used for any one or more of the terms discussed herein, nor is any special significance to be placed upon whether or not a term is elaborated or discussed herein. Synonyms for certain terms are provided. A recitation of one or more synonyms does not exclude the use of the other synonyms. The use of examples anywhere in the specification, including examples of any terms discussed herein, is illustrative only, and in no way limits the scope and meaning of the invention or any exemplified term. Likewise, the invention is not limited to its preferred embodiments.
The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. As used herein, comprising a certain sequence or a certain SEQ ID NO usually implies that at least one copy of said sequence is present in recited peptide or polynucleotide. However, two or more copies are also contemplated. The singular forms “a,” “and” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of,” and “consisting essentially of,” the embodiments or elements presented herein, whether explicitly set forth or not.
For the recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated.
The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system, e.g., the degree of precision required for a particular purpose, such as a pharmaceutical formulation. For example, “about” can mean within 1 or more than 1 standard deviations, per the practice in the art. Alternatively, “about” can mean a range of up to 20%, preferably up to 10%, more preferably up to 5%, and more preferably still up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value. Where particular values are described in the application and claims, unless otherwise stated, the term “about” meaning within an acceptable error range for the particular value should be assumed.
As used herein, the term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered, and includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art.
As used herein, the expressions “cell,” “cell line,” and “cell culture” are used interchangeably and all such designations include progeny. Thus, the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that not all progeny will have precisely identical DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
The phrase “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to use promoters, polyadenylation signals, and enhancers.
The term “heterologous” means derived from a genotypically distinct entity from that of the rest of the entity to which it is being compared. For example, a polynucleotide introduced by genetic engineering techniques into a plasmid or vector derived from a different species is a heterologous polynucleotide. A promoter removed from its native coding sequence and operatively linked to a coding sequence with which it is not naturally found linked is a heterologous promoter.
The term “in need thereof” would be a subject known or suspected of having or being at risk of having a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA).
A “host cell” refers to any cell that harbors, or is capable of harboring, a substance of interest. Often a host cell is a mammalian cell. A host cell may be used as a recipient of viral vector. The term includes the progeny of the original cell which has been transfected. Thus, a “host cell” as used herein may refer to a cell which has been transfected with an exogenous DNA sequence. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
With respect to cells, the term “isolated” refers to a cell that has been isolated from its natural environment (e.g., from a tissue or subject). The term “cell line” refers to a population of cells capable of continuous or prolonged growth and division in vitro. Often, cell lines are clonal populations derived from a single progenitor cell. It is further known in the art that spontaneous or induced changes can occur in karyotype during storage or transfer of such clonal populations. Therefore, cells derived from the cell line referred to may not be precisely identical to the ancestral cells or cultures, and the cell line referred to includes such variants. As used herein, the terms “recombinant cell” refers to a cell into which an exogenous DNA segment, such as DNA segment that leads to the transcription of a biologically-active polypeptide or production of a biologically active nucleic acid such as an RNA, has been introduced.
As used herein, “nucleic acid” or “nucleic acid sequence” refers to a polymer or oligomer of pyrimidine and/or purine bases, preferably cytosine, thymine, and uracil, and adenine and guanine, respectively (See Albert L. Lehninger, Principles of Biochemistry, at 793-800 (Worth Pub. 1982)). The present technology contemplates any deoxyribonucleotide, ribonucleotide, or peptide nucleic acid component, and any chemical variants thereof, such as methylated, hydroxymethylated, or glycosylated forms of these bases, and the like. The polymers or oligomers may be heterogenous or homogenous in composition and may be isolated from naturally occurring sources or may be artificially or synthetically produced. In addition, the nucleic acids may be DNA or RNA, or a mixture thereof, and may exist permanently or transitionally in single-stranded or double-stranded form, including homoduplex, heteroduplex, and hybrid states. In some embodiments, a nucleic acid or nucleic acid sequence comprises other kinds of nucleic acid structures such as, for instance, a DNA/RNA helix, peptide nucleic acid (PNA), morpholino nucleic acid (see, e.g., Braasch and Corey, Biochemistry, 41 (14): 4503-4510 (2002)) and U.S. Pat. No. 5,034,506), locked nucleic acid (LNA; see Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 97:5633-5638 (2000)), cyclohexenyl nucleic acids (see Wang, J. Am. Chem. Soc., 122:8595-8602 (2000)), and/or a ribozyme. Hence, the term “nucleic acid” or “nucleic acid sequence” may also encompass a chain comprising non-natural nucleotides, modified nucleotides, and/or non-nucleotide building blocks that can exhibit the same function as natural nucleotides (e.g., “nucleotide analogs”); further, the term “nucleic acid sequence” as used herein refers to an oligonucleotide, nucleotide or polynucleotide, and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin, which may be single or double-stranded, and represent the sense or antisense strand. The terms “nucleic acid,” “polynucleotide,” “nucleotide sequence,” and “oligonucleotide” are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof.
Nucleic acid or amino acid sequence “identity,” as described herein, can be determined by comparing a nucleic acid or amino acid sequence of interest to a reference nucleic acid or amino acid sequence. A number of mathematical algorithms for obtaining the optimal alignment and calculating identity between two or more sequences are known and incorporated into a number of available software programs. Examples of such programs include CLUSTAL-W, T-Coffee, and ALIGN (for alignment of nucleic acid and amino acid sequences), BLAST programs (e.g., BLAST 2.1, BL2SEQ, and later versions thereof) and FASTA programs (e.g., FASTA3x, FAS™, and SSEARCH) (for sequence alignment and sequence similarity searches). Sequence alignment algorithms also are disclosed in, for example, Altschul et al., J. Molecular Biol., 215 (3): 403-410 (1990), Beigert et al., Proc. Natl. Acad. Sci. USA, 106 (10): 3770-3775 (2009), Durbin et al., eds., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK (2009), Soding, Bioinformatics, 21 (7): 951-960 (2005), Altschul et al., Nucleic Acids Res., 25 (17): 3389-3402 (1997), and Gusfield, Algorithms on Strings, Trees and Sequences, Cambridge University Press, Cambridge UK (1997)).
“Isolated nucleic acid molecule” means a DNA or RNA of genomic, mRNA, cDNA, or synthetic origin or some combination thereof which is not associated with all or a portion of a polynucleotide in which the isolated polynucleotide is found in nature or is linked to a polynucleotide to which it is not linked in nature. For purposes of this disclosure, it should be understood that “a nucleic acid molecule comprising” a particular nucleotide sequence does not encompass intact chromosomes. Isolated nucleic acid molecules “comprising” specified nucleic acid sequences may include, in addition to the specified sequences, coding sequences for up to ten or even up to twenty or more other proteins or portions or fragments thereof, or may include operably linked regulatory sequences that control expression of the coding region of the recited nucleic acid sequences, and/or may include vector sequences.
The term “mini promoter” refers to a promoter in which certain promoter elements are selected from an endogenous full length promoter for a gene, usually to reduce the overall size of the promoter compared to the native sequence. For example, after identification of critical promoter elements, using one or more of various techniques, the native sequences that intervene between identified elements may be partially or completely removed. Other non-native sequences may optionally be inserted between the identified promoter elements. Promoter sequences, e.g., enhancer elements, may have an orientation that is different from the native orientation. For example, a promoter element may be inverted, or reversed, from its native orientation.
A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
A “peptide” or “polypeptide” is a linked sequence of two or more amino acids linked by peptide bonds. Peptides and polypeptides include proteins such as binding proteins, receptors, and antibodies. The terms “polypeptide” and “protein” are used interchangeably herein.
The term “pharmaceutically acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a host, such as gastric upset, dizziness, and the like, when administered to a human, and approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
The terms “prevent,” “prevention,” and the like refer to acting prior to overt disease or disorder onset, to prevent the disease or disorder from developing or minimize the extent of the disease or disorder, or slow its course of development.
As used herein, the terms “providing,” “administering,” and “introducing,” are used interchangeably herein and refer to the placement by a method or route which results in at least partial localization to a desired site. Administration can be by any appropriate route which results in delivery to a desired location in the cell, organism, or subject.
A “subject” or “patient” may be human or non-human and may include, for example, animal strains or species used as “model systems” for research purposes, such a mouse model as described herein. Likewise, patient may include either adults or juveniles (e.g., children). Moreover, patient may mean any living organism, preferably a mammal (e.g., human or non-human) that may benefit from the administration of compositions contemplated herein. Examples of mammals include, but are not limited to, any member of the Mammalian class: humans, non-human primates such as chimpanzees, and other apes and monkey species; farm animals such as cattle, horses, sheep, goats, swine; domestic animals such as rabbits, dogs, and cats; laboratory animals including rodents, such as rats, mice and guinea pigs, and the like. Examples of non-mammals include, but are not limited to, birds, fish, and the like. In one embodiment of the methods and compositions provided herein, the mammal is a human. In some embodiments of the present invention, the subject is known or suspected of having a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA).
The phrase “therapeutically effective amount” is used herein to mean an amount sufficient to cause an improvement in a clinically significant condition in the subject, or delays or minimizes or mitigates one or more symptoms associated with the disease or disorder, or results in a desired beneficial change of physiology in the subject.
With respect to transfected host cells, the term “transfection” is used to refer to the uptake of foreign DNA by a cell, and a cell has been “transfected” when exogenous DNA has been introduced inside the cell membrane. A number of transfection techniques are generally known in the art. Sec, e.g., Graham et al., Virology 52:456 (1973), Sambrook et al., Molecular Cloning, a Laboratory Manual, Cold Spring Harbor Laboratories, New York (1989), Davis et al., Basic Methods in Molecular Biology, Elsevier (1986), and Chu et al., Gene 13:197 (1981). Such techniques can be used to introduce one or more exogenous nucleic acids, such as a nucleotide integration vector and other nucleic acid molecules, into suitable host cells.
As used herein, “treat,” “treating,” and the like means a slowing, stopping, or reversing of progression of a disease or disorder when provided a peptide or composition described herein to an appropriate subject. The term also includes a reversing of the progression of such a disease or disorder to a point of eliminating or greatly reducing the disease. As such, “treating” means an application or administration of the peptides or compositions described herein to a subject, where the subject has a disease or a symptom of a disease, where the purpose is to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve, or affect the disease or symptoms of the disease.
The term “vector” includes any genetic element, such as a plasmid, phage, transposon, cosmid, chromosome, artificial chromosome, virus, or virion, which is capable of replication when associated with the proper control elements and which can transfer gene sequences between cells. Thus, the term includes cloning and expression vehicles, as well as viral vectors. In some embodiments, useful vectors are contemplated to be those vectors in which the nucleic acid segment to be transcribed is positioned under the transcriptional control of a promoter. A “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a gene. The phrases “operatively positioned,” “operatively linked,” “under control,” or “under transcriptional control” means that the promoter is in the correct location and orientation in relation to the nucleic acid to control RNA polymerase initiation and expression of the gene.
The term “expression vector” or “expression construct” or “construct” means any type of genetic construct containing a nucleic acid in which part or all of the nucleic acid encoding sequence is capable of being transcribed. In some embodiments, expression includes transcription of the nucleic acid, for example, to generate a biologically-active polypeptide product or inhibitory RNA from a transcribed gene.
Standard methods in molecular biology are described Sambrook, Fritsch and Maniatis Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1982 & 1989 2nd Edition, 2001 3rd Edition); Sambrook and Russell Molecular Cloning, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (2001); Wu Recombinant DNA, Vol. 217, Academic Press, San Diego, CA) (1993). Standard methods also appear in Ausbel, et al. Current Protocols in Molecular Biology, Vols. 1-4, John Wiley and Sons, Inc. New York, NY (2001).
Nucleic acid sequences of transgenes described herein may be designed based on the knowledge of the specific composition (e.g., viral vector) that will express the transgene. For example, one type of transgene sequence includes a reporter sequence, which upon expression produces a detectable signal. In another example, the transgene encodes a therapeutic protein or therapeutic functional RNA. In another example, the transgene encodes a protein or functional RNA that is intended to be used for research purposes, e.g., to create a somatic transgenic animal model harboring the transgene, e.g., to study the function of the transgene product. In another example, the transgene encodes a protein or functional RNA that is intended to be used to create an animal model of disease.
The transgenes encode more than one isoform of CRB1. Isoforms of CRB1 may include CRB1-A, CRB1-B, and CRB1-C. In some embodiments, the more than one isoform of CRB1 includes CRB1-A. In some embodiments, the more than one isoform of CRB1 includes CRB1-B. In embodiments, the composition comprises transgenes encoding CRB1-A and CRB1-B.
The CRB1-A transgene can be derived from the human CRB1-A gene (GenBank: MT470365.1).
In some embodiments, the transgene encodes human CRB1-A (SEQ ID NO: 8). The CRB1-A may have an amino acid sequence that is at least 85% identical to the amino acid sequence of human CRB1-A (SEQ ID NO: 8) (e.g., an amino acid sequence that is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of human CRB1-A). In some embodiments, the CRB1-A has an amino acid sequence that is at least 90% identical to the amino acid sequence of human CRB1-A (e.g., an amino acid sequence that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of human CRB1-A). In some embodiments, the CRB1-A has an amino acid sequence that is at least 95% identical to the amino acid sequence of human CRB1-A (e.g., an amino acid sequence that is 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of human CRB1-A).
In some embodiments, the CRB1-A has an amino acid sequence that differs from human CRB1-A (SEQ ID NO: 8) by way of one or more amino acid substitutions, insertions, and/or deletions, such as by from 1 to 10, 1 to 15, 1 to 20, 1 to 25, or more, amino acid substitutions, insertions, and/or deletions (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more, conservative amino acid substitutions). In some embodiments, the CRB1-A has an amino acid sequence that differs from human CRB1-A (SEQ ID NO: 8) by way of one or more conservative amino acid substitutions, such as by from 1 to 10, 1 to 15, 1 to 20, 1 to 25, or more, conservative amino acid substitutions (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more, conservative amino acid substitutions).
An amino acid “substitution” or “replacement” refers to the replacement of one amino acid at a given position or residue by another amino acid at the same position or residue within a polypeptide sequence. Amino acids are broadly grouped as “aromatic” or “aliphatic.” An aromatic amino acid includes an aromatic ring. Examples of “aromatic” amino acids include histidine (H or His), phenylalanine (F or Phe), tyrosine (Y or Tyr), and tryptophan (W or Trp). Non-aromatic amino acids are broadly grouped as “aliphatic.” Examples of “aliphatic” amino acids include glycine (G or Gly), alanine (A or Ala), valine (V or Val), leucine (L or Leu), isoleucine (I or He), methionine (M or Met), serine (S or Ser), threonine (T or Thr), cysteine (C or Cys), proline (P or Pro), glutamic acid (E or Glu), aspartic acid (A or Asp), asparagine (N or Asn), glutamine (Q or Gin), lysine (K or Lys), and arginine (R or Arg).
The amino acid replacement or substitution can be conservative, semi-conservative, or non-conservative. The phrase “conservative amino acid substitution” or “conservative mutation” refers to the replacement of one amino acid by another amino acid with a common property. A functional way to define common properties between individual amino acids is to analyze the normalized frequencies of amino acid changes between corresponding proteins of homologous organisms (Schulz and Schirmer, Principles of Protein Structure, Springer-Verlag, New York (1979)). According to such analyses, groups of amino acids may be defined where amino acids within a group exchange preferentially with each other, and therefore resemble each other most in their impact on the overall protein structure (Schulz and Schirmer, supra).
Examples of conservative amino acid substitutions include substitutions of amino acids within the sub-groups described above, for example, lysine for arginine and vice versa such that a positive charge may be maintained, glutamic acid for aspartic acid and vice versa such that a negative charge may be maintained, serine for threonine such that a free-OH can be maintained, and glutamine for asparagine such that a free —NH2 can be maintained. “Semi-conservative mutations” include amino acid substitutions of amino acids within the same groups listed above, but not within the same sub-group. For example, the substitution of aspartic acid for asparagine, or asparagine for lysine, involves amino acids within the same group, but different sub-groups. “Non-conservative mutations” involve amino acid substitutions between different groups, for example, lysine for tryptophan, or phenylalanine for serine, etc.
In some embodiments, the transgene encoding CRB1-A has a nucleic acid sequence that is at least 70% identical to the nucleic acid sequence of human CRB1-A (e.g., a nucleic acid sequence that is 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-A). In some embodiments, the transgene encoding CRB1-A has a nucleic acid sequence that is at least 85% identical to the nucleic acid sequence of human CRB1-A (e.g., a nucleic acid sequence that is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-A). In some embodiments, the transgene encoding CRB1-A has a nucleic acid sequence that is at least 90% identical to the nucleic acid sequence of human CRB1-A (e.g., a nucleic acid sequence that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-A). In some embodiments, the transgene encoding CRB1-A has a nucleic acid sequence that is at least 95% identical to the nucleic acid sequence of human CRB1-A (e.g., a nucleic acid sequence that is 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-A).
In some embodiments, the transgene encoding CRB1-A is codon optimized. Codon optimization, in some embodiments, may be used to match codon frequencies in target and host organisms to ensure proper folding; bias GC content to increase mRNA stability or reduce secondary structures; minimize tandem repeat codons or base runs that may impair gene construction or expression; customize transcriptional and translational control regions; insert or remove protein trafficking sequences; remove/add post translation modification sites in encoded protein (e.g., glycosylation sites); add, remove or shuffle protein domains; insert or delete restriction sites; modify ribosome binding sites and mRNA degradation sites; adjust translational rates to allow the various domains of the protein to fold properly; or to reduce or eliminate problem secondary structures within the polynucleotide. In some embodiments, codon optimization increases efficiency of transgene transcription and translation, thus increasing transgene expression.
The CRB1-B transgene can be derived from the human CRB1-B gene (GenBank: MT47036).
In some embodiments, the transgene encodes human CRB1-B (SEQ ID NO: 9). The CRB1-B may have an amino acid sequence that is at least 85% identical to the amino acid sequence of human CRB1-B (SEQ ID NO: 9) (e.g., an amino acid sequence that is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of human CRB1-B). In some embodiments, the CRB1-B has an amino acid sequence that is at least 90% identical to the amino acid sequence of human CRB1-B (e.g., an amino acid sequence that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of human CRB1-B). In some embodiments, the CRB1-B has an amino acid sequence that is at least 95% identical to the amino acid sequence of human CRB1-B (e.g., an amino acid sequence that is 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of human CRB1-B).
In some embodiments, the CRB1-B has an amino acid sequence that differs from human CRB1-B (SEQ ID NO: 9) by way of one or more amino acid substitutions, insertions, and/or deletions, such as by from 1 to 10, 1 to 15, 1 to 20, 1 to 25, or more, amino acid substitutions, insertions, and/or deletions (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more, conservative amino acid substitutions). In some embodiments, the CRB1-B has an amino acid sequence that differs from human CRB1-B by way of one or more conservative amino acid substitutions, such as by from 1 to 10, 1 to 15, 1 to 20, 1 to 25, or more, conservative amino acid substitutions (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more, conservative amino acid substitutions).
In some embodiments, the transgene encoding CRB1-B has a nucleic acid sequence that is at least 70% identical to the nucleic acid sequence of human CRB1-B (e.g., a nucleic acid sequence that is 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-B). In some embodiments, the transgene encoding CRB1-B has a nucleic acid sequence that is at least 85% identical to the nucleic acid sequence of human CRB1-B (e.g., a nucleic acid sequence that is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-B). In some embodiments, the transgene encoding CRB1-B has a nucleic acid sequence that is at least 90% identical to the nucleic acid sequence of human CRB1-B (e.g., a nucleic acid sequence that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-B). In some embodiments, the transgene encoding CRB1-B has a nucleic acid sequence that is at least 95% identical to the nucleic acid sequence of human CRB1-B (e.g., a nucleic acid sequence that is 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acid sequence of human CRB1-B).
In some embodiments, the transgene encoding CRB1-B is codon optimized
It will be appreciated that changing native codons to those most frequently used in mammals allows for maximum expression in mammalian cells (e.g., human cells). Such modified nucleic acid sequences are commonly described in the art as “codon-optimized,” or as utilizing “mammalian-preferred” or “human-preferred” codons. In some embodiments, the nucleic acid sequence is considered codon-optimized if at least about 60% (e.g., 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) of the codons encoded therein are mammalian preferred codons.
The transgenes are operably linked to control or regulatory elements which permit transcription, translation and/or expression of the transgene in a cell transfected with the transgene (e.g., on a plasmid vector) or infected by a viral vector. Regulatory elements are nucleic acid sequences or genetic elements which are capable of influencing (e.g., increasing or decreasing) expression of a gene and/or confer selective expression of a gene (e.g., a transgene) in a particular tissue or cell type of interest. In some cases, a regulatory element can be an intron, a promoter, an enhancer, UTR, insulator, a repressor, an inverted terminal repeat (ITR) sequence, a long terminal repeat sequence (LTR), stability element, posttranslational response element, or a polyA sequence, or a combination thereof. In some cases, the regulatory element is a promoter or an enhancer, or a combination thereof. In some cases, the regulatory element is derived from a human sequence.
As used herein, “operably linked” sequences include both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest. Expression control sequences include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation (polyA) or synthetic polyA (SPA) signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (e.g., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product. A great number of expression control sequences, including promoters which are native, constitutive, inducible and/or tissue-specific, are known in the art and may be utilized.
As used herein, a nucleic acid sequence (e.g., coding sequence) and regulatory sequences are said to be operably linked when they are covalently linked in such a way as to place the expression or transcription of the nucleic acid sequence under the influence or control of the regulatory sequences. If it is desired that the nucleic acid sequences be translated into a functional protein, two DNA sequences are said to be operably linked if induction of a promoter in the 5′ regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein. Thus, a promoter region would be operably linked to a nucleic acid sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide.
For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, simian virus 40, and others disclosed herein and known in the art. Vectors of the present disclosure can comprise any of a number of promoters known to the art, wherein the promoter is constitutive, regulatable or inducible, cell type specific, tissue-specific, or species specific. Many promoter/regulatory sequences useful for driving constitutive expression of a gene are available in the art and include, but are not limited to, for example, CMV (cytomegalovirus promoter), EF1a (human elongation factor 1 alpha promoter), SV40 (simian vacuolating virus 40 promoter), PGK (mammalian phosphoglycerate kinase promoter), Ubc (human ubiquitin C promoter), human beta-actin promoter, rodent beta-actin promoter, CBh (chicken beta-actin promoter), CAG (hybrid promoter contains CMV enhancer, chicken beta actin promoter, and rabbit beta-globin splice acceptor), TRE (Tetracycline response element promoter), H1 (human polymerase III RNA promoter), U6 (human U6 small nuclear promoter), CB7 (chicken β-actin promoter) and the like. Additional promoters, include, without limitation, cytomegalovirus (CMV) intermediate early promoter, a viral LTR such as the Rous sarcoma virus LTR, HIV-LTR, HTLV-1 LTR, Maloney murine leukemia virus (MMLV) LTR, myeloproliferative sarcoma virus (MPSV) LTR, spleen focus-forming virus (SFFV) LTR, the simian virus 40 (SV40) early promoter, herpes simplex tk virus promoter, elongation factor 1-alpha (EF1-α) promoter with or without the EF1-α intron. Additional promoters include any constitutively active promoter. Alternatively, any regulatable promoter may be used, such that its expression can be modulated within a cell.
N Moreover, inducible and tissue specific expression can be accomplished by placing the nucleic acid encoding such a molecule under the control of an inducible or tissue specific promoter/regulatory sequence. Examples of tissue specific or inducible promoter/regulatory sequences which are useful for this purpose include, but are not limited to, the rhodopsin promoter, the MMTV LTR inducible promoter, the SV40 late enhancer/promoter, synapsin 1 promoter, ET hepatocyte promoter, GS glutamine synthase promoter and many others. Various commercially available ubiquitous as well as tissue-specific promoters and tumor-specific are available, for example from InvivoGen. In addition, promoters which are well known in the art can be induced in response to inducing agents such as metals, glucocorticoids, tetracycline, hormones, and the like, are also contemplated for use with the invention. Thus, it will be appreciated that the present disclosure includes the use of any promoter/regulatory sequence known in the art that is capable of driving expression of the desired protein operably linked thereto.
The control or regulatory elements may direct expression of the nucleic acid in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Such regulatory elements include promoters that may be tissue specific or cell specific. The term “tissue specific” as it applies to a promoter refers to a promoter that is capable of directing selective expression of a nucleotide sequence of interest to a specific type of tissue (e.g., seeds) in the relative absence of expression of the same nucleotide sequence of interest in a different type of tissue. The term “cell type specific” as applied to a promoter refers to a promoter that is capable of directing selective expression of a nucleotide sequence of interest in a specific type of cell in the relative absence of expression of the same nucleotide sequence of interest in a different type of cell within the same tissue. The term “cell type specific” when applied to a promoter also means a promoter capable of promoting selective expression of a nucleotide sequence of interest in a region within a single tissue. Cell type specificity of a promoter may be assessed using methods well known in the art, e.g., immunohistochemical staining.
In some embodiments of the disclosure, the transgenes are operably linked to separate promoters that induce expression of the transgenes in the proper cells, e.g., CRB1-A in Müller glial cells and CRB1-B in photoreceptor cells. The promoter for CRB1-A may be, for example, RLBP1 (Retinaldehyde Binding Protein 1), GFAP (Glial fibrillary acidic protein), GfaABC1D (a truncated GFAP promoter), and synthetic promoters ProB2 and PROC17. The promoter for CRB1-B may be, for example, interphotoreceptor retinoid-binding protein (IRBP), cone arrestin (CAR), rhodopsin (RHO), PR1.7 (a truncated version of version of the L-opsin promoter), synthetic promoters: ProA1, ProA6, ProC1, ProA14, and ProA36, and G protein-coupled receptor kinase 1 (GRK1).
In some embodiments, the at least one or all of the more than one isoform of CRB1 are each individually or independently operably linked to a tissue-specific or cell type-specific control or regulatory element comprising a mini promoter. Mini promoters are minimal promoter element(s) designed for expression in specific types. For example, in some embodiments, the composition comprises transgenes encoding CRB1-A and CRB1-B either or both of which may be operably linked to a tissue-specific or cell type-specific mini promoter. In select embodiments, the composition comprises transgenes encoding CRB1-A and CRB1-B both of which are independently or individually operably linked to a tissue-specific or cell type-specific mini promoter.
In some embodiments, CRB1-A is operably linked to a mini promoter for expression in Müller glial cells. In some embodiments, CRB1-A is operably linked to a GFAP mini promoter for expression in Müller glial cells. In some embodiments, the GFAP mini promoter comprises, consists of, or consists essentially of a nucleotide sequence at least 70% similar (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% similar) to SEQ ID NO: 10. In some embodiments, the GFAP mini promoter comprises, consists of, or consists essentially of SEQ ID NO: 10.
In some embodiments, CRB1-B is operably linked to a mini promoter for expression in photoreceptor cells. In some embodiments, CRB1-B is operably linked to a GRK1 mini promoter for expression in photoreceptor cells. In some embodiments, the GRK1 mini promoter comprises, consists of, or consists essentially of a nucleotide sequence at least 70% similar (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% similar) to SEQ ID NO: 11. In some embodiments, the GRK1 mini promoter comprises, consists of, or consists essentially of SEQ ID NO: 11.
In some embodiments, CRB1-B is operably linked to a mini promoter for expression in photoreceptor cells and CRB1-A is operably linked to a mini promoter for expression in Müller glial cells. In select embodiments, CRB1-B is operably linked to a GRK1 mini promoter for expression in photoreceptor cells and CRB1-A is operably linked to a GFAP mini promoter for expression in Müller glial cells.
Other regulatory elements may also be used such as a polyadenylation sequence and post-transcriptional regulatory elements, for efficient pre-mRNA processing and increasing gene expression, respectively. For nucleic acids encoding proteins, a polyadenylation sequence generally is inserted following the transgene sequences. Examples of polyadenylation sequences include SV40, bGHpolyA, and spA. Examples of post-transcriptional regulatory elements include WPRE, WPRE3, and HPRE.
In some embodiments, optimized combinations of polyadenylation sequences and post-transcriptional regulatory elements, such as CWSL3, may be used in the vectors (Choi et al. 2014).
The precise nature of the regulatory sequences which facilitate gene expression in host cells may vary between species, tissues, or cell types, but in general include, but are not limited to, 5′ non-transcribed and 5′ non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, enhancer elements, and the like. Especially, such 5′ non-transcribed regulatory sequences will include a promoter region that includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired.
For example, some or all of the following control or regulatory elements may also be included: enhancer/promoter sequences (e.g., from the immediate early gene of human CMV for high levels of transcription); transcription termination and RNA processing signals (e.g., from SV40 for mRNA stability); 5′- and 3′-untranslated regions for mRNA stability and translation efficiency (e.g., from highly-expressed genes like α-globin or β-globin); SV40 polyoma origins of replication and ColE1 for proper episomal replication; and internal ribosome binding sites (IRESes).
The disclosed transgenes may be provided as polynucleotide segments (e.g., DNA or RNA) encoding the transgene or as vectors containing these segments. The vectors may be used to propagate the segment in an appropriate cell and/or to allow expression from the segment (e.g., an expression vector). The person of ordinary skill in the art would be aware of the various vectors available for propagation and expression of a nucleic acid sequence. In some embodiments, the polynucleotide is optimized for enhanced expression, productive co-translational protein folding, increased stability, or a combination thereof.
The vectors of the present disclosure may be delivered to a eukaryotic cell in a subject. Modification of the eukaryotic cells via the present system can take place in a cell culture, where the method comprises isolating the eukaryotic cell from a subject prior to the modification. In some embodiments, the method further comprises returning said eukaryotic cell and/or cells derived therefrom to the subject.
Viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding components of the present system into cells, tissues, or a subject. Such methods can be used to administer nucleic acids encoding components of the present system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, cosmids, RNA (e.g., a transcript of a transgene described herein), a nucleic acid, and a nucleic acid complexed with a delivery vehicle. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. Viral vectors include, for example, retroviral, lentiviral, adenoviral, adeno-associated and herpes simplex viral vectors.
A variety of viral constructs may be used with the present composition for delivery to the targeted cells and/or a subject. Nonlimiting examples of such recombinant viruses include recombinant adeno-associated virus (AAV), recombinant adenoviruses, recombinant lentiviruses, recombinant retroviruses, recombinant herpes simplex viruses, recombinant poxviruses, phages, etc. The present disclosure provides vectors capable of integration in the host genome, such as retrovirus or lentivirus. Sec, e.g., Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1989; Kay, M. A., et al., 2001 Nat. Medic. 7 (1): 33-40; and Walther W. and Stein U., 2000 Drugs, 60 (2): 249-71, incorporated herein by reference.
In some embodiments of the disclosure, the composition comprises one or more vectors, such as viral vectors, encoding the transgenes of one or more CRB1 isoforms. Viral vector(s) include, but are not limited to, an AAV, adenovirus, lentivirus, retrovirus, poxvirus, baculovirus, herpes simplex virus, vaccinia virus, or a synthetic virus (e.g., a chimeric virus, mosaic virus, or pseudotyped virus, and/or a virus that contains a foreign protein, synthetic polymer, nanoparticle, or small molecule).
In one embodiment, the vector or vectors are derived from a lentivirus. Lentiviral vectors are part of a larger group of retroviral vectors. A detailed list of lentiviruses may be found in Coffin et al. (1997) “Retroviruses” Cold Spring Harbor Laboratory Press Eds: J M Coffin, S M Hughes, H E Varmus pp 758-763). In brief, lentiviruses can be divided into primate and non-primate groups. Examples of primate lentiviruses include but are not limited to: the human immunodeficiency virus (HIV), the causative agent of human auto-immunodeficiency syndrome (AIDS), and the simian immunodeficiency virus (SIV). The non-primate lentiviral group includes the prototype “slow virus” Visna Maedi virus (VMV), as well as the related caprine arthritis-encephalitis virus (CAEV), equine infectious anemia virus (EIAV) and the more recently described feline immunodeficiency virus (FIV) and bovine immunodeficiency virus (BIV). Lentiviral vectors have been generated, for example, by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu and nef are deleted, making the vector safer for therapeutic purposes.
In some embodiments, the lentiviral vector is EIAV based.
In some embodiments, the lentiviral vector is HIV based. The HIV based vector may be an HIV-1, or HIV-2 based vector, such as a vector derived from HIV-1M, for example, from the BRU or LAI isolates.
Details on the genomic structure of some lentiviruses may be found in the art. By way of example, details on HIV and EIAV may be found from the NCBI Genbank database (e.g., Genome Accession Nos. AF033819 and AF033820 respectively). Details of HIV variants may also be found in the HIV databases maintained by Los Alamos National Laboratory. Details of EIAV clones may be found at the NCBI database maintained by the National Institutes of Health. Also see U.S. Pat. Nos. 7,790,419; 7,585,676; 7,419,829; 7,351,585; 7,303,910; 7,198,784; 7,070,994; 6,924,123; 6,818,209; 6,808,922; 6,800,281; 6,783,981; 6,541,248; 6,312,683; and 6,312,682.
A lentiviral vector, as used herein, is a vector which comprises at least one component part derivable from a lentivirus. That component part may be involved in the biological mechanisms by which the vector infects cells, expresses genes, or is replicated.
In some optional embodiments, vectors of the present invention are recombinant lentiviral vectors. The term “recombinant lentiviral vector” refers to a vector with sufficient lentiviral genetic information to allow packaging of an RNA genome, in the presence of packaging components, into a viral particle capable of infecting a target cell. Infection of the target cell may include reverse transcription and integration into the target cell genome. The recombinant lentiviral vector carries non-viral coding sequences which are to be delivered by the vector to the target cell. A recombinant lentiviral vector is incapable of independent replication to produce infectious lentiviral particles within the final target cell. Usually, the recombinant lentiviral vector lacks a functional gag-pol and/or env gene and/or other genes essential for replication. Optionally, the recombinant lentiviral vector of the present invention has a minimal viral genome. As used herein, the term “minimal viral genome” means that the viral vector has been manipulated so as to remove the non-essential elements and to retain the essential elements in order to provide the required functionality to infect, transduce and deliver a nucleotide sequence of interest to a target host cell.
In one embodiment, the vector or vectors are derived from or based on adeno-associated viruses (AAVs). Adeno-associated viruses (AAV), from the parvovirus family, are small viruses with a genome of single stranded DNA. Because AAV are not associated with pathogenic disease in humans, AAV vectors are able to deliver therapeutic proteins and agents to human patients without causing substantial AAV pathogenesis. The adeno-associated virus may be of any serotype, a mixture of serotypes, or variants thereof. Exemplary AAV serotypes include AAV1, AAV 2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, and AAV11. For example, when the viral transfer vector is based on a mixture of serotypes, the viral transfer vector may contain the capsid signal sequences taken from one AAV serotype (for example selected from any one of AAV serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11) and packaging sequences from a different serotype (for example selected from any one of AAV serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11).
An AAV vector, as used herein, is a vector which comprises at least one component part derivable from adeno-associated viruses. That component part may be involved in the biological mechanisms by which the vector infects cells, expresses genes, or is replicated. In some embodiments, all or a part of the viral genome has been replaced with a transgene, which is a non-native nucleic acid with respect to the AAV nucleic acid sequence. AAV vectors generally have had up to approximately 96% of the parental genome deleted, such that only the terminal repeats (ITRs), which contain recognition signals for DNA replication and packaging, remain. Thus, the AAV vector may be a recombinant AAV vector.
For a description of AAV-based vectors, see, for example, U.S. Pat. Nos. 8,679,837, 8,637,255, 8,409,842, 7,803,622, and 7,790,449, and U.S. Publication Nos. 20150065562, 20140155469, 20140037585, 20130096182, 20120100606, and 20070036757, incorporated herein by reference in their entirety.
In some embodiments, the vector(s) may be configured or modified to confer increased infectivity of one or more types of cells. In the case of two or more vectors, each vector may be configured to confer increased infectivity in the same or different cell types. In some embodiments, the vector(s) may be configured to confer increased infectivity in one or more types of retinal cells (e.g., a photoreceptor cell (e.g., rods; cones), a retinal ganglion cell (RGC), a glial cell (e.g., a Müller glial cell, a microglial cell), a bipolar cell, an amacrine cell, a horizontal cell, and/or a retinal pigmented epithelium (RPE) cell). See for example, International Patent Publication No. WO2019104279, incorporated herein by reference in its entirety.
Due to size constraints of viral genomes for packaging, the transgenes of more than one isoform of CRB1 can be engineered and packaged in two or more vectors/stocks. Whether packaged in one vector or stock which is used as a composition according to the invention, or in two or more vectors or stocks which form a virus composition of the invention, the composition collectively contains the transgenes of more than one isoform of CRB1.
In some embodiments, the composition comprises two vectors, e.g., two viral vectors, each encoding a transgene of at least one CRB1 isoform. For example, the composition may comprise a first vector encoding a first CRB1 isoform and a second vector encoding a second CRB1 isoform. In some embodiments, the composition comprises a first vector encoding a CRB1-A transgene and a second vector encoding a CRB1-B transgene, as described herein.
In some embodiments, the two viral vectors are derived from the same or different virus. For example, the two viral vectors may each be AAV-based vectors or lentivirus-based vectors. Alternatively, the first vector may be an AAV-based vector and the second vector may be a lentivirus-based vectors.
Additionally, the vector(s) may contain, for example, some or all of the following: a selectable marker gene, such as the neomycin gene for selection of stable or transient transfectants in host cells; a “suicide switch” or “suicide gene” which when triggered causes cells carrying the vector to die (e.g., HSV thymidine kinase, an inducible caspase such as iCasp9), and reporter gene for assessing expression of the chimeric receptor. Suitable vectors and methods for producing vectors containing transgenes are well known and available in the art.
In some embodiments, the viral vector may further comprise sequences which facilitate packaging into a viral vector, such as AAV inverted terminal repeats (ITRs) or lentiviral long terminal repeats (LTRs.)
In some embodiments, the viral vector further comprises an enhancer, such as the CMV enhancer. Enhancer sequences near or far, upstream or downstream, from their target promoters, contain DNA motifs that act as binding sites for transcription factors and other cofactors.
Selectable markers also include chloramphenicol resistance, tetracycline resistance, spectinomycin resistance, streptomycin resistance, erythromycin resistance, rifampicin resistance, bleomycin resistance, thermally adapted kanamycin resistance, gentamycin resistance, hygromycin resistance, trimethoprim resistance, dihydrofolate reductase (DHFR), GPT; the URA3, HIS4, LEU2, and TRP1 genes of S. cerevisiae. In some embodiments, the viral vector further comprises an antibiotic resistance marker (e.g., AmpR).
In some embodiments, a dual expression vector further comprises a sequence encoding a reporter, such as a sequence encoding a fluorescent protein (e.g., GFP, mCherry, Kusabira-Orange).
In some embodiments of the disclosure, the composition comprises one or more viral vectors, collectively encoding two or more CRB1 isoforms, wherein one or more of the two or more CRB1 isoforms are operably linked to a tissue-specific or cell type-specific control or regulatory element (e.g., a promoter). In some embodiments, each of the two or more CRB1 isoforms are operably linked to the same or different tissue-specific or cell type-specific control or regulatory element. In some embodiments, the two or more CRB1 isoforms comprise CRB1-A and CRB1-B.
In some embodiments, the composition comprises a single viral vector, encoding CRB1-A and CRB1-B, wherein one or both of CRB1-A and CRB1-B are operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, the composition comprises a single viral vector, encoding CRB1-A and CRB1-B, wherein CRB1-A is operably linked to a ubiquitous control or regulatory element and CRB1-B is operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, the composition comprises a single viral vector encoding CRB1-A and CRB1-B, wherein both CRB1-A and CRB1-B are operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, the single viral vector is derived from a lentivirus.
In some embodiments, the composition comprises two viral vectors, collectively encoding CRB1-A and CRB1-B, wherein the first viral vector encodes CRB1-A and the second viral vector encodes CRB1-B, and one or both of CRB1-A and CRB1-B are operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, the composition comprises two viral vectors, wherein the first viral vector encodes CRB1-A operably linked to a ubiquitous control or regulatory element and the second viral vector encodes CRB1-B operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, the composition comprises two viral vectors, wherein the first viral vector encodes CRB1-A and the second viral vector encodes CRB1-B, and both of CRB1-A and CRB1-B are operably linked to a tissue-specific or cell type-specific control or regulatory element. In some embodiments, at least one or both of the two viral vectors are derived from an AAV virus.
In some embodiments, the CRB1-A transgene is operably linked to a Müller glial regulatory element (e.g., a regulatory element (e.g., a promoter) that confers selective or predominantly selective expression of the operably linked gene in a Müller glial cell). In select embodiments, the Müller glial regulatory element comprises a promoter selected from: RLBP1 (Retinaldehyde Binding Protein 1), GFAP (Glial fibrillary acidic protein), GfaABC1D (a truncated GFAP promoter), and synthetic promoters ProB2 and PROC17. In select embodiments, the Müller glial regulatory element comprises a GFAP mini promoter.
In some embodiments, the composition comprises a single viral vector (e.g., lentivirus vector) comprising a CRB1-A transgene operably linked to a Müller glial regulatory element. In some embodiments, the composition comprises two viral vectors, wherein one of the viral vectors comprises a CRB1-A transgene operably linked to a Müller glial regulatory element.
In some embodiments, the CRB1-B transgene is operably linked to a photoreceptor regulatory element (e.g., a regulatory element that confers selective or predominantly selective expression of the operably linked gene in a photoreceptor cell). Suitable photoreceptor-specific regulatory elements include, but are not limited to, a rhodopsin promoter; a rhodopsin kinase promoter; a beta phosphodiesterase gene promoter; a retinitis pigmentosa gene promoter; an interphotoreceptor retinoid-binding protein (IRBP) gene enhancer; an IRBP gene promoter, an opsin gene promoter, a retinoschisin gene promoter, a CRX homeodomain protein gene promoter, a guanine nucleotide binding protein alpha transducing activity polypeptide 1 (GNAT1) gene promoter, a neural retina-specific leucine zipper protein (NRL) gene promoter, human cone arrestin (hCAR) promoter, and the PR2.1, PR1.7, PR1.5, and PR1.1 promoters. In select embodiments, the photoreceptor-specific regulatory element comprises a promoter selected from: interphotoreceptor retinoid-binding protein (IRBP), cone arrestin (CAR), rhodopsin (RHO), PR1.7 (a truncated version of version of the L-opsin promoter), synthetic promoters: ProA1, ProA6, ProC1, ProA14, and ProA36, and G protein-coupled receptor kinase 1 (GRK1). In select embodiments, the photoreceptor-specific regulatory element comprises a GRK1 mini promoter.
In some embodiments, the composition comprises a single viral vector (e.g., lentivirus vector) comprising a CRB1-B transgene operably linked to a photoreceptor regulatory element. In some embodiments, the composition comprises two viral vectors, wherein one of the viral vectors comprises a CRB1-B transgene operably linked to a photoreceptor regulatory element.
The current disclosure provides for compositions containing a recombinant lentivirus containing a nucleic acid that encodes CRB1-A and CRB1-B on the same dual expression vector under control of separate promoters that induce expression of the transgenes in the proper cells, e.g., CRB1-A in a Müller glial cells and CRB1-B in photoreceptor cells.
An exemplary CRB1 Isoform Dual Expression Vector is shown in
In some embodiments, a dual expression vector comprises, from 5′ to 3′, a sequence encoding a first CRB1 isoform and a second CRB1 isoform. In some embodiments, the first and second CRB1 isoforms are independently selected from CRB1-A and CRB1-B. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a sequence encoding a CRB1-A transgene and a sequence encoding a CRB1-B transgene. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a sequence encoding a CRB1-B transgene and a sequence encoding a CRB1-A transgene.
In some embodiments, a dual expression vector comprises, from 5′ to 3′, a first promoter, a sequence encoding a CRB1-A transgene, a second promoter, and a sequence encoding a CRB1-B transgene. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a first promoter, a sequence encoding a CRB1-B transgene, a second promoter, and a sequence encoding a CRB1-A transgene. In some embodiments, the CRB1-A transgene is a human CRB1-A transgene. In some embodiments, the CRB1-B transgene is a human transgene. In some embodiments, the CRB1-A transgene is a human CRB1-A transgene and the CRB1-B transgene is a human transgene.
In some embodiments, the CRB1-A transgene comprises one or more amino acid mutations relative to the human CRB1-A sequence. In some embodiments, the CRB1-B transgene comprises one or more amino acid mutations relative to the human CRB1-B sequence. In some embodiments, both the CRB1-A transgene and the CRB1-B transgene comprise one or more amino acid mutations relative to their respective human sequences.
In some embodiments, a dual expression vector further comprises an enhancer, such as the CMV enhancer.
In some embodiments, a dual expression vector further comprises a sequence encoding a reporter, such as a sequence encoding GFP or mCherry.
In some embodiments, a dual expression vector further comprises sequences which facilitate packaging into a viral vector, e.g., lentiviral long terminal repeats (LTRs.)
In some embodiments, a dual expression vector comprises, from 5′ to 3′, a first lentiviral LTR, a sequence encoding a CRB1-A transgene, a sequence encoding a CRB1-B transgene, and a second lentiviral LTR. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a sequence encoding a first lentiviral LTR, a CRB1-B transgene, a sequence encoding a CRB1-A transgene, and a second lentiviral LTR. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a first lentiviral LTR, a first promoter, a sequence encoding a CRB1-A transgene, a second promoter, a sequence encoding a CRB1-B transgene, and a second lentiviral LTR. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a first lentiviral LTR, a first promoter, a sequence encoding a CRB1-B transgene, a second promoter, a sequence encoding a CRB1-A transgene, and a second lentiviral LTR.
In some embodiments, a dual expression vector, as described herein, does not include any heterologous control or regulatory sequences, as described above, between the two CRB1 transgenes. For example, in some embodiments, a dual expression vector comprises, from 5′ to 3′, a sequence encoding a first CRB1 isoform operably linked to a promoter and a second CRB1 isoform operably linked to a promoter without any heterologous control or regulatory sequences (e.g., polyadenylation sequence) between the two transgenes, e.g., 3′ of the sequence encoding a first CRB1 isoform and 5′ of the promoter of a second CRB1 isoform. Exclusion of heterologous control or regulatory sequences between the two transgenes may confer increased expression of one or both of the transgenes compared to a vector including heterologous control or regulatory sequences between the two transgenes. Alternatively or additionally, exclusion of heterologous control or regulatory sequences between the two transgenes may decrease gene truncation events of one or both of the transgenes.
In some embodiments, a dual expression vector, as described herein, includes endogenous, or viral vector derived, control, regulatory, or packaging sequences between the two CRB1 transgenes. In some embodiments, a dual expression vector comprises, from 5′ to 3′, a sequence encoding a first CRB1 isoform operably linked to a promoter and a second CRB1 isoform operably linked to a promoter, separated by endogenous, or viral vector derived, control, regulatory, or packaging sequences. In some embodiments, the endogenous, or viral vector derived, transcription or translational regulatory or packaging sequences include a sequence comprising a central polypurine tract (cPPT) with downstream central termination sequence (CTS).
The compositions may further comprise excipients or pharmaceutically acceptable carriers. The choice of excipients or pharmaceutically acceptable carriers will depend on factors including, but not limited to, the particular mode of administration, the effect of the excipient on solubility and stability, and the nature of the dosage form.
Excipients and carriers may include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents. Some examples of materials which can serve as excipients and/or carriers are sugars including, but not limited to, lactose, glucose and sucrose; starches including, but not limited to, corn starch and potato starch; cellulose and its derivatives including, but not limited to, sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients including, but not limited to, cocoa butter and suppository waxes; oils including, but not limited to, peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols; including propylene glycol; esters including, but not limited to, ethyl oleate and ethyl laurate; agar; buffering agents including, but not limited to, magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants including, but not limited to, sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants. The compositions of the present invention and methods for their preparation will be readily apparent to those skilled in the art. Techniques and formulations may be found, for example, in Remington's Pharmaceutical Sciences, 19th Edition (Mack Publishing Company, 1995).
Patients who would benefit from the administration of the described compositions include those diagnosed with a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA).
In some embodiments, the present disclosure provides methods of treating, preventing, curing, and/or reducing the severity or extent of a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) by administering to a subject in need thereof a therapeutically effective amount of a composition as described herein. For example, The methods may comprise administering a viral vector or vectors, comprising a nucleic acid encoding more than one isoform of CRB1, such as CRB1-A and CRB1-B. In some embodiments, the methods comprise administering to a subject in need thereof a dual expression vector, as described herein.
In some embodiments, the methods comprise administering to a subject in need thereof a composition comprising more than one vector, each vector comprising at least one isoform of CRB1. For example, the composition may comprise a first vector encoding a first CRB1 isoform and a second vector encoding a second CRB1 isoform. In some embodiments, the methods comprise administering to a subject in need thereof a composition comprising a first vector encoding a CRB1-A transgene and a second vector encoding a CRB1-B transgene, as described herein.
In some embodiments, the composition (e.g., viral vector or vectors) comprising a nucleic acid encoding more than one isoform of CRB1, such as CRB1-A and CRB1-B, is administered as soon as the disease or disorder is characterized by CRB1 mutations. The disease or disorder may include, but is not limited to, autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA).
In some embodiments, the present disclosure provides methods of treating, preventing, curing, and/or reducing the severity or extent of a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) by administering to a subject in need thereof a therapeutically effective amount of a composition, such as a viral vector, comprising a nucleic acid encoding an isoform of CRB1, such as CRB1-A or CRB1-B, configured to allow expression of the CRB1 isoform in more than one retinal cell type (e.g., Müller glial cells and photoreceptor cells).
In some embodiments, the composition comprises a viral vector encoding CRB1-A. In some embodiments, the composition comprises a viral vector encoding CRB1-B. In some embodiments, the transgenes and vector are configured to allow expression in Müller glial cells and photoreceptor cells.
The current disclosure provides for compositions and vectors for use in methods of treating, preventing, and/or curing a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) and/or alleviating in a subject at least one of the symptoms associated with a disease or disorder characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA). In some embodiments, methods involve administration of the compositions and vectors, in a pharmaceutically acceptable carrier to the subject in an amount and for a period of time sufficient to treat, prevent and/or cure the characterized by CRB1 mutations including but not limited to autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA).
In certain embodiments, the route of administration is subretinal injection or intravitreal injection.
The vector can be formulated into a pharmaceutical composition intended for subretinal or intravitreal injection. Such formulation involves the use of a pharmaceutically and/or physiologically acceptable vehicle or carrier, particularly one suitable for administration to the eye, e.g., by subretinal injection, such as buffered saline or other buffers, e.g., HEPES, to maintain pH at appropriate physiological levels, and, optionally, other medicinal agents, pharmaceutical agents, stabilizing agents, buffers, carriers, adjuvants, diluents, etc. For injection, the carrier will typically be a liquid. Exemplary physiologically acceptable carriers include sterile, pyrogen-free water and sterile, pyrogen-free, phosphate buffered saline.
In one embodiment, the carrier is an isotonic sodium chloride solution. In another embodiment, the carrier is balanced salt solution. In one embodiment, the carrier includes tween. If the virus is to be stored long-term, it may be frozen in the presence of glycerol or Tween-20.
In another embodiment, the pharmaceutically acceptable carrier comprises a surfactant, such as perfluorooctane (Perfluoron liquid). In certain embodiments, the pharmaceutical composition described above is administered to the subject by subretinal injection. In other embodiments, the pharmaceutical composition is administered by intravitreal injection.
Other forms of administration that may be useful in the methods described herein include, but are not limited to, direct delivery to a desired organ (e.g., the eye), oral, inhalation, intranasal, intratracheal, intravenous, intramuscular, subcutaneous, intradermal, and other parental routes of administration. Additionally, routes of administration may be combined, if desired.
Suitable carriers may be readily selected by one of skill in the art in view of the indication. For example, one suitable carrier includes saline, which may be formulated with a variety of buffering solutions (e.g., phosphate buffered saline). Other exemplary carriers include sterile saline, lactose, sucrose, calcium phosphate, gelatin, dextran, agar, pectin, peanut oil, sesame oil, and water. The selection of the carrier is not a limitation of the present invention.
Optionally, the compositions may contain, in addition to the vector and carrier(s), other conventional pharmaceutical ingredients, such as preservatives, or chemical stabilizers. Suitable exemplary preservatives include chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, parabens, ethyl vanillin, glycerin, phenol, and parachlorophenol. Suitable chemical stabilizers include gelatin and albumin.
Formulation of pharmaceutically acceptable excipients and carrier solutions is well-known to those of skill in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens. Typically, these formulations may contain at least about 0.1% of the active ingredient or more, although the percentage of the active ingredient(s) may, of course, be varied and may conveniently be between about 1% or 2% and about 70% or 80% or more of the weight or volume of the total formulation. Naturally, the amount of active ingredient in each therapeutically useful composition may be prepared in such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.
The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms. In many cases the form is sterile and fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
For administration of an injectable aqueous solution, for example, the solution may be suitably buffered, if necessary, and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous, and intraperitoneal administration. In this connection, a sterile aqueous medium that can be employed will be known to those of skill in the art. For example, one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion. Some variation in dosage will necessarily occur depending on the condition of the host. The person responsible for administration will, in any event, determine the appropriate dose for the individual host.
Sterile injectable solutions are prepared by incorporating the active vector in the required amount in the appropriate solvent with various of the other ingredients enumerated herein, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
The present invention provides stable pharmaceutical compositions comprising virions. The compositions remain stable and active even when subjected to freeze/thaw cycling and when stored in containers made of various materials, including glass.
Appropriate doses will depend on the subject being treated (e.g., human or nonhuman primate or other mammal), age and general condition of the subject to be treated, the severity of the condition being treated, the mode of administration of the vector, among other factors. An appropriate effective amount can be readily determined by one of skill in the art.
The dose of vector required to achieve a desired effect or “therapeutic effect,” e.g., the units of dose in vector genomes/per kilogram of body weight (vg/kg), will vary based on several factors including, but not limited to: the route of administration; the level of gene or RNA expression required to achieve a therapeutic effect; the specific disease or disorder being treated; and the stability of the gene or RNA product. An effective amount is generally in the range of from about 10 μl to about 100 ml of solution containing from about 109 to 1016 genome copies per subject. Other volumes of solution may be used. The volume used will typically depend, among other things, on the size of the subject, the dose, and the route of administration.
Dosage treatment may be a single dose schedule or a multiple dose schedule to ultimately deliver the amount specified above. Moreover, the subject may be administered as many doses as appropriate.
Pharmaceutical compositions will thus comprise sufficient genetic material to produce a therapeutically effective amount of the protein of interest, e.g., an amount sufficient to reduce or ameliorate symptoms of the disease state in question or an amount sufficient to confer the desired benefit. Thus, the vector will be present in the subject compositions in an amount sufficient to provide a therapeutic effect when given in one or more doses.
Toxicity and therapeutic efficacy of the therapeutic compositions, administered alone or in combination with another agent, can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index (LD50/ED50). In particular aspects, therapeutic compositions exhibiting high therapeutic indices are desirable. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration.
Determination of the appropriate dose is made by the clinician, e.g., using parameters or factors known or suspected in the art to affect treatment. Generally, the dose begins with an amount somewhat less than the optimum dose and it is increased by small increments thereafter until the desired or optimum effect is achieved relative to any negative side effects. Important diagnostic measures include those of symptoms of, e.g., the inflammation or level of inflammatory cytokines produced. In general, it is desirable that a biologic that will be used is derived from the same species as the animal targeted for treatment, thereby minimizing any immune response to the reagent.
The present invention may be better understood by reference to the following non-limiting examples, which are presented in order to more fully illustrate the preferred embodiments of the invention. They should in no way be construed to limit the broad scope of the invention.
It was found that approximately 70% of novel CRB1 patient mutations affect both CRB1-A and CRB1-B (
Using in situ hybridization (Basescope), isoform specific distribution of CRB1-A, B and C was found in the human donor retina and human retinal organoids (ROs) (
A probe which targeted all three isoforms at exon 6 (PAN-CRB1) localized in both the ONL and the INL as well as the inner segments of the photoreceptor. The CRB1-A probe targeted exon 12 (
The CRB1-B probe targeted its unique exon 1. The signal for CRB1-B was primarily expressed in the ONL and inner segments and to a lesser extent the INL.
The CRB1-C probe targeted its unique exon 6. The signal was localized in both the ONL and INL and to a lesser extent than CRB1-B in the inner segments.
The expression patterns of CRB1-B and CRB1-C appear more evenly distributed between the ONL and INL of maturating retinal organoids.
Thus, it was determined that CRB1-A is predominantly expressed in Müller glial cells and CRB1-B in photoreceptor cells.
Additionally, the phenotypes observed in CRB1 LCA ROs are similar to those exhibited in patients suffering from LCA (
Using the information in Example 1 that CRB1-A is predominantly expressed in Müller glial cells and CR1-B in photoreceptor cells, a dual expression vector was designed which mediates concomitant CRB1-A and CRB1-B expression to their predominately expressed cell types as found in wild-type retina.
CRB1-A, which is predominantly expressed in Müller glial cells, is linked to promoters including but not limited to RLBP1, GFAP, and PROC17. CRB1-B, which is predominantly expressed in photoreceptor cells, is linked to promoters including but not limited to IRBP and GRK1. See
An alternative approach targets both isoforms concomitantly to both cell types using ubiquitous promoters such as CMV, EF1, CAG, and SFFV. Both isoforms along with cell type specific or ubiquitous promoters along with post-transcriptional regulatory elements (e.g., WPRE) and polyadenylation sequences for efficient pre-mRNA processing (e.g., SV40) is placed in HIV and EIAV lentiviral based vectors for testing.
Previous work has produced multiple CRB1-A lentiviral based vectors (
An alternative approach targets both isoforms concomitantly to both cell types using mini promoters such as a GRK1 mini promoter for expression in photoreceptor cells and a GFAP mini promoter for expression in Müller glial cells, as exemplified in
Three CRB1 patients, all having mutations that affect CRB1-A and CRB1-B (Table 1 and 2), have been recruited. Induced pluripotent stem cells and retinal organoids have been derived from P001 and P002 (Table 1). CRB1 patient derived retinal organoids have a phenotype, the failure in biosynthesis of photoreceptor outer segments, which can be used as an outcome measurement for therapeutic efficacy. See
As an additional strategy, CRB1 null iPSCs are generated for their derivation to CRB1 Null retinal organoids. These can be utilized as optimal model for testing CRB1 gene augmentation. See
Previous studies have demonstrated that ROs can be generated from CRB1 Retinitis pigmentosa patient derived iPSCs and that these ROs exhibit a morphological phenotype of outer limiting membrane disruptions (OLM) and ectopic photoreceptor localization. To test this hypothesis, patient iPSCs were used to generate CRB1 LCA retinal organoids (ROs). Initial data suggest that the phenotypes observed in CRB1 RP and LCA organoids are similar to those exhibited in patients and that the therapeutic agents can successfully target ROs. These data align with the hypothesis that patient iPSC ROs will be clinically-relevant recipients of therapeutic agents. The rationale for this project is that iPSC ROs recapitulate both human retinal development and the naive protein expression patterns of CRB1 and also phenocopy retinal disease pathogenesis, rendering them an excellent tool for understanding disease mechanisms and a platform for testing therapeutic strategies.
The following vectors are administered to the retinal organoids generated from patients with either RP or LCA described in Example 3:
The same vectors are also administered to rat models of disease both via subretinal injection or intravitreal injection.
Both the ROs and the rats are assessed for the following:
The dual expression vectors show greater improvement in morphology, function, and survival than either single expression vector. Moreover, as expected only the ROs or rats that received the dual expression vector expressed both of the wild-type isoforms. The CRB1 isoforms are expressed in the correct cells when the dual expression vector is administered.
As an additional model, a mouse model of spontaneous retinal vascularization JR5558 B6. Cg-Crb1rd8Jak3mIJ/Boc mice (Chang, et al., Invest Ophthalmol Vis Sci. 2018; 59:5127-5139, incorporated herein by reference in its entirety), which shows diminished ERG from 2 months of age, are utilized in a similar manner to the rat model described above.
RNA in-situ hybridization was performed using CRB1 isoform-specific probes in human cadaveric retina (
Viral delivery to the sub-retinal space of one or more isoforms of human CRB1 to their predominately cell-specific localization may halt or slow the diseases progression exhibited in the Crb1-associated inherited retinal disease mouse models (B6.Cg-Crb1rd8 Jak3m1J/BocJ). Using the subretinal injection route, AAV2/9-mediated delivery of codon-optimized CRB1-A (including a spiking construct 1/10, with AAV2/9.sCMV.GFP) or CRB1-B cDNAs alone or concomitantly (including a spiking construct 1/10, with AAV2/9.sCMV.GFP) in C57BL6/J and B6.Cg-Crb1rd8 Jak3m1J/BocJ mice were assessed (
Immunostaining from mouse number 217 injected with CRB1-A and CRB1-B in a Crb1 mouse model at 6-months timepoint is shown in
Differences in localization of all three CRB1 isoforms were found in human cadaveric retina. CRB1-A and CRB1-B predominately localized to different cell types, Müller glial cells and photoreceptors, respectively. Using CRB1-A and CRB1-B gene augmentation vectors, overexpression of CRB1-A and CRB1-B was safe and tolerable.
This application is a continuation of International Application No. PCT/US2023/068529, filed Jun. 15, 2023, which claims the benefit of U.S. Provisional Application Nos. 63/352,462, filed Jun. 15, 2022, and 63/498,379, filed Apr. 26, 2023, the contents of which are herein incorporated by reference in their entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63498379 | Apr 2023 | US | |
| 63352462 | Jun 2022 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US2023/068529 | Jun 2023 | WO |
| Child | 18981112 | US |
