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WO2024171063A1 - Nucleic acids encoding bcl2-associated athanogene 3 (bag3) for gene therapy - Google Patents

Nucleic acids encoding bcl2-associated athanogene 3 (bag3) for gene therapy
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WO2024171063A1
WO2024171063A1PCT/IB2024/051345IB2024051345WWO2024171063A1WO 2024171063 A1WO2024171063 A1WO 2024171063A1IB 2024051345 WIB2024051345 WIB 2024051345WWO 2024171063 A1WO2024171063 A1WO 2024171063A1
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raav vector
bag3
nucleotide sequence
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sequence
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Nicolas CHRISTOFOROU
Suryanarayan SOMANATHAN
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AstraZeneca Ireland Ltd
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Abstract

The present disclosure relates to recombinant nucleic acids and gene therapy vectors comprising a nucleic acid encoding a Bcl2-associated anthanogene3 (BAG3) polypeptide, and variants thereof, for use in the treatment of cardiac-related diseases and disorders, including those associated with a deficiency or dysfunction of BAG3, such as dilated cardiomyopathy (DCM), and those not associated with a deficiency or dysfunction of BAG3, such as heart failure unrelated to BAG3 expression.

Description

NUCLEIC ACIDS ENCODING BCL2-ASSOCIATED ATHANOGENE 3 (BAG3) FOR GENE THERAPY
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of priority of U.S. Provisional Patent Application No. 63/484,630, filed February 13, 2023, and U.S. Provisional Patent Application No. 63/501 ,898, filed May 12, 2023, the entire contents of each of which are incorporated herein by reference, including all text, tables, and drawings.
REFERENCE TO SEQUENCE LISTING
This application is being filed electronically and includes an electronically submitted sequence listing. The sequence listing is entitled “24-0147-WO_SequenceListing.xml” and was created on February 13, 2024, and has a size of 67,384 bytes. The sequence listing contained in this .xml file is part of the specification and is herein incorporated by reference in its entirety.
BACKGROUND
Bcl2-associated athanogene 3 (BAG3) has been implicated in a diverse array of cellular functions, including but not limited to excitation-contraction coupling, maintenance of sarcomere integrity, and regulation of autophagy (Kirk et al., J. Clin. Invest. 131 (16): e149415 (2021)). BAG3 has four protein-protein binding domains and acts through binding interactions with a range of other proteins (Qu et al., J. Am. Heart Assoc. 11 (23): e027373 (2022)). Various functions of BAG3 are thought to be protective in cardiomyocytes, including modulation of apoptosis, protein homeostasis, mitochondrial stability, myocardial contraction, and heart rhythm (Liu et al., Heart Fail. Rev. 26(1): 183-94 (2021)).
Mutations in BAG3 have been associated with dilated cardiomyopathy (DCM) in humans (Myers et al., JAMA Cardiol. 3(10): 929-38 (2018)). BAG3-associated DCM (BAG3 DCM) is an autosomal dominant primary DCM. It is not associated with other systemic involvement (non-syndromic). Patients with BAG3 DCM present with severely reduced heart function and moderate to severe symptoms of heart failure. BAG3 DCM is characterized by an early heart failure presentation (80% of genotype-positive patients older than age 40 exhibit DCM), with a high incidence of heart failure in genotype-positive, phenotype-negative patients (26.1 % in approximately 2 years follow-up) and poor prognosis once heart failure symptoms present as demonstrated by a 5.1% per year rate of death or major cardiovascular events (LVAD implantation, heart transplant or SCD or equivalent). At present, heritable DCM patients lack precision medicines to address their underlying pathophysiology and therapies remain undifferentiated from guideline-directed medical therapy (GDMT) for heart failure with reduced ejection fraction (HFrEF). The implementation of GDMT and device therapy for heart failure in DCM patients have improved overall prognosis. However, DCM patients face a persistently high unmet medical need. BAG3 DCM is a rare clinical indication with an estimated genetic prevalence of approximately 1% of all DCM patients, based on the literature, who could benefit from a gene therapy treatment.
In addition to DCM and heart disease in general, BAG3 is a multifunctional protein that is involved in cell stress response through its participation in several regulatory pathways, which control cell homeostatic response in physiological and pathological conditions. Thus, there is a need for treatment of any disease or disorder mediated by or associated with decreased expression and/or activity of BAG3, and where a moderate increase in protein expression of BAG3 can lead to alleviation of a disease phenotype. Provided herein are tools and methods that function in human cells for precise administration of BAG3. The compositions and methods provided herein can modulate BAG3 levels, target diseases, and serve as the basis of curative therapies for many previously untreatable diseases and/or disorders, including but not limited to dilated cardiomyopathy.
SUMMARY OF THE DISCLOSURE
The disclosure provides a gene therapy that delivers BAG3 protein expression to a desired target tissue (e.g., cardiac tissues). In some embodiments, the therapy can be used for the treatment of cardiac-related diseases or disorders, including, for example, cardiac- related diseases or disorders associated with a deficiency or dysfunction of BAG3. It is also intended for the treatment of cardiac-related diseases or disorders not associated with a deficiency or dysfunction of BAG3. Examples of cardiac-related diseases or disorders associated with a deficiency or dysfunction of BAG3 include, for example, BAG3-associated dilated cardiomyopathy (DCM), and BAG3-associated heart failure. Examples of cardiac- related diseases or disorders not associated with a deficiency or dysfunction of BAG3 include, for example, heart failure unrelated to BAG3 expression.
In one aspect, the disclosure provides a nucleic acid molecule comprising a nucleotide sequence encoding a Bcl2-associated athanogene 3 (BAG3) polypeptide, or variant thereof.
In another aspect, the disclosure provides a recombinant adeno-associated virus (rAAV) vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof.
In another aspect, the disclosure provides an rAAV vector comprising, in 5’ to 3’ order: (a) at least one 5’ ITR sequence; (b) at least one cardiac promoter; (c) at least one intron; (d) at least one nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, operably linked to the at least one cardiac promoter; (e) at least one transcription terminator sequence; (f) at least one stutter or filler sequence; and (g) at least one 3’ ITR sequence.
In another aspect, the disclosure provides an rAAV vector plasmid comprising, in 5’ to 3’ order: (a) at least one left spacer sequence; (b) the at least one 5’ ITR sequence; (c) the at least one cardiac promoter; (d) the at least one intron; (e) the at least one nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, operably linked to the at least one cardiac promoter; (f) the at least one transcription terminator sequence; (g) the at least one stuffer or filler sequence; (h) the at least one 3’ ITR sequence; and (i) at least one right spacer sequence.
In another aspect, the disclosure provides a pharmaceutical composition comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, or an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, and at least one pharmaceutically acceptable salt.
In another aspect, the disclosure provides a method for treating a cardiac-related disease or disorder in a subject, the method comprising administering to the subject a therapeutically effective amount of: (a) a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof; or (b) an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof; or (c) a pharmaceutical composition comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, or an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, and at least one pharmaceutically acceptable salt.
In another aspect, the disclosure provides a method for reducing the frequency or severity of at least one symptom associated with a cardiac-related disease or disorder in a subject, the method comprising administering to the subject: (a) a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof; or (b) an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof; or (c) a pharmaceutical composition comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, or an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, and at least one pharmaceutically acceptable salt; in an amount effective to reduce the frequency or severity of the at least one symptom.
In another aspect, the disclosure provides the use of a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
In another aspect, the disclosure provides the use of an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
In another aspect, the disclosure provides the use of a pharmaceutical composition comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, or an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof, and at least one pharmaceutically acceptable salt, in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
In another aspect, the disclosure provides a plasmid comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof. The disclosure also provides a host cell for rAAV vector production comprising such a plasmid.
In another aspect, the disclosure provides a plasmid comprising an rAAV vector comprising a nucleic acid molecule comprising a nucleotide sequence encoding a BAG3 polypeptide, or variant thereof. The disclosure also provides a host cell for rAAV vector production comprising such a plasmid.
In another aspect, the disclosure provides a method of making an rAAV vector comprising: (a) incubating a host cell for rAAV vector production under conditions sufficient to allow the production of rAAV vectors; and (b) purifying the rAAV vectors produced thereby. The disclosure also provides an rAAV vector produced by such method.
These and other features and advantages of the present disclosure will be more fully understood from the following detailed description taken together with the accompanying claims. It is noted that the scope of the claims is defined by the recitations therein and not by the specific discussion of features and advantages set forth in the present description.
BRIEF DESCRIPTION OF THE FIGURES
The accompanying drawings are included to provide a further understanding of the methods and compositions of the disclosure. The drawings illustrate one or more embodiments of the disclosure, and together with the description serve to explain the principles and operation of the disclosure.
FIG. 1 depicts an exemplary potency evaluation of Compound A (multiplicity of infection (MOI): 3E4, 1 E5, 3E5 vg/cell) in HiPSC-CM, based on detection of transgene mRNA (ddPCR) and total BAG3 protein (Wes™ (automated capillary-based immunoassay)).
FIG. 2 depicts an exemplary potency evaluation of Compound A in HiPSC-CM, based on knockdown of endogenous BAG3 using siRNA resulting in HSPB8 destabilization. Cells were subsequently transduced with AAVs (MOI: 1 E5, 3E5 vg/cell), driving BAG3 expression and resulting in stabilization of HSPB8.
FIG. 3A-3F depict an exemplary biodistribution and expression evaluation of human BAG3 in wild-type mice (C57BL/6J) following administration of Compound A at 3- and 8- weeks post dosing. Dose: 3E13 vg/kg (n:12, male), control (n:12). Note: 6 mice were sacrificed at 3-weeks and 6 mice were sacrificed at 8-weeks post dosing. FIG.3A depicts exemplary longitudinal body weight measurements for the two groups. FIG. 3B depicts exemplary viral genome biodistribution in the heart at 3- and 8-weeks (left graph) and the heart, skeletal muscle (quadriceps), liver at 8-weeks post dosing (right graph). FIG. 3C depicts exemplary transgene expression (mRNA) in heart, skeletal muscle (quadriceps), and liver at 8-weeks post dosing. Normalized to murine TBP gene expression levels. FIG. 3D depicts exemplary human only BAG3 protein expression in the heart, skeletal muscle and liver (left panel). Total BAG3 expression (mouse endogenous & human transgene) in the heart (right panel). FIG. 3E depicts exemplary ejection fraction and left ventricular end diastolic volume determined using echocardiography at 4- and 7-weeks post dosing. FIG. 3F depicts exemplary spatial biodistribution of transgene determined using immunohistochemistry (antibody specific for human specific BAG3) at 3- and 8-weeks post dosing.
FIG. 4A-4H depict exemplary characterization of mouse disease model. FIG. 4A-4B depicts exemplary ejection fraction and left ventricular end diastolic volume data measured using echocardiography in a cohort of mice with complete cardiac specific knockdown of BAG3 (BAG3 cKO, n: 10) and wild-type control (n :10). A mixed effects model with an AR(1) covariance structure was implemented to compare the genotypes (BAG3 cKO vs. WT control). # denotes statistical significance (p<0.05). FIG. 4C depicts exemplary longitudinal body weight measurements. FIG. 4D-4E depict exemplary BAG3 and HSPB8 protein expression levels quantified in the heart, liver, and skeletal muscle (quadriceps). # denotes statistical significance (p<0.05). FIG. 4F-4G depict exemplary biomarkers of heart failure (Nppa, Nppb, Myh7/Myh6 ratio) and fibrosis (Col1a1 , Col1a2, Postn, Fn1 , Timpl) quantified at the mRNA level (qRT-PCR) using RNA collected from heart tissue. # denotes statistical significance (p<0.05). FIG. 4H depicts an exemplary proportion of fibrotic area determined using Picrosirius red staining.
FIG. 5A-5K depict an exemplary in vivo dose response study to determine effective dose and transgene expression associated with efficacy in mouse model of disease. cKO control mice (n:20), Compound A 1 E13 vg/kg (n:15), Compound A 3E13 vg/kg (n:14), Compound A 9E13 vg/kg (n:14), wild-type control (n:20). FIG. 5A-5B depict exemplary ejection Fraction (EF, %) and Left Ventricular End Diastolic Volume (LVEDV, uL) data determined using echocardiography 4-, 8-, and 12-weeks post dosing. A longitudinal mixed effects model was implemented to test the % change from baseline of EF and LVEDV over the course of the study while controlling for sex. # denotes statistical significance (p<0.05). FIG. 5C depicts exemplary longitudinal body weight measurements (male). A longitudinal mixed effects model with an AR(1) covariance structure was implemented to compare body weights over the course of the study. FIG. 5D depicts exemplary tissue-specific biodistribution of Compound A as determined by measuring viral genomes (ddPCR) in heart, liver, and skeletal muscle tissue collected at necropsy. FIG. 5E depicts exemplary tissuespecific expression of Compound A as determined by measuring mRNA expression (RT- ddPCR) in heart, liver, and skeletal muscle tissue collected at necropsy. FIG. 5F depicts exemplary quantification of BAG3 protein expression in the heart (mouse endogenous + human transgene, Simple Western). FIG. 5G depicts exemplary quantification of HESPB8 protein expression in the heart (Simple Western). FIG. 5H depicts exemplary quantification of human BAG3 protein expression in the heart (LCMS). FIG. 5I-5J depict exemplary spatial biodistribution expression analysis of transgene mRNA (/n situ hybridization, ISH) and transgene protein (immunohistochemistry, IHC). FIG. 5K depicts exemplary biomarkers of heart failure (Nppa, Myh7/Myh6 ratio) and fibrosis (Postn) measured (qRT-PCR) in heart tissue of wild-type control mice, BAG3 cKO control mice or BAG3 cKO mice treated with Compound A at 3E13 vg/kg or 9E13 vg/kg. Statistical significance was determined using one-way ANOVA. * denotes statistical significance (p<0.05).
FIG. 6A-6F depict exemplary biodistribution and expression evaluation of human BAG3 in non-human primates (NHPs, Macaca fascicularis) following administration of Compound A. Doses: 4E13 vg/kg (n: 2, male & female), 1 .3E14 vg/kg (n:2 male & female), vehicle control (n:2, male & female). Note: It was determined that the female animal dosed with the 1.3E14 vg/kg dose seroconverted before dosing resulting in very low biodistribution and transgene expression. Data from this animal was excluded from panels. FIG. 6A depicts exemplary biodistribution of viral genomes in three cardiac regions (R11 , R12, R13), liver (right medial lobe), dorsal root ganglia (DRG, thoracic), spinal cord (thoracic), skeletal muscle (gastrocnemius), and testis or ovary. FIG. 6B-6C depict exemplary transgene mRNA expression levels normalized to endogenous HPRT or endogenous BAG3 gene expression levels measured in three cardiac regions (R11 , R12, R13), liver (right medial lobe), dorsal root ganglia (DRG, thoracic), spinal cord (thoracic), and skeletal muscle (gastrocnemius). FIG. 6D depicts exemplary spatial cardiac biodistribution of transgene mRNA (proportion of positive cardiomyocytes) as determined by in situ hybridization (ISH, RNAScope). FIG. 6E- 6F depict exemplary BAG3 protein expression levels in the heart measured using Liquid Chromatography-Mass Spectrometry (LCMS) in three cardiac regions (R11 , R12, R13), liver (right medial lobe), dorsal root ganglia (DRG, thoracic), spinal cord (thoracic), and skeletal muscle (gastrocnemius). Quantification of total BAG3 determined using a peptide conserved to both human and cynomolgus BAG3. Quantification of human BAG3 determined using a peptide specific to the human protein.
FIG. 7 depicts exemplary LCMS data demonstrating dose-dependent increase of human BAG3 protein localized in purified heart sarcomeres of cynomolgus monkeys treated with Compound A.
FIG. 8 depicts exemplary immunohistochemistry data for human BAG3 protein in hearts of individual WT mice dosed with Compound A at 3- and 8-weeks post dose.
FIG. 9 depicts exemplary in situ hybridization data for human BAG3 mRNA shown as brown granules in heart, liver and DRG (from left to right) of individual WT mice treated with Compound A at 8 weeks post dose. Skeletal muscle (not shown) was negative.
FIG. 10 depicts exemplary H&E, immunohistochemistry, and in situ hybridization for human BAG3 protein and mRNA in hearts of cKO mice treated with Compound A.
FIG. 11A-11 B depict exemplary liver enzyme (ALT) elevation at > 4E13 vg/kg (FIG. 11 A) and cytokine (TNF) response at 1.3E14 vg/kg (FIG. 11B).
FIG. 12 depicts exemplary in situ hybridization for human BAG3 RNA in hearts of cyno treated with Compound A.
FIG. 13A-13D depict exemplary determination of target therapeutic level of BAG3 expression. Change in Ejection Fraction in BAG3-cKO mice treated with Compound A as a function of BAG3 protein (FIG. 13A) and ISH-based BAG3-mRNA cardiomyocyte coverage (FIG. 13B). Circles denote observed results for individual animals. Change in Ejection Fraction in BAG3-cKO mice treated with Compound A in bins of BAG3 expression - BAG3 protein (FIG. 13C) and ISH-based BAG3-mRNA cardiomyocyte coverage (FIG.13D). Mice that had >20% protein expression or ISH+ cardiomyocyte coverage had a better ejection fraction change than mice that had <20% expression but were comparable to mice that had >40% expression suggesting saturation of cardiac function response above 20% BAG3 protein/ISH-based expression. Group mean comparisons used the unpaired two-sample t- test. N for each binned expression group is indicated below the respective box-plots. ** = p<0.01 and ns = p>0.05.
Figure 14A-14C depict exemplary determination of human efficacious dose for Compound A. FIG. 14A depicts exemplary dose-dependence of Compound A heart transduction measured as VCN/dge in cynomolgus monkeys (blue triangles) is consistent with historical data-based QSP model projection (black line). Historical literature/in-house data for AAV9 heart transduction is also shown for comparison. Note that the model prediction that human dose transduction relationship was similar in Cyno and Humans was consistent with reported clinical data for AAV9 (red symbols). FIG.14B depicts exemplary dose-dependence of Compound A hBAG3 ISH-based cardiomyocyte coverage in cynomolgus monkeys. The target level of hBAG3 tissue coverage was achieved above 4E13 vg/kg in monkeys and a similar dose-response is expected in humans. Circles show measurements for individual heart sections from the monkey studies (8 heart sections/monkey; n=2 at 4E13 and n = 1 at 1 .3E14 vg/kg). Points and error bars show mean and standard deviations. FIG.14C depicts exemplary dose-dependence of Compound A hBAG3 protein level in cynomolgus monkeys. The target level of hBAG3 protein expression (22 ng BAG3/mg protein; dashed line) was exceeded at the 1.3E14 vg/kg in monkeys and is predicted to be achieved in humans at a 1 E14 vg/kg dose. Lines and circles show the model prediction and individual monkey observed data respectively. Points and error bars show mean and standard deviations (3 heart sections/monkey; n=2 at 4E13 and n = 1 at 1.3E14 vg/kg).
FIG. 15A-15C depict exemplary data from an in vivo dose response study to determine effective dose and transgene expression associated with survival and efficacy in mouse model of disease. cHET untreated control mice (Group 1 , n:14), cHET mice treated with Compound A at 3E13 vg/Kg (Group 2, n:13), cHET mice treated with Compound A at 1 E14 vg/Kg (Group 3, n:14), and cWT untreated control mice. FIG. 15A depicts ejection fraction (EF, %), FIG. 15B depicts left ventricular end diastolic volume (LVEDV, uL), and FIG. 15C depicts left ventricular end systolic volume (LVESV, uL) all of which were determined using echocardiography at baseline (2 week prior to treatment) and 3-, 8-, and 13-weeks post-treatment.
FIG. 16A depicts exemplary mouse survival following treatment. Untreated control cHET mice (Group 1 , n:14), cHET mice treated with Compound A at 3E13 vg/Kg (Group 2, n:14), cHET mice treated with Compound A at 1 E14 vg/Kg (Group 3, n:14), untreated control cWT mice (Group 4, n:15). A Kaplan-Meier survival analysis and pairwise log rank test between the groups was used to compare survival rates between the three groups. There were no significant differences in survival between the treatment groups.
FIG. 16B depicts exemplary longitudinal body weight measurements collected at baseline (2-weeks prior to treatment) and up to 15-weeks post treatment.
FIG. 17A-17D depict exemplary AAV biodistribution, transgene mRNA expression, BAG3 protein and HSPB8 protein expression in the heart. FIG.17A depicts exemplary tissue-specific biodistribution (heart) determined by measuring viral genomes (ddPCR) in heart tissue collected at necropsy from cHET mice treated with Compound A at 3E13 vg/Kg (Group 2), and Compound A at 1 E14 vg/Kg (Group 3). Two control cohorts of mice were included: Untreated cHET mice (Group 1), and untreated cWT mice (Group 4). FIG.17B depicts exemplary Transgene expression determined by measuring mRNA expression (ddPCR) in heart tissue collected at necropsy from the same cohorts of mice. FIG.17C depicts exemplary BAG3 protein expression determined by measuring its level in heart tissue collected at necropsy from the same cohorts of mice. FIG.17D depicts exemplary HSPB8 protein expression determined by measuring its level in heart tissue collected at necropsy from the same cohorts of mice. Statistical analysis was performed using one-way ANOVA with multiple comparisons (Tukey’s). (ns = p>0.05, * = p<0.05, ** = p<0.01 , *** = p<0.001 , *** = p<0.0001).
FIG. 18A-18E depict exemplary expression of fibrosis-related biomarkers in the hearts of cHET mice treated with Compound A at 3E13 vg/Kg (Group 2), and Compound A at 1 E14 vg/Kg (Group 3). Two control cohorts of mice were included: Untreated cHET mice (Group 1), and untreated cWT mice (Group 4). FIG. 18F-18H depict exemplary expression of heart failure-related biomarkers in the hearts of cHET mice treated with Compound A at 3E13 vg/Kg (Group 2), and Compound A at 1 E14 vg/Kg (Group 3). Two control cohorts of mice were included: Untreated cHET mice (Group 1), and untreated cWT mice (Group 4). Statistical analysis was performed using one-way ANOVA with multiple comparisons (Tukey’s). (ns = p>0.05, * = p<0.05, ** = p<0.01 , *** = p<0.001 , *** = p<0.0001).
FIG. 19A depicts exemplary mouse survival following treatment. Untreated control Bag3 cKO mice (Group 1 , n:13), Bag3 cKO mice treated with Compound A at 3E13 vg/Kg (Group 2, n:16), and Bag3 cKO mice treated with Compound A at 1 E14 vg/Kg (Group 3, n:15). A Kaplan-Meier survival analysis and pairwise log rank test between the groups was used to compare survival rates between the three groups. Group 1 had a significantly lower survival rate when compared to Group 2 and Group 3.
FIG. 19B depicts exemplary longitudinal body weight measurements (males & females) collected at baseline (2-weeks prior to treatment) and up to 20-weeks post treatment.
FIG. 20A-20C depict an exemplary in vivo dose response study to determine effective dose and transgene expression associated with survival and efficacy in mouse model of disease. Untreated control Bag3 cKO mice (Group 1 , n:13), Bag3 cKO mice treated with Compound A at 3E13 vg/Kg (Group 2, n:16), and Bag3 cKO mice treated with Compound A at 1 E14 vg/Kg (Group 3, n:15), FIG. 20A depicts exemplary ejection Fraction (EF, %) data, FIG. 20B depicts exemplary left ventricular end diastolic volume (LVEDV, uL) data, and FIG. 20C depicts exemplary left ventricular end systolic volume (LVESV, uL) data determined using echocardiography at baseline (1 week prior to treatment) and 2-, 5-, 9-, and 13-weeks post-treatment. A longitudinal mixed effects model with an AR(1) covariance structure was implemented to compare each variable between groups over time while controlling for gender. Symbol represents mean and error bars represent standard deviation, (ns = p>0.05, * = p<0.05, ** = p<0.01 , *** = p<0.001 , *** = p<0.0001).
FIG. 21 A depicts exemplary tissue-specific biodistribution (heart) determined by measuring viral genomes (ddPCR) in heart tissue collected at necropsy from untreated control Bag3 cKO mice (Group 1), Bag3 cKO mice treated with Compound A at 3E13 vg/Kg (Group 2), and Bag3 cKO mice treated with Compound A at 1 E14 vg/Kg (Group 3).
FIG. 21 B depicts exemplary transgene expression determined by measuring mRNA expression (ddPCR) in heart tissue collected at necropsy.
FIG. 21 C depicts exemplary transgene BAG3 protein expression determined by measuring its levels in heart tissue collected at necropsy. BAG3 protein expression was normalized to BAG3 levels detected in the hearts of wild type mice. Statistical analysis was performed using one-way ANOVA with multiple comparisons (Tukey’s). (ns = p>0.05, * = p<0.05, ** = p<0.01 , *** = p<0.001 , *** = p<0.0001).
DETAILED DESCRIPTION
The following discussion is directed to various embodiments. The disclosure is not intended to refer to any particular embodiment or otherwise limit the scope of the disclosure. Although one or more of these embodiments may be preferred, the embodiments disclosed should not be interpreted, or otherwise used, as limiting the scope of the disclosure, including the claims. In addition, one skilled in the art will understand that the following description has broad application, and the discussion of any embodiment is meant only to be an example of that embodiment, and not intended to intimate that the scope of the disclosure, including the claims, is limited to that embodiment.
The disclosure provides a gene therapy that delivers BAG3 protein expression to a desired target tissue (e.g., cardiac tissues). In some embodiments, the therapy can be used for the treatment of cardiac-related diseases or disorders, including, for example, cardiac- related diseases or disorders associated with a deficiency or dysfunction of BAG3. It is also intended for the treatment of cardiac-related diseases or disorders not associated with a deficiency or dysfunction of BAG3. Examples of cardiac-related diseases or disorders associated with a deficiency or dysfunction of BAG3 include, for example, BAG3-associated dilated cardiomyopathy (DCM), and BAG3-associated heart failure. Examples of cardiac- related diseases or disorders not associated with a deficiency or dysfunction of BAG3 include, for example, heart failure unrelated to BAG3 expression.
The extent and level of BAG3 protein expression needed to arrest decline in cardiac structure and function was evaluated in a BAG3 cardiac knockout (cKO) mouse model. These biodistribution targets were demonstrated in non-human primates (NHPs) at clinically- feasible dose levels and with acceptable safety. Toxicology assessments in mice (WT and cKO) and NHPs provided an adequate safety profile. Modeling predicts a clinically efficacious dose level of 3E13 vg/kg - 1 E14 vg/kg, and doses up to 1 .3E14 vg/kg were tested in NHPs.
Certain Definitions As used herein, the terms “about” and “approximately” refer to an amount that is ± 10 % of the recited value and is optionally ± 5 % of the recited value, or more optionally ± 2 % of the recited value. The terms “about” and “approximately” also are used to provide literal support for the exact number that it precedes, as well as a number that is near to or approximately the number that the term precedes. In determining whether a number is near to or approximately a specifically recited number, the near or approximating unrecited number may be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number.
As used herein, “adeno-associated virus vector” means an adeno-associated virus (AAV) comprising a naturally occurring or non-naturally occurring AAV capsid encapsidating a vector. Adeno-associated virus vector may be abbreviated “AAV vector,” and depending on context, may be referred to by synonymous terms, such as “recombinant AAV vector,” “rAAV vector,” “rAAV,” or just “vector.”
As used herein, “administering” and “administration” refers to any method of providing a pharmaceutical preparation to a subject. The vectors described herein (e.g., recombinant AAV vector) may be administered by any method known to those skilled in the art. Suitable methods for administering a vector may include, for example, by infusion or injection (e.g., intravenously, intraperitoneally, intramuscularly, intravitreally, and subcutaneously), drop infusion preparations, and the like. Methods of administering a vector may include subcutaneous administration. Vectors prepared as described herein may be administered in various forms, depending on the disorder to be treated and the age, condition, and body weight of the subject, as is known in the art. A preparation can be administered prophylactically; that is, administered to decrease the likelihood of developing a disease or condition.
As used herein, the term “at least” prior to a number or series of numbers is understood to include the number adjacent to the term "at least," and all subsequent numbers or integers that could logically be included, as clear from context. For example, the number of nucleotides in a nucleic acid molecule must be an integer. For example, "at least 10 nucleotides of a 21 -nucleotide nucleic acid molecule" means that a range of from 10-21 nucleotides, such as, e.g., 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 nucleotides, have the indicated property. When “at least” is present before a series of numbers or a range, it is understood that "at least" can modify each of the numbers in the series or range.
As used herein, the term “cardiac promoter” refers to a nucleotide sequence which, when operably linked with a polynucleotide 'which encodes or specifies a gene product, causes the gene product to be produced in a living cell substantially when the cell is a cell of the cardiac tissue. As used herein, the terms “complementary DNA” or “cDNA” are interchangeable and refer to a nucleic acid sequence that is a DNA equivalent of an mRNA sequence (/.e., having uridine substituted with thymidine). Generally, the terms cDNA and mRNA may be used interchangeably in reference to a particular gene (e.g., BAG3 gene) as one of skill in the art would understand that a cDNA sequence is the same as the mRNA sequence with the exception that uridines are read as thymidines.
As used herein, the term “disease” refers to an interruption, cessation, or disorder of body functions, systems, or organs. Diseases or disorders of interest include those that would benefit from treatment with a vector as described herein that delivers BAG3 expression to a target tissue. For example, diseases or disorders of interest include those that would benefit from treatment with a rAAV vector as described herein that delivers BAG3 expression to card io myocytes, such as by a treatment method described herein. Nonlimiting examples of diseases or disorder mediated by or associated with BAG3 protein expression that can be treated using the compositions and methods described herein include, for example, BAG3 DCM and BAG3-associated heart failure.
As used herein, the terms “effective amount,” pharmaceutically effective amount,” and “therapeutically effective amount,” of an agent (e.g., a rAAV vector described herein) that delivers human BAG3 protein expression to cardiomyocytes (e.g., in a subject) refers to a quantity sufficient to, when administered to the subject, including a human, effect beneficial or desired results, including clinical results, and, as such, an “effective amount” or synonym thereto depends on the context in which it is being applied. For example, in the context of treating a disease associated with BAG3 protein expression, it is an amount of the agent that delivers BAG3 protein expression sufficient to achieve a treatment response or a beneficial or desired result as compared to the response obtained without administration of the agent.
As used herein, the term “excipient” refers to a non-therapeutic agent that may be included in a formulation or composition, for example, to provide or contribute to a desired consistency or stabilizing effect.
As used herein, “expression cassette” means a nucleotide sequence comprising a transgene operably linked with promoters, regulatory regions, or elements for controlling the initiation and termination of transcription of the transgene from DNA into RNA.
As used herein, the terms “formulation,” “pharmaceutical formulation,” and “pharmaceutical composition,” as they relate to the vectors described herein, are meant to describe the vector (e.g., a rAAV) in combination with one or more pharmaceutically acceptable excipients comprising, for example, a buffer, a salt, a cryoprotectant, and/or a surfactant, optionally wherein the pH is defined, and further optionally where the formulation is manufactured or sold with the approval of a governmental regulatory agency as part of a therapeutic regimen for the treatment of disease in a mammal. A “pharmaceutical formulation” or “pharmaceutical composition” is a preparation which is in such form as to permit the biological activity of the active ingredients to be effective. Pharmaceutical formulations and compositions can be formulated, for example, for subcutaneous administration, for intravenous administration (e.g., as a sterile solution free of particulate emboli and in a solvent system suitable for intravenous use); for intrathecal injection; for intracerebroventricular injections; for intraparenchymal injection; for oral administration in unit dosage form (e.g., a tablet, capsule, caplet, gelcap, or syrup); or for topical administration (e.g., as a cream, gel, lotion, or ointment; or in any other pharmaceutically acceptable formulation.
As used herein, “heterologous nucleotide sequence” means a nucleotide sequence that is introduced into an organism (including a virus) from a different organism (including an organism). The sequence of a heterologous nucleotide sequence may be the same as one that occurs in nature, or may be a modified version thereof, or even partially or entirely synthetic.
As used herein, “host cell” means a cell in which viral vectors are produced. Producer cells and packaging cells are examples of host cells. Host cells can be mammalian or insect, or from other organisms, whether single or multi-cellular.
As used herein, “percent (%) sequence identity” with respect to a reference nucleic acid or polypeptide sequence is defined as the percentage of nucleotides or amino acids in a candidate sequence that are identical to the nucleotides or amino acids in the reference nucleic acid or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid or amino acid sequence identity can be achieved in various ways that are within the capabilities of one of skill in the art, for example, using publicly available computer software such as BLAST, BLAST-2, or Megalign software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For example, percent sequence identity values may be generated using the sequence comparison computer program BLAST. As an illustration, the percent sequence identity of a given nucleotide or amino acid sequence, A, to, with, or against a given nucleotide or amino acid sequence, B, (which can alternatively be phrased as a given nucleotide or amino acid sequence, A that has a certain percent sequence identity to, with, or against a given nucleotide or amino acid sequence, B) is calculated as follows:
100 multiplied by (the fraction X/Y) where X is the number of nucleotides or amino acids scored as identical matches by a sequence alignment program (e.g., BLAST) in that program’s alignment of A and B, and where Y is the total number of nucleotides in B. It will be appreciated that where the length of nucleotide or amino acid sequence A is not equal to the length of nucleotide or amino acid sequence B, the percent sequence identity of A to B will not equal the percent sequence identity of B to A.
As used herein, the term “purify,” and the related terms “purified,” “purification,” and “isolated,” when used in connection with the vectors as described herein, or sample or preparation thereof, indicates a relative increase or improvement in purity compared with a starting material containing the vector, and/or a prior intermediate purification step in some scheme of sequential purification steps intended to purify the biological product, and does not require a particular qualitative or quantitative degree of purity, unless otherwise specified.
As used herein, “subject” means an organism to which a vector (e.g. a rAAV) is administered for purposes of preventing or treating a disease, disorder, or condition. Moreover, the term “subject” refers to any organism to which a composition in accordance with the disclosure may be administered, e.g., for experimental, diagnostic, prophylactic, and/or therapeutic purposes. Typical subjects include any animal (e.g., mammals, such as mice, rats, rabbits, non-human primates, and humans). A subject may seek or be in need of treatment, require treatment, be receiving treatment, be receiving treatment in the future, or be a human or animal who is under care by a trained professional for a particular disease or condition.
As used herein, “target cell” means a cell that a vector (e.g., a rAAV) is designed or intended to transduce, or is experimentally observed to be transduced by the vector, whether in vitro, or in vivo in a subject.
As used herein, “transduction” means the introduction into a target cell of the genome of a vector (e.g.. a rAAV). Transduction is distinguished from infection, the latter term being used to refer to the introduction into a cell of the genome of a replication-competent virus.
As used herein, “transgene” means a nucleotide sequence that encodes at least one polypeptide, and/or the nucleotide sequence coding for at least one functional RNA molecule. Transgene may be referred to by the synonymous term “gene of interest.”
As used herein, the term “treat” refers to the act of providing care to a subject in need thereof, e.g., through the administration of a therapeutic agent (e.g., a rAAV as described herein) to the subject, for purposes of improving the health and/or well-being of the subject with respect to an existing condition (e.g., a disease, disorder) or to prevent or decrease the likelihood of the occurrence of a condition. In some embodiments, treatment involves reducing the frequency or severity of at least one sign, symptom, or contributing factor of a condition (e.g., disease, disorder) experienced by a subject.
As used herein, “vector” means an AAV genome modified both to include a heterologous nucleotide sequence and to render any AAV vector containing the vector replication incompetent, such as by inactivating or deleting an endogenous AAV rep and/or cap gene.
BAG3
The BAG3 gene is located on chromosome 10q26.11 (MIM: 603883) (Nucleotide NCBI Reference Sequence: NM_004281 .4; Protein NCBI Reference Sequence No.: NP_004272.2) and is referred to as “BCL2-ASSOCIATED ATHANOGENE 3” or “BAG cochaperone 3” or “BAG family molecular chaperone regulator 3.” BAG3 is a multifunctional protein that is involved cell stress response through its participation in several regulatory pathways which control cell homeostatic response in physiological and pathological conditions. BAG proteins compete with Hip for binding to the Hsc70/Hsp70 ATPase domain and promote substrate release. The BAG domains of BAG1 , BAG2, and BAG3 interact specifically with the Hsc70 ATPase domain in vitro and in mammalian cells and inhibit its chaperone activity in a Hip-repressible manner.
BAG3 Mutations
BAG3 mutations in humans are mainly nonsense, deletions, or frameshifts and different mutations that all lead to a similar disease phenotype. Cardiac BAG3 knockout (cKO) mice present with heart failure, dilatation, and fibrosis. Delivery of BAG3 by an adeno- associated virus (AAV) vector results in stabilization of cardiac structure and function as well as decreased biomarkers of heart failure and fibrosis. Furthermore, BAG3 protein levels are decreased in failing human hearts (no BAG3 mutation) and AAV delivery of BAG3 protects WT mouse hearts from ischemia/reperfusion injury.
Mutations in BAG3 are associated with a rare autosomal dominant form of non- syndromic dilated cardiomyopathy (DCM 1 HH/BAG3; OMIM 613881), at an estimated genetic prevalence of approximately 1 % of all DCM patients, based on literature.
Patients with BAG3 associated DCM present with severely reduced heart function and moderate to severe symptoms of heart failure. Once diagnosed, patients with BAG3 associated DCM demonstrate a high cardiac event rate of approximately 25-30% (e.g., death, LVAD, heart transplant, sustained VT) and a mortality rate of 5% over 4 to 5 years (Dominguez et al., J. Am. Coll. Cardiol. 72(20): 2471-81 (2018)). BAG3 expression may be down-regulated in heart failure in general and thus may be a target in acquired heart failure.
Adeno-Associated Virus (AAV)
The disclosure provides vectors created from recombinantly modified adeno- associated virus (AAV). AAV vectors are capable of delivering genes, which may be under the control of transcriptional and other regulatory elements, into targeted cells via transduction. By supplying a functional copy of a gene to a target cell in which the endogenous version is missing or mutated, AAV vectors are useful in gene therapy for a variety of diseases and disorders.
AAV is a small non-enveloped, non-pathogenic parvovirus that depends on certain other viruses to supply gene products, known as helper factors, essential to its own replication, that has made AAV well-suited to serve as a recombinant vector. For example, adenovirus (AdV) can serve as a helper virus by providing certain adenoviral factors, such as the E1A, E1 B55K, E2A, and E4ORF6 proteins, and the VA RNA, in cells co-infected by adenovirus and AAV. Other helper viruses, such as herpes simplex virus, have been identified as well. The dependence of AAV replication on accessory factors supplied by other viruses led AAV to be characterized as a type of dependovirus. AAV virions have two major structural features, called the capsid and genome, respectively. The capsid is an icosahedral protein shell that encloses and protects (encapsidates) the viral genome, which contains genes and other sequences required for viral replication in infected cells.
The AAV genome is a single strand of DNA containing two genes called rep and cap. In AAV9, for example, a naturally occurring AAV that infects humans and is well characterized biologically, the genome is about 4.7 kilobases long. By virtue of alternative splicing of the transcripts from two promoters, the rep gene is capable of producing four related multifunctional proteins called Rep (e.g., Rep 78, Rep 68, Rep 52, and Rep 40, named according to their apparent molecular weights) that are involved in viral gene expression, and replication and packaging of genomes. Alternative splicing of the transcript from the single promoter controlling the single cap gene produces three related structural proteins, VP1 , VP2, and VP3, a total of 60 of which self-assemble to form the virus’s icosahedral capsid in a ratio of approximately 1 :1 :10, respectively. VP1 is longest of the three VP proteins and contains amino acids in its amino terminal region that are absent from VP2, which in turn is longer than VP3 and contains amino acids in its amino terminal region that are absent from VP3. In addition to containing the genome, capsid proteins mediate specific binding interactions with receptors on the surface of target cells, based on which AAV can be restricted in their ability to infect certain animal species, and even tissues within the same type of animal, a phenomenon called tropism. For example, one type of AAV may preferentially infect liver cells (e.g., hepatocytes) as compared to muscle or neuronal cells.
In addition to the rep and cap genes, intact AAV genomes have a relatively short (145 nucleotides) sequence element positioned at each of their 5' and 3' ends called an inverted terminal repeat (ITR). ITRs contain nested palindromic sequences that can selfanneal through Watson-Crick base pairing to form a T-shaped, or hairpin, secondary structure. ITRs have been demonstrated to have important functions required for the viral life cycle, including converting the single stranded DNA genome into double stranded form required for gene expression, as well as packaging by Rep proteins of single stranded AAV genomes into capsid assemblies.
Numerous naturally occurring types of AAV have been discovered in different species. At one time, only six types of primate AAV had been isolated from biological samples (AAV1 , AAV2, AAV3, AAV4, AAV5, and AAV6), the first five of which were sufficiently distinct structurally to be classified as different serotypes based on antibody cross reactivity experiments. Later, two novel AAVs, called AAV7 and AAV8 were discovered by PCR amplification of DNA from rhesus monkeys using primers targeting highly conserved regions in the cap genes of the previously discovered AAVs (Gao et al., Proc. Natl. Acad. Sci. U.S.A. 99(18): 11854-59 (2002)). Subsequently, a similar approach was used to clone numerous novel AAVs from human and non-human primate tissues, vastly expanding the scope of AAV capsid protein sequences (Gao et al., J. Virol. 78(12): 6381-88 (2004)). Many AAV capsid protein sequences are highly similar to each other, or previously identified AAVs, and while often referred to as distinct AAV “serotypes,” not all such capsids would necessarily be expected to be immunologically distinguishable if tested by antibody cross reactivity. AAVs, or AAV capsids, which are not serologically distinguishable from a defined serotype but contain capsid proteins with a different amino acid sequence are better termed variants of the known serotype. Numerous capsids made from naturally and non-naturally occurring capsid proteins have found utility in creating AAV gene therapy vectors.
After binding one or more receptor molecules on a cell surface, the AAV viral particle enters the cell via endocytosis. Upon reaching the low pH of lysosomes, capsid proteins undergo a conformational change that allows the capsid to escape into the cytosol and then be transported into the nucleus. Once there, the capsid disassembles, releasing the genome that is acted on by cellular DNA polymerases to synthesize the second DNA strand starting at the ITR at the 3' end, which functions as a primer after self-annealing. Expression of the rep and cap genes can then commence, followed by formation and release from the cell of new viral particles.
AAV9 is a human AAV serotype that has enhanced transduction efficiency in cardiac and skeletal muscle, liver and pancreatic tissue, and the eye relative to other serotypes. Similar to other AAVs, AAV9 can transduce nondividing cells, including hepatocytes, which normally express factor IX (FIX). AAV9 can also cross the blood-brain barrier, and among all of the AAVs, it targets the central nervous system with high efficiency. Furthermore, while preexisting antibodies to AAVs have been shown to be detrimental to AAV gene delivery, the prevalence of antibodies to AAV9 is lower in humans than those of other serotypes, for example, AAV1 and AAV2, making this serotype a more attractive candidate for development as a gene delivery vector. AAV Vectors
The relative simplicity of AAV structure and life cycle, and the fact that it is not known to be pathogenic in humans, inspired researchers to engineer AAV and investigate if it could be converted from a virus to a recombinant vector for gene therapy. Briefly, this was done by cloning the entire genome of AAV2, including both ITRs, into a plasmid, removing the rep and cap genes into a separate plasmid, and replacing them with a heterologous gene expression cassette comprising a promoter controlling a protein encoding transgene. Thus, the only viral genomic sequences retained in the vector were the ITRs, due to their critical function in packaging and gene expression, and without which AAV vectors could not be produced or function to express the transgene after transduction of target cells. Finally, to avoid the need for co-infection with a helper virus, necessary for replication of AAV virions, genes for the so-called helper factors (such as, in the case of AdV, the E1A, E1 B55K, E2A, E4ORF6, and VA RNA helper factors) were cloned into a third plasmid.
When the three plasmids (which are sometimes called the transgene, rep/cap, and helper plasmids) were transfected together into mammalian host cells, Rep and capsid proteins, and the helper virus factors were expressed from their respective plasmids. These gene products then functioned in the host cells to replicate the vector into single stranded DNA from the plasmid on which its sequence resided, assemble capsids, and package the single stranded genomes into the capsids, forming vectors. The vectors could then be purified from the host cells. Because the rep and cap genes existed in trans on a different plasmid, outside their usual context flanked by ITRs, they were not packaged into the vectors. Consequently, while AAV vectors produced this way were able to bind to and convey the expression cassette within their genomes into target cells, they are unable to replicate and create new vector particles.
If vectors function as intended, after transduction, the expression cassette will be transcriptionally active and produce the gene product encoded by the transgene in the target cell. AAV vectors are highly versatile because vectors comprising a variety of transgenes under the control of different functional sequences and regulatory elements in various configurations can be designed and paired with a variety of naturally occurring and engineered capsids, with different tropisms and other properties. Many types of gene products can therefore be produced, with a degree of control over the types of cells that are transduced and amount of gene product that is made.
AAV vectors comprise a vector encapsidated by an AAV capsid. In some embodiments, the AAV vector comprises at least one AAV inverted terminal repeat (ITR) and a heterologous nucleotide sequence with a desired function when present or expressed in a transduced target cell. In some embodiments, the heterologous nucleotide sequence originates from a different type of virus, or an entirely different type of organism, such as an animal, plant, protist, fungus, bacteria, archaea, or other type of organism. In some embodiments, the heterologous nucleotide sequence replaces some or all of the native AAV rep and/or cap genes so that the vector is incapable of expressing functional Rep or VP proteins in transduced target cells. In some embodiments, the entire sequence of the vector consists of heterologous nucleotide sequences except for AAV inverted terminal repeat sequences positioned at the ends of the genome.
The length of a genome of the AAV vectors of the disclosure, inclusive of ITRs, can be any suitable length, which typically, but not necessarily, will not exceed the average genome size packaging capacity of the particular AAV capsid, which may be selected in the design and production of a particular AAV vector. Accordingly, in some non-limiting embodiments, the length of a genome of an AAV vector of the disclosure, inclusive of ITRs, can be at least or about 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, or 5200 nucleotides (or basepairs when the genome sequence is embodied in a plasmid for vector production), or an integer value between or range encompassing any of the foregoing specifically enumerated values.
The length of the AAV plasmid based vectors of the disclosure can be any suitable length. In some non-limiting embodiments, the length AAV plasmid based vectors of the disclosure, can be at least or about 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300, 5400, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10000, 10500, 11000, 11500, or 12000 nucleotides, or an integer value between or range encompassing any of the foregoing specifically enumerated values.
AAV Capsid Proteins
AAV vectors of the disclosure can utilize any AAV capsid protein, whether naturally occurring, modified, or engineered, including those presently known, or yet to be discovered or developed, which are suitable for transducing cells in a subject to express BAG3 protein, or a variant thereof, from a vector transgene.
Choice of which capsid proteins to use in designing and producing an AAV vector (and the corresponding cap gene sequence to be used in its production) can be guided by many considerations and factors. As noted above, by virtue of interacting specifically with certain cell surface receptors, different AAV capsids can have different cell or tissue tropisms, which can be an advantage when it is desired to transduce certain tissues versus others. For example, to express a transgene product in the heart, such as in a cardiomyocyte, one might design and produce a vector using a capsid with greater tropism for cardiomyocytes compared to, for example, neurons or hepatocytes. Conversely, to express a transgene product in the liver, one might design and produce a vector using a capsid with greater tropism for hepatocytes compared to neurons, muscle, or other tissues.
Other factors may be important as well. It has been reported, for example, that some humans have high neutralizing antibody titers to certain capsids as a result of exposure to naturally occurring AAVs, which can interfere with the ability of AAV vectors with the same or similar capsids to transduce target cells. Thus, in designing a vector for gene therapy, choice of capsid may in some cases be guided by the immunogenicity of the capsid, and/or the seroprevalence of the patients to be treated. Other considerations that may influence capsid choice include manufacturability and stability during storage, with other relevant guiding factors being known in the art.
AAV vectors of the disclosure can use capsids made from capsid proteins from naturally occurring AAVs, as well as modified or engineered capsid proteins. For example, naturally occurring capsid proteins can be modified by inserting or deleting amino acids or peptides, or by introducing amino acid substitutions, in the VP1 , VP2, and/or VP3 protein sequence intended to improve capsid function in some way, such as tissue tropism, immunogenicity, stability, or manufacturability. Other examples include novel capsids with improved properties created by swapping amino acids or domains from one known capsid to another (e.g., mosaic or chimeric capsids), or using DNA shuffling and directed evolution methods to discover capsid protein sequences with desired properties.
In some embodiments, AAV vectors of the disclosure can comprise a capsid from known AAV serotypes and variants, as well as non-naturally occurring capsids, including, without limitation serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype 9 (AAV9), serotype 10 (AAV10), serotype 11 (AAV11), or serotype 12 (AAV12), with others being possible. In some embodiments, capsids of AAV vectors of the disclosure include a VP1 , a VP2, and/or a VP3 AAV capsid protein that is a variant or derivative of a known VP1 , VP2, or VP3 AAV capsid protein. In some embodiments, the amino acid sequence of such variant or derivative AAV capsid protein can be at least or about 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 95.5%, 96%, 96.5%, 97%, 97.5%, 98%, 98.5%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to the amino acid sequence of any known AAV capsid VP1 , VP2, or VP3 protein sequence, including, without limitation, the AAV capsid VP1 , VP2, or VP3 proteins of AAV1 , AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11 , or AAV12, or any other suitable AAV capsid, including, for example, the cardiac capsids discussed below. In some other embodiments, the amino acid sequence of such variant or derivative AAV capsid protein differs (whether due to deletion, insertion, or substitution of amino acids) 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, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more amino acids from a known AAV capsid VP1 , VP2, or VP3 protein amino acid sequence including, without limitation, the AAV capsid VP1 , VP2, or VP3 proteins of AAV1 , AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11 , or AAV12, or any other suitable AAV capsid, including, for example, the cardiac capsids discussed below.
Cardiotropic AAV Capsids
The heart is a key target organ for BAG3 gene therapy. In some embodiments, an rAAV vector comprising a BAG3 transgene comprises a capsid protein known in the art as cardiotropic. Non-limiting examples of cardiotropic capsid proteins include one or more AAV1 , AAV4, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11 , and AAV12 capsid proteins. For example, AAV9 is known to transduce the heart in non-human primates (Pacak et a!., Giro. Res. 99(4): e3-9 (2006)). A cTNT cardiac promoter can be used to express BAG3 transgene in transduced cardiomyocytes and to restrict expression outside the heart (Prasad et al., Gene Ther. 18(1): 43-52 (2011)).
In some embodiments, the AAV vector comprises AAV9 capsid proteins. AAV9 capsid proteins may comprise VP1 protein (e.g., the amino acid sequence of SEQ ID NO: 1), VP2 protein (e.g., the amino acid sequence of SEQ ID NO: 2), and VP3 protein (e.g., the amino acid sequence of SEQ ID NO: 3), or a functional subsequence, modification, or variant respectively thereof.
Expression Cassettes
In some embodiments, the heterologous nucleotide sequence comprises or consists of an expression cassette or “payload” comprising a transgene operably linked with a promoter and optionally one or more enhancers, serving to control transcription initiation of the transgene from DNA into RNA, as well as a transcription termination element, such as a polyadenylation signal sequence, serving to terminate transcription of the transgene into RNA. AAV vectors can comprise more than one transgene, either as part of one transcriptional unit, or each being part of its own transcriptional unit. As described in later sections, expression cassettes can further comprise additional sequence elements designed to influence transcription, transcript stability, translation, or other functions.
As AAV vectors are typically designed, the structure of the expression cassette, and the genome overall, is limited by the packaging capacity of the capsid, so that the length of the transgene when combined with all other elements in the genome required for vector function, such as the transcriptional control elements and ITRs, does not exceed approximately 4.7 kilobases in the case of AAV9, although other types of capsids may have greater or smaller packaging limits. Within the size constraints, however, there is great flexibility in choice of transgenes, ITRs, and the other elements required for the vector to function for its intended purpose.
In some embodiments, the expression cassette of the rAAVs of the disclosure ranges in size from about 3.5 to about 4,7 kb. In certain embodiments, the expression cassette of the rAAVs of the disclosure is about 4.2 kb in size.
BAG3 Transgenes
In some embodiments, AAV vectors of the disclosure comprise a vector comprising an expression cassette comprising a nucleotide coding sequence (transgene) for a BAG3 protein, or variant thereof. In some embodiments, the BAG3 protein is identical to the 575 amino acid human BAG3 protein (NCBI Reference Sequence NP_004272.2 or SEQ ID NO: 10).
In yet other embodiments, the BAG3 protein can include any naturally occurring variant of human BAG3 protein that does not contain pathogenic mutations, such as premature translation termination codons, or amino acid substitutions, insertions, or deletions that substantially impair BAG3 activity and/or protein stability. In yet further embodiments, the BAG3 protein can include engineered variants of human BAG3 protein that retain BAG3 activity, such as the chimeric variants and variants with amino acid substitutions, insertions, or deletions designed to modulate BAG3 activity, add or remove glycosylation sites, add or remove or change internal cleavage sites or sites for other post- translational modifications, or alter other aspects of BAG3 structure or function.
In certain other embodiments, the BAG3 protein variant comprises at least one amino acid substitution mutation compared to the full-length wild-type human BAG3 protein amino acid sequence (such as that provided by SEQ ID NO: 10), such as 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, or 20, or more amino acids are changed from their wildtype counterpart. In some of these embodiments, a substitution mutation may be a conservative amino acid substitution, in which an amino acid ordinarily present is substituted by another amino acid with an R group having similar physico-chemical and/or or size characteristics. Alternatively, in other embodiments, a substitution mutation may be a nonconservative amino acid substitution, in which an amino acid ordinarily present is substituted by another amino acid with an R group having non-similar physico-chemical and/or or size characteristics.
For use in AAV vectors of the disclosure, the nucleotide sequence encoding the BAG3 protein can be any nucleotide sequence capable of encoding the desired BAG3 protein in the type of cell desired to be transduced by the vector, such as a cardiomyocyte. In some embodiments, the nucleotide sequence encoding BAG3 protein (/.e., the transgene) is the same as exists in a naturally occurring gene encoding BAG3 (/.e., the exons of such gene), or is the DNA sequence that corresponds to the mRNA sequence transcribed from such gene. In some embodiments, wherein the BAG3 protein is full-length wild-type human BAG3 protein, the encoding nucleotide sequence is SEQ ID NO: 4.
In other embodiments, the nucleotide sequence encoding BAG3 protein can differ at one or more nucleotide positions compared to a naturally occurring nucleotide sequence and, by virtue of the redundancy in the genetic code, still encode the identical BAG3 protein as the naturally occurring gene sequence, or BAG3 protein variant that, but for the differences in the polypeptide relative to wild-type BAG3, is otherwise encoded by the naturally occurring gene sequence. In some embodiments, the nucleotide sequence encoding BAG3 protein can be intentionally modified to affect its function in transduced cells, such as to eliminate sequence motifs capable of stimulating an innate immune response, to eliminate cryptic splice junctions, to eliminate alternative start codons, to increase the stability of the corresponding mRNA, and/or to increase the rate of translation of mRNA into protein. In other embodiments, the nucleotide sequence encoding BAG3 protein can be intron-less, or can include one or more introns interrupting the coding sequence, but that are removed by the splicing apparatus in transduced cells so as to allow translation of the desired BAG3 protein.
In some embodiments of the AAV vectors of the disclosure, the transgene encodes a protein sequence that is highly similar to, or identical with the protein sequence encoded by a certain nucleotide reference sequence, but where the nucleotide sequences of the transgene and reference sequence are not identical, but rather share a certain percent identity, the differences corresponding to positions within codons that do not change the corresponding amino acid (/.e., are silent changes). For example, in some embodiments, the transgene comprises or consists of a nucleotide sequence that encodes the same full- length BAG3 protein as set forth in SEQ ID NO: 10 wherein the nucleotide sequence is at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 95.5%, 96%, 96.5%, 97%, 97.5%, 98%, 98.5%, 99%, 99.1 %, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to the nucleotide sequence of SEQ ID NO: 4.
The percentage of nucleotide sequence identity between a reference sequence and a transgene can be determined by any method known in the art. For example, in some embodiments, the nucleotide sequences of the reference sequence and the transgene (or the amino acid sequences encoded by them) can be aligned and compared over their entire lengths and a percent nucleotide sequence identity calculated using a computer algorithm. An exemplary algorithm for globally aligning and comparing nucleotide sequences is the Needleman-Wunsch algorithm. In other embodiments, however, a local alignment algorithm, such as the BLAST algorithm can be used (Needleman et al., J. Mol. Biol., 48(3): 443-53 (1970); States et al., Methods, 3(1): 66-70 (1991); Pearson, Curr. Protoc. Bioinformatics, 43:3.5.1-3.5.9 (2013)). In some embodiments, where one orthe other of the reference and transgene sequences contains a non-coding sequence, such as an intron or a stop codon, then the non-coding sequence(s) are ignored and only the protein coding sequence within the reference and transgene sequences are aligned and compared. Once the optimal global alignment between a reference sequence and a transgene is established, the percent of identical nucleotides between the aligned sequences can be calculated.
As is known in the art, sequence comparison algorithms can allow users to define substitution scores and gap penalties, parameters used to calculate alignment scores for the numerous possible alignments that can be made. The alignment with the highest score is then considered optimal. The substitution score involves assigning a numerical reward for matches and penalty for mismatches. Exemplary sets of respective match and mismatch scores include 1 ,-1 ; 1 ,-2; 1 ,-3; 1 ,-4; 2,-3; 4,-5, although others are possible. The gap cost involves assigning a numerical penalty for existence of a gap (insertion or deletion of a nucleotide) as well as penalty for extending the width of the gap once formed. Increasing the gap costs will result in alignments that decrease the number of gaps introduced. Exemplary sets of respective costs for gap existence and extension include 0,-4; -2,-2; -2,-4; -3,-3; -4,-2; -4,-4; -5,-2; -6,-2, although others are possible. In some embodiments, the alignment and comparison of the reference and transgene sequences is carried out using the default substitution scores and gap penalties, and any other default settings, provided with computer software or algorithm for performing the analysis.
Sequence Optimization
In some embodiments, one or more sequences within an AAV vector can be optimized to improve its functional characteristics relative to a starting reference sequence. For example, and without limitation, any protein coding sequence in a vector can be codon- optimized relative to the wild-type sequence, based on the degeneracy of the genetic code and codon usage biases known to exist between different species and between proteins expressed at high or low levels in the same species. Such codon biases can be identified using a codon adaptation index for a particular species, for example. Codon adaptation index (CAI) is explained in more detail in Sharp et al., Nucleic Acids Res. 15(3): 1281-95 (1987). In some embodiments, coding sequences are human codon-optimized, meaning the coding sequences are optimized based on human codon biases. Codon-optimization can be facilitated using various algorithms known in the art. As is known in the art, different CAI can be constructed based upon which highly expressed genes, such as human genes, are analyzed. An exemplary human CAI is reported in Haas et al., Curr. Biol. 6(3): 315-24 (1996). If desired, protein coding sequences can be codon-optimized for species other than human as well.
With the goal of increasing protein expression levels, different codon-optimization strategies have been proposed and implemented. For example, the most frequently used synonymous codon (/.e., one coding for the same amino acid) can be substituted at each position where it does not occur. Alternatively, codon usage can be adjusted over the entire coding sequence so that it is proportional to the natural codon bias distribution of the host organism. In some embodiments, codon replacement is limited to ones that occur relatively rarely in highly expressed proteins in a species, for example, with a frequency of 10% of less, as reflected in a CAI.
In some embodiments, a protein coding sequence to be expressed by a AAV vector of the disclosure can be codon-optimized by substituting at least one rare codon with a more common synonymous codon. In some embodiments, at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95%, and in some embodiments 100% of rare codons in the protein coding sequence are replaced with a more frequently used synonymous codon as reflected in a CAI, such as a human CAI. In some embodiments, a rare codon is one that occurs at a frequency of less than or equal to 10%, 9%, 8%, 7%, 6%, or 5%, as reflected in a CAI, such as a human CAI.
In some embodiments, a protein coding sequence to be expressed by an AAV vector of the disclosure can be codon-optimized by replacing one or more codons with a more frequently used synonymous codon as reflected in a CAI, such as a human CAI, so that the CAI value calculated for the overall coding sequence is increased relative to the starting noncodon optimized sequence, which in some embodiments is the wild-type coding sequence of a protein. Thus, in some embodiments, the CAI value of a starting reference sequence is calculated with reference to a particular CAI reference table and one or more codons are replaced with more frequent synonymous codons so that the overall CAI value of the now codon-optimized coding sequence is increased by at least or about 0.01 , 0.02, 0.03, 0.04,
0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11 , 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20,
0.21 , 0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31 , 0.32, 0.33, 0.34, 0.35, 0.36,
0.37, 0.38, 0.39, 0.40, 0.41 , 0.42, 0.43, 0.44, 0.45, 0.46, 0.47, 0.48, 0.49, 0.50, 0.55, 0.60, or
0.70.
As is known in the art, the presence of hypomethylated CpG dinucleotides in nucleic acid can stimulate immune responses that eliminate transduced cells. Depleting CpG dinucleotides in vectors can therefore increase the likelihood that vector transduction will result in long-term gene expression (Wright, Mol. Ther. 28(3): 701-03 (2020)). In view of the potentially detrimental effects of CpG dinucleotides, in some embodiments, any sequence within the genome, including for example, enhancers, promoters, introns, open reading frames that encode protein or functional RNA, transcriptional terminators, 5' and/or 3' untranslated region (UTR) sequences, ITRs, or any other sequence can be modified to remove one or more CpG dinucleotides, as long as doing so does not unacceptably interfere with or disrupt some desirable function of the modified element. Because the function of certain elements within vectors, such as ITRs, promoters, and enhancers, can be highly dependent on the identity of particular nucleotides in certain positions, there may be more limited opportunities to significantly deplete such elements of CpG dinucleotides. Because AAV vectors of both polarities (e.g., sense and antisense, with respect to the coding sequence of a transgene within the genome) are packaged into capsids in about equal proportions, a strategy of CpG depletion can, in some embodiments, be directed to reducing or eliminating CpG motifs from the nucleotide sequence of vectors of both polarities, not just vectors that contain protein coding sequence in the sense orientation.
In some embodiments, at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% of CpG dinucleotides in a coding sequence or the overall vector sequence (with respect to the sense and/or antisense strand) are deleted, or replaced, relative to a reference starting sequence. In other embodiments at least 1 , 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more CpG dinucleotides, or a range between any of the foregoing values, are deleted, or replaced, relative to a starting reference sequence. In other embodiments, between 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50, 50-55, 55-60, 60-65, 65-70, 70-75, 75-80, 80-85, 85-90, 90-95, or 95-100, CpG dinucleotides are deleted, or replaced, relative to a reference starting sequence.
In other embodiments, sequence optimization can increase or decrease the overall GC content relative to a starting reference sequence. Thus, in some embodiments, the overall percentage of G or C nucleotides in a transgene or the genome overall, can be increased, relative to a starting reference sequence, such as a wild-type protein encoding sequence, by at least or about 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, 26, 27, 28, 29, 30, 35, or 40 percent, or more. In other embodiments, the overall percentage of G or C nucleotides in a transgene or the genome overall, can be decreased, relative to a starting reference sequence, such as a wild-type protein encoding sequence, by at least or about 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, 26, 27, 28, 29, 30, 35, or 40 percent, or more.
As will be appreciated by those of ordinary skill, when optimizing coding sequence, the goal of substituting with more prevalent codons for any particular amino acid in a species (such as human) may be incompatible with other optimization strategies because introduction of more frequently used codons could introduce CpG motifs, or elimination of CpG might require use of rarely occurring codons, or codon optimization might increase or decrease GO content in undesired ways. In these instances, it may be necessary to design and test different optimized coding sequences (encoding the same polypeptide) to identify versions that strike an acceptable balance between the different optimization strategies to achieve improved protein expression.
Transgene and vector sequence can be optimized by changing features in addition to codon bias and CpG content. For example, any of the following features that sometimes occur in sequences and negatively impact transgene expression can be identified (either conceptually, such as by using algorithms, or empirically) and altered or eliminated so as to reduce their effect: cryptic splice sites; premature transcriptional termination signal sequences (e.g., polyA sequences); translational start sites (e.g., IRES) other than for the intended initiator methionine; sequence regions with high GC content; mRNA 5' end sequences that can form hairpins; and AU rich elements (ARE) in mRNA 3' untranslated regions that can be bound by destabilizing RNA binding proteins. Other sequence features that can appear in transgenes and vectors that, when altered, can enhance transgene expression will be familiar to those of ordinary skill in the art.
In other embodiments, transgene or vector sequence can be modified to enhance functionality. For example, the first intended start codon in a protein coding sequences may only weakly support translation initiation from that site, in which case, the surrounding sequence can be altered to match the so-called Kozak consensus sequence for translation initiation in eukaryotes (Kozak, Gene 234(2):187-208 (1999)).
In some embodiments, CpG depletion (partial or complete), or other types of sequence optimization of the transgene coding sequence, such as codon-optimization, can improve protein expression from the transgene compared to the same vector including a non-optimized reference starting sequence, such as a wild-type coding sequence from which the optimized sequence is derived. Thus, for example, the optimized coding sequence of a transgene may express at least 25%, 50%, 75%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, or more efficiently as compared to a non-optimized reference starting sequence, such as the wild-type version of the coding sequence.
In some embodiments of the nucleic acid molecules of the disclosure, the nucleic acid molecule comprises a codon-optimized nucleotide sequence encoding a BAG3 polypeptide. In certain embodiments, the codon-optimized nucleotide sequence encoding the BAG3 polypeptide is the nucleotide sequence set forth in SEQ ID NO: 19 (CpG5), SEQ ID NO: 20 (CpG6), SEQ ID NO: 21 (CpG21), SEQ ID NO: 22 (CpG22), SEQ ID NO: 23 (CpG23), or SEQ ID NO: 24 (CpG24), or a functional subsequence, modification, or variant respectively thereof. Transcription Control Regions - Promoters and Enhancers
AAV vectors of the disclosure intended to express BAG3 protein in and/or from transduced cells can further comprise, as part of the expression cassette of the vector, one or more transcription control regions in operable linkage with the transgene encoding the BAG3 polypeptide sequence. As discussed below, different types of transcription control regions are known in the art that can be used to control initiation of transcription of the transgene into RNA. As used herein, the term “operable linkage,” and variations such as “operative linkage,” “operably linked,” and “operatively linked,” refer to a functional relationship between the transcription control region and transgene, so that the control region can affect transcription of the transgene (whether positively or negatively), without specifying any particular spatial or structural relationship between them. Thus, for example, a transcription control region could be operably linked with a transgene even though it is positioned 5' or 3' of the transgene and/or positioned immediately adjacent to or distal from the transgene. Transcription control regions can be constitutively active, active in specific cells or tissues, inducibly active in response to some environmental stimulus, be derived from a naturally occurring gene (of any suitable species) and can be modified to improve or change its function, or even be entirely synthetic.
In some embodiments, a transcription control region comprises a promoter region, which comprises the minimal DNA sequence required to initiate transcription by the transcription apparatus in transduced cells (e.g., a TATA box or initiator sequence), often as well as one or more additional proximal elements that act singly or cooperatively to increase the rate of transcription from the basal promoter. Depending on its sequence, a promoter can initiate transcription by RNA polymerase I, II, or III, but promoters from protein encoding genes, which are usually transcribed by RNA pol II, are often used in AAV vectors intended to express a polypeptide, such as BAG3 or variant thereof, in transduced cells.
In other embodiments, a transcription control region comprises or further comprises at least one enhancer region, which functions to further increase the rate of gene transcription beyond what the basal promoter alone can sustain. In their natural context, enhancers are often positioned distally from the promoter of the gene on which they act, sometimes tens to hundreds or thousands of basepairs upstream (/.e., 5'), but enhancers can also occur elsewhere, such as in introns or downstream (/.e., 3') of the gene on which they act. While promoter regions may contain proximal enhancer elements (subsequences that, if removed, would reduce transcription from the basal promoter), enhancers do not usually contain sequences that can function as a basal promoter. Although enhancer regions in nature are often positioned distally to the promoter of the gene on which they act, enhancer regions, or enhancer elements from within larger enhancer regions (such elements often corresponding to DNA binding sites fortranscription factors), can sometimes retain at least some of their transcription enhancing function when removed from their natural context and repositioned much closer to a promoter, whether from the same or even a different gene.
Enhancer and promoter regions of genes described in the scientific literature may be too large to be accommodated by the packaging capacity of AAV capsids when combined with a transgene and other genomic elements required for vector function. Accordingly, in some embodiments, functional subsequences within longer enhancer or promoter regions can be identified using methods familiar to those of ordinary skill, and the shorter functional subsequences incorporated into transcription control regions for use in the vectors of the disclosure. In this manner, the size of transcription control regions can be reduced while maintaining their desired function. Using this approach, functional elements from naturally occurring enhancers or promoters can be combined in novel ways, such as by modifying their number, spacing and/or arrangement, to create hybrid or synthetic enhancers and/or promoters with improved properties. In some embodiments, the enhancer and promoter can each be derived from the same, naturally occurring gene, whereas in other embodiments, the enhancer and promoter can originate from entirely different genes, including genes of different species.
In some embodiments, from the perspective of a coding strand (/.e., plus strand) single stranded DNA AAV vector, a promoter sequence is positioned 5' of a downstream sequence to be transcribed into RNA, such as a transgene encoding a protein, such as BAG3 or variant thereof. In some embodiments, an enhancer element or region, if present, can be positioned 5' of the promoter sequence, or instead be positioned elsewhere in the genome, such as in a 5' or 3' untranslated region (UTR) adjacent the transgene, in an intron, 3' of a transcription termination signal sequence, or elsewhere. In some embodiments, a vector can comprise more than one enhancer region (of same or different types), which can be positioned adjacent to each other, or spaced apart, and/or separated by other functional elements within the genome. In some embodiments, the same enhancer element or region is provided in a tandemly arranged array of repeating units, such as 2, 3, 4, or more.
In some embodiments, transcription control regions for use in the AAV vectors of the disclosure are non-tissue specific, meaning that they are constitutively active in many different cell types, although not necessarily all. According to some embodiments, nontissue specific transcription control regions include promoters (which may include enhancer elements proximal to a basal promoter) derived from certain viruses, such as the human cytomegalovirus major immediate early gene (CMV-IE) (Boshart et al., 06114 (2)-. 521-30 (1985); Yew et al., Hum. Gene Ther. 8(5): 575-84 (1997)); simian virus 40 (SV40); as well as the retroviral long terminal repeat (LTR) promoters from Rous sarcoma virus (RSV) and Moloney murine leukemia virus (MoMLV). In other embodiments, non-tissue specific transcription control regions include promoters (which may include proximal enhancer elements) that can be derived from genes active in many different cell types (which are sometimes referred to as “housekeeping” genes), including from different types of animals, such as the human polypeptide chain elongation factor (EF1a) gene; the phosphoglycerate kinase (PGK) gene; the ubiquitin C (UbiC) gene; the chicken beta-actin (CBA) gene; the U1a1 or U1 b2 small nuclear RNA promoters (Bartlett et al., Proc. Natl. Acad. Sci. U.S.A. 93(17): 8852-57 (1996); Wu et al., Mol. Ther. 16(2): 280-89 (2008)); or the histone H2 or histone H3 promoters (Hurt et al., Mol. Cell Biol. 11 (6): 2929-36 (1991)).
Likewise, enhancer regions can be derived from viruses and genes active in different cell types from different types of animals. As noted, in some embodiments, a promoter and enhancer derived from the same gene can be combined to create a transcription control region for use in the vectors of the disclosure, but enhancers and promoters from different genes can be combined to create hybrid transcription control regions. A commonly used example is the 1.6 kilobase hybrid enh/pro region called CAG (or CAGGS) comprising the CMV immediate-early enhancer, the chicken beta actin (CBA) gene promoter and the CBA intron/exon 1 (Niwa et al., Gene 108(2): 193-99 (1991)); Ikawa et al., Dev. Growth Differ. 37(4): 455-59 (1995)), and later modifications that reduced its size, including one in which the CBA intron was replaced with a smaller simian virus 40 (SV40) intron (Wang et al., Gene Ther. 10(26): 2105-11 (2003)), and another called CBA hybrid intron (CBh) that replaced the SV40 intron with a hybrid intron composed of a 5' donor splice site from the CBA 5' UTR and a 3' acceptor splice site from the MVM intron (Gray et al., Hum. Gene Ther. 22(9): 1143-53 (2011)).
In some embodiments, transcription control regions for use in the AAV vectors of the disclosure can be cardiac tissue specific, meaning that they are more or most active in directing expression of a transgene in cell types within the heart, compared to cells of other tissues or organs, such as the muscle, brain, or liver. In some embodiments, the cardiac cell types in which transcription control regions of AAV vectors of the disclosure are active include, without limitation, cardiomyocytes, with other cell types being possible. Without wishing to be bound by any particular theory of operation, one mechanism by which cardiac tissue or cardiac cell gene transcriptional specificity may occur is the presence in an enhancer and/or promoter of one or more specific binding sites for DNA binding transcriptional activator proteins preferentially expressed in cardiac cells, such as cardiomyocytes or other cell types in the heart. Use of a cardiac tissue or cardiac cell specific transcription control region can be advantageous, in some embodiments, by reducing or even preventing transgene expression in cells outside of the heart or noncardiac cells (or other cardiac cell type) that may be transduced by a vector, which can desirably reduce the risk of off-target effects.
In some embodiments, transcription control regions for use in the AAV vectors of the disclosure are tissue specific, meaning that they are constitutively active in specific cell types, for example cardiac cell types. Non-limiting examples of cardiac promoters include chicken troponin T (cTNT) (for example, as in SEQ ID NO: 5), CAG (for example, as in SEQ ID NO: 28), MHCK7 (for example, as in SEQ ID NO: 25), CK7 (for example, as in SEQ ID NO: 27), endogenous BAG promoter (for example, as in SEQ ID NO: 26), desmin (Des), alpha-myosin heavy chain (a-MHC), myosin light chain 2 (MLC-2), and cardiac troponin C (TNNC1 or cTnC) promoters, as well as the 600 base pair cardiac troponin T (TNNT2) promoter, or a functional subsequence, modification, or variant respectively thereof.
Transcription Terminator Sequence
In some embodiments, for example when the transgene contains a protein encodingsequence (as opposed to the sequence of an RNA with some function other than encoding protein), the transcription terminator sequence can be a polyadenylation signal sequence (abbreviated variously as “polyA,” “pA,” “poly(A)” or “p(A)”). In some embodiments, polyA signal sequences can be derived from naturally occurring genes and used in vectors, whereas in other embodiments, polyA signals can be modified, such as by shortening them compared to their natural counterparts or altering their sequence to make them more efficient at transcription termination. In other embodiments, polyA signals can be hybrid sequences, combining polyA sequences from different genes, or synthetic.
Non-limiting examples of polyA signals that may be used in the vectors of the disclosure include the polyA signal from the bovine growth hormone gene (bGH pA); human, mouse or rabbit beta-globin gene; SV40 late gene; sNRP1 ; spA; herpes simplex virus thymidine kinase gene (HSV TK); or adenovirus type 5 L3 polyadenylation site, with others being possible. In other embodiments, transcription terminators for use in vectors of the disclosure include those that terminate RNA transcripts without directing polyadenylation, such as the histone H4 gene mRNA 3' end processing signal (Whitelaw et al., Nucleic Acids Res. 14(17): 7059-70 (1986)).
In some embodiments, AAV vectors of the disclosure comprise expression cassettes comprising a transgene, transcription of which is terminated by inclusion (1) of a poly(A) site derived from the bovine growth hormone gene (bGH) that, in some embodiments, comprises or consists of the nucleotide sequence of SEQ ID NO: 32 or a functional subsequence, modification, or variant respectively thereof; (2) of a poly(A) site from SV40 virus that, in some embodiments, comprises or consists of the nucleotide sequence of SEQ ID NO: 7 or a functional subsequence, modification, or variant respectively thereof; or (3) of a poly(A) site from the rabbit beta-globin gene or a functional subsequence, modification, or variant respectively thereof.
Other Vector Genomic Elements
In addition to transcription control regions and transcription termination signal, other sequences, including cis-regulatory elements, can be included in genomes of AAV vectors of the disclosure to improve, control or modulate transgene expression and/or translation in transduced cells, or confer other functions to the vectors. Such elements include, without limitation, untranslated regions from the 5' and/or 3' ends of genes, non-coding exons, introns, splice donor and acceptor sites, lox sites, internal ribosome entry sites (IRES), sequence encoding 2A peptides, elements that stabilize RNA transcripts, binding sites for regulatory miRNAs, micro RNA (miRNA) sequences, elements that enhance nuclear export of mRNAs, including viral post-transcriptional regulatory elements, such as the woodchuck hepatitis virus post-transcriptional regulatory element (WPRE), as well as any other element demonstrated empirically to improve transgene expression, even if the mechanism may be uncertain. In other embodiments, vectors can include so-called stuffer or filler sequences, which are intended only to increase the overall length of the vector to a desired size, for example, to achieve a length close to but still under the packaging capacity of a particular capsid, and thereby reduce the likelihood of adventitiously packaging truncated vectors or non-vector DNA into capsids.
Introns
Introns can, in some embodiments, be included in vectors to increase transgene expression and/or transcript stability. In some embodiments, a protein encoding transgene is provided in which the sequence of exons and introns is the same as in the naturally occurring gene. In a gene possessing multiple exons and introns, however, one or more of the introns can be removed so as to minimize the overall length to facilitate the inclusion of other elements while not exceeding the capsid packaging capacity. In other embodiments, however, an intron can be provided from an entirely different gene than the gene providing the coding sequence for the vector transgene. Whether the intron is from the same or a different gene as the transgene, the intron can be modified from its original sequence, for example by changing certain nucleotides, or removing internal sequences to reduce its overall length while maintaining the splice donor and acceptor sequence motifs required for efficient splicing to occur, or other intronic cis elements important for function (for example, enhancers that may reside in the original unmodified intron sequence). Introns can also be hybrid, where the splice donor portion of the intron from one gene is paired with the splice acceptor portion of the intron from a different gene, or synthetic, with sequence that does not correspond to any known gene’s intron. Introns, in some embodiments, can be positioned within, and therefore interrupt, the coding sequence of a transgene (and be provided with the donor and acceptor sites necessary for efficient splicing to occur), whereas in other embodiments an intron is present, but does not interrupt the protein coding sequence, and is instead positioned either 5' or 3' of the coding sequence. Where an intron does not interrupt coding sequence, it may be provided with some exonic sequence carried over from its original genetic context, so long as the exonic sequence does not contain a cryptic translation start signal. In some embodiments, an intron can be positioned 3' of a promoter (from the perspective of plus strand ssDNA vector) and 5' of the coding sequence. In other embodiments, an intron can be positioned distally from coding sequence in a vector, either upstream or downstream.
Non-limiting examples of introns that may be used in the AAV vectors of the disclosure, such as in the expression cassette, include introns having nucleotide sequence of SEQ ID NOs: 6 or 29-31 , or a functional subsequence, modification, or variant respectively thereof. Other non-limiting examples include the small intron from the minute virus of mice (MVM) (Haut et al., J. Virol. 72(3): 183443 (1998); Haut et al., Virology 258(1): 8494 (1999)); internally deleted intron 1 from human clotting factor IX (FIXml and FIXm2) (Kurachi et al., J. Biol. Chem. 270(10): 527681 (1995)); chimeric beta globin splice donor and immunoglobulin heavy chain splice acceptor intron (GenBank U47120.2 nucleotides 890-1022); intron 1 from the mouse alpha globin gene; and the SV40 small t antigen intron that can comprise or consist of base pairs 4644 to 4552 of GenBank record J02400.1 , and that can be modified at positions 4582 (g to c), 4580 (g to c), 4578 (a to c), and 4561 (a to t) (Nathwani et al., Blood 107 (7): 265361 (2006)).
AAV Inverted Terminal Repeats (ITRs)
Positioned at the termini of the adeno-associated virus genome are unique nucleotide sequences called inverted terminal repeats (abbreviated, “ITR”) that function as origins of viral DNA replication and as priming sites to support the conversion, in infected cells, of the single-stranded (ssDNA) genome into a double-stranded form (dsDNA) competent to support transcription of the rep and cap protein-encoding genes, also contained in the virus genome. The ITRs also function in packaging of replicated ssDNA genomes into AAV capsids. AAV ITRs contain multipalindromic sequences that can fold back on themselves via intra-strand complementary base pairing to form dsDNA T-shaped hairpin secondary structures.
As explained further below, expression cassettes of AAV vectors of the disclosure can include one or more AAV ITRs, which function similarly as they do in unmodified virus. Unless otherwise, use of the term “inverted terminal repeat” or “ITR” herein includes intact full-length ITRs, as well as ITRs with modified sequences (such as truncations, internal deletions (such as of a trs or D sequence), additions, and substitutions of one or more nucleotides) that retain one or more of the functions attributable to ITRs (even if less efficiently compared to an intact ITR of the same type), including but not limited to rescue of vector from recombinant DNA (such as a plasmid), vector replication, and/or packaging of vector into assembled capsids.
As they exist in packaged viral and vectors, the ITR positioned at the 3' end of the ssDNA genome will have a free 3' hydroxyl group, whereas the ITR positioned at the opposite 5' end of the ssDNA genome will have a free 5' end. The 5' ITR can also referred to as the “left” ITR, and the 3' ITR can also referred to as the “right” ITR. In the context of a plasmid, however, such as might be used in vector production, the vector sequence will exist in double-stranded form, such that there will be two sets each of 5' ITRs and 3' ITRs. To avoid ambiguity therefore, it should be specified which strand an ITR sits on to distinguish among them. In the absence of such specification, reference to the ITRs of a vector in double-stranded form, such as in a plasmid, is with respect to the plus or sense strand, i.e., the DNA strand on which the sequence of the transgene is the same as the coding sequence for a polypeptide product of the transgene, or of a functional RNA, where the transgene is not protein encoding.
In some non-limiting and purely exemplary embodiments, the expression cassettes of the rAAV vectors of the disclosure can contain one or more ITRs comprising, consisting essentially of, or consisting of the nucleotide sequence of any one or more of SEQ ID NO: 8 and SEQ ID NO: 9 or a functional subsequence, modification, or variant respectively thereof, with other ITR sequences being possible, or the complement or reverse complement of any of the foregoing specifically recited sequences.
In some embodiments, the rAAV vectors disclosed herein comprise at least one 5’ ITR. In some embodiments, the at least one 5’ ITR comprises the nucleotide sequence of SEQ ID NO: 8, or a functional subsequence, modification, or variant thereof.
In some embodiments, the rAAV vectors disclosed herein comprise at least one 3’ ITR. In some embodiments, the at least one 3’ ITR comprises the nucleotide sequence of SEQ ID NO: 9, or a functional subsequence, modification, or variant thereof.
Stuffer or Filler Sequences
In some embodiments, rAAV vectors of the disclosure further comprise at least one stuffer or filler nucleotide sequence. In some embodiments, the at least one stuffer or filler sequence is an inert nucleotide sequence positioned inside the 5’-ITR to 3’-ITR payload (aka expression cassette). In some embodiments, the at least one stuffer or filler sequence is positioned 3' of the poly(A) signal sequence and 5' of an ITR. The at least one stuffer or filler may have any desired design, and use of a stuffer or filler sequence, as defined herein, is intended to result in a reduction of contaminating nucleic acids packaged into a viral particle/capsid. In some embodiments, a stuffer or filler sequence can be a random sequence of nucleotides. In some embodiments, the at least one stuffer or filler sequence is derived from a human sequence. In some embodiments, the stuffer or filler sequence is derived from an intron of a gene, such as the Factor 9 gene or the gene encoding the TATA box binding protein (TBP) of human or another species, or a functional subsequence, modification, or variant thereof. In some embodiments, the stuffer or filler sequence is a TBP gene intron, or functional subsequence, modification, or variant thereof. In some embodiments, at least one stuffer or filler sequence can be one or more intronic sequences which have been modified, for example, to deplete CpGs. In some embodiments, the stuffer or filler sequence has 97% sequence identity to intron 1 of the Factor 9 gene. In some embodiments, the stuffer or filler sequence has the nucleotide sequence of SEQ ID NO: 11 .
Spacers
In some embodiments, rAAV vector plasmids of the disclosure comprise at least one spacer sequence. The spacer is an inert nucleotide sequence outside the 5’-ITR to 3’-ITR payload (aka expression cassette) - i.e., the spacer is part of the rAAV vector plasmid. The spacer may have any desired design, and use of a spacer sequence, as defined herein, is intended to result in a reduction of contaminating nucleic acids packaged into a viral particle/capsid. In some embodiments, a spacer sequence can be a random sequence of nucleotides. In other embodiments, it can encode a gene product, such as a marker gene. In certain embodiments, a spacer can be one or more intronic sequences from the Factor 9 gene which have been modified, for example, to deplete CpGs. In some embodiments, the length of the spacer may range from about 10 nucleotides to about 10,000 nucleotides, such as in the range of about 100 nucleotides to about 8,000 nucleotides. In certain embodiments, a spacer sequence is less than 2,000 nucleotides in length.
In some embodiments, the rAAV vector plasmids disclosed herein comprise at least one left (i.e., 5’ of the 5’ ITR) spacer sequence. In some embodiments, the at least one left spacer comprises the nucleotide sequence of SEQ ID NO: 12, or a functional subsequence, modification, or variant thereof.
In some embodiments, the rAAV vector plasmids disclosed herein comprise at least one right (i.e., 3’ of the 3’ ITR) spacer sequence. In some embodiments, the at least one right spacer comprises the nucleotide sequence of SEQ ID NO: 13, or a functional subsequence, modification, or variant thereof.
In some embodiments, the rAAV vector plasmids of the disclosure, including the expression cassette, must be greater than about 4.7 kilobases, such as greater than about 5 kilobases. In some embodiments, the rAAV vector plasmids of the disclosure, including the expression cassette, range in size from about 4.7 kilobases to about 12 kilobases.
In some embodiments, the rAAV vector plasmid comprises at least one left spacer and/or at least one right spacer, such that the at least one left spacer and/or at least one right spacer increases the entire length of the rAAV vector plasmid to about 4.7 to about 12 kilobases, such as about 9 to about 10 kilobases.
Compound A
Some embodiments comprise Compound A, an AAV9 gene therapy vector that delivers BAG3 protein expression to the heart under the control of a cardiac specific promoter (for example, the troponin T (cTNT) promoter). It is intended for the treatment of diseases or disorders (1) associated with mutations in Bcl2-associated athanogene 3 (BAG 3) or (2) mediated by or associated with BAG3 protein expression. Compound A is a heart-directed gene therapy, and AAV9 is known to transduce the heart in mice, non-human primates, and humans. In addition, the cTNT promoter confers transgene expression that is strongly cardiac-biased (Prasad et al., Gene Ther. 18(1): 43-52 (2011)). In some embodiments, one-time intravenous administration may be used to transduce a substantial proportion of cardiomyocytes in the heart. BAG3 cKO mice show substantial deficits in left ventricular ejection fraction and left ventricular end diastolic volume at 18-21 weeks of age. When 12 -week old BAG3 cKO mice with low and declining heart function were dosed intravenously with Compound A at 1 E13, 3E13 and 9E13 vg/kg, cardiac function (ejection fraction) and structure (diastolic volume) were dose-dependently improved relative to untreated cKO controls. The mid- and high-dose levels stabilized ejection fraction relative to the time of dosing. Analysis of BAG3 mRNA biodistribution in heart by in situ hybridization showed that the effect on cardiac function increased with increasing heart coverage and plateaued at 20 - 80% coverage. Analysis of BAG3 protein levels in heart similarly showed an increase in efficacy from 0% to 20% of the wild-type BAG3 level and a plateau from 20 - 120%. These correlations defined the targets for heart biodistribution and expression required for cardiac efficacy.
In a non-human primate biodistribution and safety study, the human BAG3 protein level in the heart exceeded target threshold of 20% of wild type (WT) at 1 .3E14 vg/kg, and the percentage of human BAG3 mRNA positive cardiomyocytes in the heart exceeded target threshold of about 20% at about 4E13 and about 1 .3E14 vg/kg. In some embodiments, the clinically-efficacious dose is projected to be between about 3E13 and about 1 E14 vg/kg, inclusive. There were no development-limiting safety findings.
Compound A is intended to be an AAV gene therapy for cardiac-related diseases and disorders, such as BAG3 DCM. This vector differentiates from other vectors through the use of intravenous delivery (broader and more even heart transduction than intracoronary) and a cardiac specific promoter (e.g., greater safety and potentially more durable expression than CMV).
Pharmaceutical Composition
In some embodiments, the present disclosure provides a pharmaceutical composition, or medicament, for preventing or treating a disease, disorder or condition mediated by or associated with decreased expression and/or activity of BAG3, e.g., dilated cardiomyopathy. In some embodiments, a pharmaceutical composition comprises a modified nucleic acid, a recombinant nucleic acid, a viral vector genome, an expression vector, a host cell or a rAAV vector, and a pharmaceutically acceptable carrier.
In some embodiments, a pharmaceutical composition comprises a therapeutically effective amount of a vector (e.g., viral vector genome, expression vector, rAAV vector) or host cell comprising a modified nucleic acid encoding BAG3 which can increase the level of expression and/or the level of activity of BAG3 in a cell.
The rAAV vector or vector genome dose to achieve a therapeutic effect, e.g., the dose in vector genomes/per kilogram of body weight (vg/kg), will vary based on several factors including, but not limited to: route of administration, the level of heterologous polynucleotide expression required to achieve a therapeutic effect, the specific disease treated, any host immune response to the viral vector, a host immune response to the heterologous polynucleotide or expression product (protein), and the stability of the protein expressed. Generally, doses will range from at least 1 E8, or more, for example, 1 E9, 1 E10, 1 E11 , 1 E12, 1 E13 or 1 E14, 1 E15, 1 E16, 1 E17, or more, vector genomes per kilogram (vg/kg) of the weight of the subject, to achieve a therapeutic effect. In some embodiments, a pharmaceutically effective amount of the rAAV vector ranges from about 1 E10 to about 1 E17 vector genomes per kilogram (vg/kg) of subject body weight.
In some embodiments, a pharmaceutical composition comprises a therapeutically effective amount of a vector (e.g., viral vector genome, expression vector, rAAV vector) or host cell (e.g., for ex vivo gene therapy) comprising a nucleic acid encoding BAG3 wherein the composition further comprises a pharmaceutically-acceptable carrier, adjuvant, diluent, excipient, other medicinal agents or a combination thereof. A pharmaceutically acceptable carrier, adjuvant, diluent, excipient or other medicinal agent is one that is not biologically or otherwise undesirable, e.g., the material may be administered to a subject without causing undesirable biological effects which outweigh the advantageous biological effects of the material.
Any suitable pharmaceutically acceptable carrier or excipient can be used in the preparation of a pharmaceutical composition according to the invention (see, e.g., Remington The Science and Practice of Pharmacy, Alfonso R. Gennaro (Editor) Mack Publishing Company, April 1997).
A pharmaceutical composition is typically sterile, pyrogen-free and stable under the conditions of manufacture and storage. A pharmaceutical composition may be formulated as a solution (e.g., water, saline, dextrose solution, buffered solution, or other pharmaceutically sterile fluid), microemulsion, liposome, or other ordered structure suitable to accommodate a high product (e.g., viral vector particles, microparticles or nanoparticles) concentration. In some embodiments, a pharmaceutical composition comprising a modified nucleic acid, vector genome comprising the modified nucleic acid, host cell or rAAV vector of the disclosure is formulated in water or a buffered saline solution. A carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. Proper fluidity can be maintained, for example, by use of a coating such as lecithin, by maintenance of a required particle size, in the case of dispersion, and by the use of surfactants. In some embodiments, it may be preferable to include isotonic agents, for example, a sugar, a polyalcohol such as mannitol, sorbitol, or sodium chloride in the composition. Prolonged adsorption of an injectable composition can be brought about by including, in the composition, an agent which delays absorption, e.g., a monostearate salt and gelatin. In some embodiments, a nucleic acid, vector and/or host cell of the disclosure may be administered in a controlled release formulation, for example, in a composition which includes a slow-release polymer or other carrier that protects the product against rapid release, including an implant and microencapsulated delivery system.
In some embodiments, a pharmaceutical composition of the disclosure is a parenteral pharmaceutical composition, including a composition suitable for intravenous, intraarterial, subcutaneous, intradermal, intraperitoneal, intramuscular (e.g., cardiac muscle) and/or intraarticular. In some embodiments, a pharmaceutical composition comprising a rAAV vector comprising a nucleic acid encoding BAG3 is formulated for administration by intravenous injection.
In some embodiments, the pharmaceutical composition of the disclosure comprises at least one pharmaceutically acceptable salt in an amount ranging from about 1 mM to about 450 mM, or from about 2 mM to about 350 mM, or from about 20 mM to about 200 mM. In certain embodiments, the at least one pharmaceutically acceptable salt is present in the pharmaceutical composition at about 150 mM. In other embodiments, the at least one pharmaceutically acceptable salt is present in the pharmaceutical composition at about 350 mM. In certain embodiments, the at least one pharmaceutically acceptable salt is sodium chloride, magnesium chloride, potassium chloride, calcium chloride, calcium phosphate, or combinations thereof. In certain embodiments, the at least one pharmaceutically acceptable salt comprises sodium chloride and magnesium chloride. In certain embodiments, the at least one pharmaceutically acceptable salt comprises sodium chloride at about 5 mM to about 6 mM and magnesium chloride at about 45 mM to about 55 mM. In other embodiments, the least one pharmaceutically acceptable salt comprises sodium chloride and potassium chloride. In other embodiments, the least one pharmaceutically acceptable salt comprises sodium chloride at about 300 mM to about 400 mM and potassium chloride at about 2 mM to about 3 mM.
In some embodiments, the pharmaceutical composition of the disclosure further comprises at least one buffer. In certain embodiments, the buffer is citrate, histidine, acetate, phosphate, tris hydrochloride, tromethamine, or combinations thereof. In an embodiment, the buffer is phosphate (for example, at about 5 mM to about 15 mM). In another embodiment, the buffer is tris hydrochloride (for example, at about 2 mg/mL to about 3 mg/mL) and tromethamine (at about 0.25 mg/mL to about 0.75 mg/mL). In certain embodiments, the least one buffer is present in an amount ranging from about 10 mM to about 40 mM. In some embodiments, the at least one buffer is present in an amount of about 20 mM.
In some embodiments, the pharmaceutical composition of the disclosure further comprises at least one cryoprotectant. In certain embodiments, the at least one cryoprotectant is a sugar or a sugar alcohol. In some embodiments, the least one cryoprotectant is trehalose, sucrose, sorbitol, mannitol, or a combination thereof. In an embodiment, the at least one cryoprotectant is sucrose (for example, at about 30 mg/mL to about 50 mg/mL). In another embodiment, the at least one cryoprotectant is sorbitol (for example, at about 2% to about 10%). In certain embodiments, the at least one cryoprotectant is present in an amount of up to about 20%. In some embodiments, the at least one cryoprotectant is present in an amount ranging from about 3% to about 15%. In some embodiments, the at least one cryoprotectant is present in an amount of about 4% or about 5%.
In some embodiments, the pharmaceutical composition of the disclosure further comprises at least one surfactant. In certain embodiments, the at least one surfactant is a polaxamer or a polysorbate. In some embodiments, the at least one surfactant is polaxamer 188, polysorbate 20, or polysorbate 80. In some embodiments, the at least one surfactant is polaxamer 188 at about 0.1 % to about 0.5%. In certain embodiments, the at least one surfactant is present in an amount ranging from about 0.0001% to about 1 %. In an embodiment, the at least one surfactant is present in an amount of about 0.02%. In another embodiment, the at least one surfactant is present in an amount of about 0.002%.
In some embodiments, the pharmaceutical composition of the disclosure has a pH ranging from about 6 to about 8. In some embodiments, the pharmaceutical composition has a pH ranging from about 7 to about 8. In an embodiment, the pharmaceutical composition has a pH of about 7.6. In another embodiment, the pharmaceutical composition has a pH of about 7.4.
In some embodiments, a rAAV vector comprising a BAG3 transgene is purified and suspended in a formulation comprising: 10 mM phosphate, 350 mM NaCI, 2.7 mM KCI, 5% sorbitol, and 0.002% pluronic, at pH 7.4. In some embodiments, a rAAV vector comprising a BAG3 transgene is purified and suspended in a formulation comprising tromethamine 0.47 mg/mL, Tris 2.54 mg/mL (Tris and tromethamine combined being 20 mM), MgCI2 10.17 mg/mL (50 mM), NaCI 5.84 mg/mL (100 mM), sucrose 40 mg/mL (4%), polaxamer188 0.2 mg/mL (0.02%), at pH 7.6.
AAV Vector Production
As known in the art, AAV vectors can be produced, including at large scale, in a variety of ways. AAV vectors, for example, can be made in mammalian or insect cells and then purified. The traditional approach, which does not rely on coinfection with a helper virus, involves use of three plasmids as discussed above. One plasmid contains genes for helper virus factors, a second contains the AAV genome sequence in double stranded form, and the third contains AAV rep and cap genes. In practice, the three plasmids are often separately replicated in bacteria, purified, mixed in solution together in predetermined proportions, and then mixed with a transfection agent. The transfection mixture is then used to transfect suitable mammalian host cells (in adherent or suspension cell culture) that are incubated for sufficient time (e.g., 48 to 72 hours, etc.) and under conditions sufficient for the host cells to express the helper factors and the rep and cap genes, and for AAV vector to be replicated from its plasmid template and packaged into capsids. In some embodiments, the host cells are HEK293 cells or derivatives thereof, which constitutively express AdV helper factors E1A and E1 B, such that the helper plasmid only need contain the AdV E2A, E4ORF6, and VA RNA genes. Use of other mammalian host cells that do not produce AdV or other viral helper factor on their own would necessitate use of a helper plasmid containing whichever helper factors are missing or are otherwise required. Although the so-called triple transfection method described above is commonly employed, there is no requirement that the genes for the helper factors, and rep and cap genes, be provided on separate plasmids. In principle all these genes could be housed in one plasmid, for example, in which case two plasmids can be used in the transfection.
Seeking more efficient methods of producing AAV vector at large scale, stable cell lines have been created that contain some but not all the components that would otherwise need to be introduced into cells by transient transfection. Packaging cell lines contain stably integrated AAV rep and cap genes. Production of AAV in packaging cells requires them to be transiently transfected with a plasmid containing an AAV vector and infected with a helper virus. It is also possible to produce AAV vectors in packaging cells without transfection by first infecting them with an AdV (either wild-type or in which the E2b gene is deleted) that supplies AdV E1 gene products, which induce rep and cap expression in the cells, as well as helper factors required for AAV replication, followed by infection with a replication deficient hybrid AdV in which an AAV vector replaces the E1 gene in the genome of the hybrid virus.
In another option, producer cell lines contain stably integrated AAV rep and cap genes, and also an AAV vector. Production of AAV in producer cells requires them to be infected with a helper virus. Packaging and producer cells have been described (Martin et al., Hum. Gene Ther. Methods 24(4): 253-69 (2013); Gao et al., Hum. Gene Ther. 9(16): 2353-62 (1998); Clement et al., Mol. Ther. Methods Clin. Dev. 3: 16002 (2016)). Other cellular systems for producing AAV vectors in mammalian cells, including at commercial scale, are possible.
The baculovirus system has also been employed to produce AAV vectors, in which Sf9 insect cells are infected with recombinant baculovirus vectors that variously contain the AAV rep and cap genes and the AAV genome. The exogenous genes are expressed, followed by genome packaging into vector particles within the cells. In early versions of the system, each component, rep, cap, and genome, were carried by three separate baculoviruses. Later, modifications were made, such as combining rep and cap into a single baculovirus, so that only two types of baculovirus were required, as well as producing Sf9 cell lines containing stably integrated AAV rep and cap genes, which only require infection with a single type of recombinant baculovirus containing an AAV vector (Urabe et al., Hum. Gene Ther. 13(16): 1935-43 (2002); Virag et al., Hum. Gene Ther. 20(8): 807-17 (2009); Smith et al., Mol. Ther. 17(11): 1888-96 (2009); Mietzsch et al., Hum. Gene. Ther. 25(3): 212-22 (2014)). Other cellular systems for producing AAV vectors in insect cells, including at commercial scale, are possible.
Host Cells
As used herein, “host cells” means cells suitable for or adapted to in vitro production of AAV vectors. Host cells are often clonal cell lines capable of dividing for multiple generations before senescence stops growth or may even be immortal. To produce vectors, host cells can be modified, transiently or non-transiently, through the introduction of exogenous genetic information designed to direct biosynthesis in host cells of the various components required for AAV vector assembly, notably the AAV capsid proteins, Rep proteins, helper virus factors, and vectors. For example, host cells can be transfected with exogenously supplied nucleic acid, such as in the form of one or more DNA plasmids, containing nucleotide sequences coding for the required vector components.
Various ways are known in the art for transfecting host cells with nucleic acid. These include, without limitation, mixing nucleic acid with certain compounds that can complex with nucleic acids and then be taken up into the cells, including calcium phosphate or cationic organic compounds, such as DEAE-dextran, polyethylenimine (PEI), polylysine, polyornithine, polybrene, cyclodextrin, cationic lipids, and others known in the art. Transfection can also be performed non-chemically via electroporation and more exotic technologies, such as biolistic particle delivery. As known in the art, transfection can be transient or stable. With transient transfection, the transfected nucleic acid exists in the cell for a limited period of time and, in the case of DNA, does not integrate into the genome. With stable transfection, DNA introduced into the cell can persist for long periods either as an episomal plasmid or integrated into a chromosome. Usually, to produce stably transfected cells, a plasmid containing a selection marker gene, as well as nucleotide sequence coding for one or more of the required vector components, is transfected into the cells that are then grown and maintained under selective pressure, i.e., conditions that kill non-transfected cells or transfected cells from which the exogenous DNA, including its selection marker, are lost for some reason. For example, plasmids can contain an antibiotic resistance gene and transfected cells can be selected for by adding the antibiotic to the media in which the cells are grown. In some embodiments, the nucleotide sequence coding for one or more of the required vector components introduced into stably transfected host cells is under the control of an inducible promoter and is not expressed, or only at a low level, unless an environmental factor, such as a drug, metal ion, or temperature increase, which induces the promoter, is introduced as the cells are grown.
In other embodiments, host cell genomes can be modified in a non-transient and targeted fashion using genetic engineering methods, such as knock-in, or gene editing methods, to direct host cells to produce one or more of the required vector components. In other embodiments, nucleotide sequence coding for one or more of the required vector components can be introduced into host cells for purposes of directing production of AAV vectors via transduction, in which host cells are infected with modified viruses containing such nucleotide sequences. Examples of viral vectors useful for such purposes include adenovirus, retroviruses (including lentiviruses), baculoviruses, vaccinia virus, and herpes simplex virus, with others being possible.
Host cells can be any type of cell known in the art to be useful for the purpose of producing AAV vectors. Host cells are often animal cells, with different types or species being possible, such as insect cells or mammalian cells, including rat, mouse, or human cells, with others being possible. In some embodiments, host cells useful for producing AAV vectors of the disclosure are mammalian host cells, examples of which include HeLa cells, Cos cells, HEK293 cells (and variants of HEK293 cells, such as HEK293E, HEK293F, HEK293H, HEK293T or HEK293FT cells), A549 cells, BHK cells, Vero cells, NIH 3T3 cells, HT-1080 cells, Sp2/0 cells, NSO cells, C127 cells, AGE1.HN cells, CAP cells, HKB-11 cells, WI-38 cells, MRC-5 cells, or PER.C6 cells, with many others being possible. In some embodiments, host cells useful for producing AAV vectors of the disclosure are insect host cells, examples of which include Sf9 cells, ExpiSf9, Sf21 cells, S2 cells, D.Mel2 cells, Tn-368 cells, or BTI-Tn-5B1-4 cells, with many others being possible. In some embodiments, host cells, including without limitation HEK293 cells, and its variants, can be adapted to growth in suspension culture.
For purposes of producing AAV vectors, host cells are often grown or maintained in culture under controlled conditions conducive to their growth and vector biosynthesis. For example, host cells can be grown in liquid media of defined chemical composition that provides all the nutrients necessary for cell growth and biosynthesis. Exemplary media includes DMEM, DMEM/F12, MEM, RPMI 1640, for mammalian host cells, and Express Five SFM, Sf-900 II SFM, Sf-900 III, or ExpiSf CD, for certain insect cells. Such media may be supplemented with antibiotics, growth factors or cytokines (produced recombinantly or present in animal serum, such as FBS) known to stimulate growth of the particular type of cells in use, as well as other ingredients that may be required for optimal biosynthesis of AAV vectors, but that would otherwise be in limiting supply. Exemplary supplements include essential amino acids, glutamine, vitamin K, insulin, BSA, or transferrin. In addition to the growth media, other culture conditions may be controlled to optimize growth and/or productivity of the cells, such as pH, temperature and CO2 and oxygen concentration.
Host cells in culture can be grown or maintained in many containers known in the art, such as stirred tank bioreactors, wave bags, spinner flasks, hollow fiber bioreactors, or roller bottle, some of which can be designed and configured for single use or multiple use. Depending on the characteristics of the host cells in question, host cells can be grown in adherent cell culture, where the cells attach to and grow while in contact with a physical substrate, or in suspension cell culture, either where single cells float free in the media that sustains them, or while attached to bead microcarriers, which are suspended in the media. As known in the art, various technologies have been developed and can be used to grow host cells to high cell density, such as perfusion culture, which can increase the overall amount of AAV vector generated per production run.
As known in the art, samples of host cells are often maintained in frozen cell banks, such as master cell banks and working cell banks, which facilitate production of biological products in many batches over time, while ensuring consistent performance by the host cells. Before a campaign to produce an AAV vector, a frozen sample of host cells from a cell bank would typically be thawed, seeded into a small culture volume, and grown to ever higher densities or numbers in cultures of increasing volume. When host cells have reached a desired cell density and/or volume in culture, exogenous genetic material can be introduced, such as by transfection with plasmid DNA or infection or transduction with viral vectors, to cause them to begin producing the AAV vector. Alternatively, if using non- transiently modified host cells in which the nucleotide sequence coding for one or more of the required vector components is under inducible control, the environmental factor necessary to induce expression can be introduced. Host cells can then be grown or maintained in culture for time and under conditions sufficient forthem to produce the AAV vectors.
Embodiments
Embodiment 1 : A nucleic acid molecule comprising a nucleotide sequence encoding a Bcl2- associated athanogene 3 (BAG3) polypeptide, or variant thereof.
Embodiment 2: The nucleic acid molecule of embodiment 1 , wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is a codon-optimized nucleotide sequence.
Embodiment 3: The nucleic acid molecule of either embodiment 1 or embodiment 2, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 4: The nucleic acid molecule of any one of embodiments 1-3, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 5: The nucleic acid molecule of any one of embodiments 1-4, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 85% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 6: The nucleic acid molecule of any one of embodiments 1-5, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 90% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 7: The nucleic acid molecule of any one of embodiments 1-6, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 95% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 8: The nucleic acid molecule of any one of embodiments 1-7, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 98% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 9: The nucleic acid molecule of any one of embodiments 1-8, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 99% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24. Embodiment 10: The nucleic acid molecule of any one of embodiments 1-9, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 11 : A recombinant adeno-associated virus (rAAV) vector comprising the nucleic acid molecule of any one of embodiments 1-10.
Embodiment 12: The rAAV vector of embodiment 11 , wherein the rAAV vector comprises serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype 9 (AAV9), serotype 10 (AAV10), serotype 11 (AAV11), or serotype 12 (AAV12) capsid protein.
Embodiment 13: The rAAV vector of either embodiment 11 or embodiment 12, wherein the rAAV vector comprises AAV9 capsid protein.
Embodiment 14: The rAAV vector of embodiment 13, wherein the AAV9 capsid protein is a VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, a VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, or a VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
Embodiment 15: The rAAV vector of either embodiment 13 or embodiment 14, wherein the AAV9 capsid protein comprises the VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, the VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, and the VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
Embodiment 16: The rAAV vector of any one of embodiments 11-15, wherein the rAAV vector further comprises at least one cardiac promoter operably linked to the nucleic acid molecule comprising the nucleotide sequence encoding a BAG3 polypeptide, or variant thereof.
Embodiment 17: The rAAV vector of embodiment 16, wherein the at least one cardiac promoter is chicken troponin T (cTNT), CAG, MHCK7, CK7, endogenous BAG promoter, desmin (Des), alpha-myosin heavy chain (a-MHC), myosin light chain 2 (MLC-2), cardiac troponin C (TNNC1 or cTnC), human cardiac troponin T (TNNT2) promoter, or a functional subsequence, modification, or variant respectively thereof.
Embodiment 18: The rAAV vector of either embodiment 16 or embodiment 17, wherein the at least one cardiac promoter is cTNT promoter or a functional subsequence, modification, or variant thereof. Embodiment 19: The rAAV vector of either embodiment 17 or embodiment 18, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5, or a functional subsequence, modification, or variant thereof.
Embodiment 20: The rAAV vector of either embodiment 17 or embodiment 18, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5.
Embodiment 21 : The rAAV vector of any one of embodiments 11-20, wherein the rAAV vector further comprises at least one intron.
Embodiment 22: The rAAV vector of embodiment 21 , wherein the intron comprises the nucleotide sequence of SEQ ID NO: 6, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31 , or a functional subsequence, modification, or variant thereof.
Embodiment 23: The rAAV vector of either embodiment 21 or embodiment 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 6.
Embodiment 24: The rAAV vector of either embodiment 21 or embodiment 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 29.
Embodiment 25: The rAAV vector of either embodiment 21 or embodiment 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 30.
Embodiment 26: The rAAV vector of either embodiment 21 or embodiment 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 31 .
Embodiment 27: The rAAV vector of any one of embodiments 11-26, wherein the rAAV vector further comprises at least one 5’ inverted terminal repeat (ITR) sequence.
Embodiment 28: The rAAV vector of embodiment 27, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8, or a functional subsequence, modification, or variant thereof.
Embodiment 29: The rAAV vector of either embodiment 27 or embodiment 28, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8.
Embodiment 30: The rAAV vector of any one of embodiments 11-29, wherein the rAAV vector further comprises at least one 3’ ITR sequence.
Embodiment 31 : The rAAV vector of embodiment 30, wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9, or a functional subsequence, modification, or variant thereof.
Embodiment 32: The rAAV vector of either embodiment 30 or embodiment 31 , wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9.
Embodiment 33: The rAAV vector of any one of embodiments 11-32, wherein the rAAV vector further comprises at least one transcription terminator sequence.
Embodiment 34: The rAAV vector of embodiment 33, wherein the at least one transcription terminator sequence is an SV40 polyA sequence, a bovine growth hormone (BGH) polyA sequence, a rabbit b-globin (rPg) polyA sequence, or a functional subsequence, modification, or variant thereof.
Embodiment 35: The rAAV vector of either embodiment 33 or embodiment 34, wherein the at least one transcription terminator sequence is an SV40 polyA sequence.
Embodiment 36: The rAAV vector of any one of embodiments 33-35, wherein the at least one transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7, or a functional subsequence, modification, or variant thereof.
Embodiment 37: The rAAV vector of any one of embodiments 33-36, wherein the at least transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7. Embodiment 38: The rAAV vector of either embodiment 33 or embodiment 34, wherein the at least one transcription terminator sequence is a BGH polyA sequence.
Embodiment 39: The rAAV vector of any one of embodiments 33, 34, or 38, wherein the at least one transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 32, or a functional subsequence, modification, or variant thereof.
Embodiment 40: The rAAV vector of any one of embodiments 33, 34, 38, or 39, wherein the at least transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 32.
Embodiment 41 : The rAAV vector of any one of embodiments 11-40, wherein the rAAV vector further comprises at least one stuffer or filler sequence, preferably wherein the at least one stuffer of filler sequence increases the entire length of the nucleic acid molecule of the rAAV vector, inclusive of the ITR sequences, to approximately 4.2 to 4.7 kilobases.
Embodiment 42: The rAAV vector of embodiment 41 , wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 , or a functional subsequence, modification, or variant thereof.
Embodiment 43: The rAAV vector of either embodiment 41 or embodiment 42, wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 . Embodiment 44: An rAAV vector comprising, in 5’ to 3’ order:
(a) at least one 5’ ITR sequence;
(b) at least one cardiac promoter;
(c) at least one intron;
(d) at least one nucleotide sequence encoding a Bcl2-associated athanogene 3 (BAG3) polypeptide, or variant thereof, operably linked to the at least one cardiac promoter;
(e) at least one transcription terminator sequence;
(f) at least one stuffer or filler sequence; and
(g) at least one 3’ ITR sequence.
Embodiment 45: The rAAV vector of embodiment 44, wherein the rAAV vector comprises serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype 9 (AAV9), serotype 10 (AAV10), serotype 11 (AAV11), or serotype 12 (AAV12) capsid protein.
Embodiment 46: The rAAV vector of either embodiment 44 or embodiment 45, wherein the rAAV vector comprises AAV9 capsid protein.
Embodiment 47: The rAAV vector of embodiment 46, wherein the AAV9 capsid protein is a VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, a VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, or a VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
Embodiment 48: The rAAV vector of either embodiment 46 or embodiment 47, wherein the AAV9 capsid protein comprises the VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, the VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, and the VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
Embodiment 49: An rAAV vector plasmid comprising, in 5’ to 3’ order:
(a) at least one left spacer sequence;
(b) the at least one 5’ ITR sequence;
(c) the at least one cardiac promoter;
(d) the at least one intron;
(e) the at least one nucleotide sequence encoding a Bcl2-associated athanogene 3 (BAG3) polypeptide, or variant thereof, operably linked to the at least one cardiac promoter;
(f) the at least one transcription terminator sequence;
(g) the at least one stuffer or filler sequence;
(h) the at least one 3’ ITR sequence; and
(i) at least one right spacer sequence.
Embodiment 50: The rAAV vector of any one of embodiments 44-48 or rAAV vector plasmid of embodiment 49, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is a codon-optimized nucleotide sequence.
Embodiment 51 : The rAAV vector of any one of embodiments 44-48 or 50 or rAAV vector plasmid of any one of embodiments 49 or 50, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 52: The rAAV vector of any one of embodiments 44-48, 50, or 51 or rAAV vector plasmid of any one of embodiments 49-51 , wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 53: The rAAV vector of any one of embodiments 44-48 or 50-52 or rAAV vector plasmid of any one of embodiments 49-52, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 85% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 54: The rAAV vector of any one of embodiments 44-48 or 50-53 or rAAV vector plasmid of any one of embodiments 49-53, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 90% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 55: The rAAV vector of any one of embodiments 44-48 or 50-54 or rAAV vector plasmid of any one of embodiments 49-54, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 95% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 56: The rAAV vector of any one of embodiments 44-48 or 50-55 or rAAV vector plasmid of any one of embodiments 49-55, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 98% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 57: The rAAV vector of any one of embodiments 44-48 or 50-56 or rAAV vector plasmid of any one of embodiments 49-56, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 99% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 58: The rAAV vector of any one of embodiments 44-48 or 50-57 or rAAV vector plasmid of any one of embodiments 49-56, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is the nucleotide sequence of SEQ ID NO: 4 or 19-24.
Embodiment 59: The rAAV vector of any one of embodiments 44-48 or 50-58 or rAAV vector plasmid of any one of embodiments 49-58, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8, or a functional subsequence, modification, or variant thereof.
Embodiment 60: The rAAV vector of any one of embodiments 44-48 or 50-59 or rAAV vector plasmid of any one of embodiments 49-59, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8.
Embodiment 61 : The rAAV vector of any one of embodiments 44-48 or 50-60 or rAAV vector plasmid of any one of embodiments 49-60, wherein the at least one cardiac promoter is chicken troponin T (cTNT), CAG, MHCK7, CK7, endogenous BAG promoter, desmin (Des), alpha-myosin heavy chain (a-MHC), myosin light chain 2 (MLC-2), cardiac troponin C (TNNC1 or cTnC), human cardiac troponin T (TNNT2) promoter, or a functional subsequence, modification, or variant thereof.
Embodiment 62: The rAAV vector or rAAV vector plasmid of embodiment 61 , wherein the at least one cardiac promoter is cTNT promoter or a functional subsequence, modification, or variant thereof.
Embodiment 63: The rAAV vector or rAAV vector plasmid of either embodiment 61 or embodiment 62, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5, or a functional subsequence, modification, or variant thereof.
Embodiment 64: The rAAV vector or rAAV vector plasmid of any one of embodiments 61- 63, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5. Embodiment 65: The rAAV vector of any one of embodiments 44-48 or 50-64 or rAAV vector plasmid of any one of embodiments 49-64, wherein the at least one intron comprises the nucleotide sequence of SEQ ID NO: 6, or a functional subsequence, modification, or variant thereof.
Embodiment 66: The rAAV vector of any one of embodiments 44-48 or 50-65 or rAAV vector plasmid of any one of embodiments 49-65, wherein the at least one intron comprises the nucleotide sequence of SEQ ID NO: 6.
Embodiment 67: The rAAV vector of any one of embodiments 44-48 or 50-66 or rAAV vector plasmid of any one of embodiments 49-66, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 29.
Embodiment 68: The rAAV vector of any one of embodiments 44-48 or 50-67 or rAAV vector plasmid of any one of embodiments 49-67, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 30.
Embodiment 69: The rAAV vector of any one of embodiments 44-48 or 50-68 or rAAV vector plasmid of any one of embodiments 49-68, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 31 .
Embodiment 70: The rAAV vector of any one of embodiments 44-48 or 50-69 or rAAV vector plasmid of any one of embodiments 49-69, wherein the at least one transcription terminator sequence is an SV40 polyA sequence, a bovine growth hormone (BGH) polyA sequence, a rabbit b-globin (rPg) polyA sequence, or a functional subsequence, modification, or variant thereof.
Embodiment 71 : The rAAV vector of any one of embodiments 44-48 or 50-70 or rAAV vector plasmid of any one of embodiments 49-70, wherein the at least one transcription terminator sequence is an SV40 polyA sequence.
Embodiment 72: The rAAV vector of any one of embodiments 44-48 or 50-71 or rAAV vector plasmid of any one of embodiments 49-71 , wherein the at least one transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7, or a functional subsequence, modification, or variant thereof.
Embodiment 73: The rAAV vector of any one of embodiments 44-48 or 50-72 or rAAV vector plasmid of any one of embodiments 49-72, wherein the at least transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7.
Embodiment 74: The rAAV vector of any one of embodiments 44-48 or 50-70 or rAAV vector plasmid of any one of embodiments 49-70, wherein the at least one transcription terminator sequence is a BGH polyA sequence.
Embodiment 75: The rAAV vector of any one of embodiments 44-48, 50-70, or 74 or rAAV vector plasmid of any one of embodiments 49-70 or 74, wherein the at least one transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 32, or a functional subsequence, modification, or variant thereof.
Embodiment 76: The rAAV vector of any one of embodiments 44-48, 50-70, 74, or 75 or rAAV vector plasmid of any one of embodiments 49-70, 74, or 75, wherein the at least transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 32. Embodiment 77: The rAAV vector of any one of embodiments 44-48 or 50-76 or rAAV vector plasmid of any one of embodiments 49-76, wherein at least one stuffer or filler sequence increases the entire length of the nucleic acid molecule of the rAAV vector or rAAV vector plasmid, inclusive of the ITR sequences and excluding the spacer sequences, to approximately 4.2 to 4.7 kilobases.
Embodiment 78: The rAAV vector of any one of embodiments 44-48 or 50-77 or rAAV vector plasmid of any one of embodiments 49-77, wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 , or a functional subsequence, modification, or variant thereof.
Embodiment 79: The rAAV vector of any one of embodiments 44-48 or 50-78 or rAAV vector plasmid of any one of embodiments 49-78, wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 .
Embodiment 80: The rAAV vector of any one of embodiments 44-48 or 50-79 or rAAV vector plasmid of any one of embodiments 49-79, wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9, or a functional subsequence, modification, or variant thereof.
Embodiment 81 : The rAAV vector of any one of embodiments 44-48 or 50-80 or rAAV vector plasmid of any one of embodiments 49-80, wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9.
Embodiment 82: The rAAV vector plasmid of any one of embodiments 49-81 , wherein the at least one left spacer sequence comprises the nucleotide sequence of SEQ ID NO: 12, or a functional subsequence, modification, or variant thereof. Embodiment 83: The rAAV vector plasmid of any one of embodiments 49-82, wherein the at least one left spacer sequence comprises the nucleotide sequence of SEQ ID NO: 12.
Embodiment 84: The rAAV vector plasmid of any one of embodiments 49-83, wherein the at least one right spacer sequence comprises the nucleotide sequence of SEQ ID NO: 13, or a functional subsequence, modification, or variant thereof.
Embodiment 85: The rAAV vector plasmid of any one of embodiments 49-84, wherein the at least one right spacer sequence comprises the nucleotide sequence of SEQ ID NO: 13. Embodiment 86: The rAAV vector plasmid of any one of embodiments 49-85, wherein the rAAV vector plasmid further comprises at least one left spacer and/or at least one right spacer, preferably wherein the at least one left spacer and/or at least one right spacer increases the entire length of the rAAV vector plasmid to approximately 4.7 to 12 kilobases, preferably to approximately 9 to 10 kilobases.
Embodiment 87: The rAAV vector of any one of embodiments 11-48 or 50-81 or rAAV vector plasmid of any one of embodiments 49-86, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 14, or a functional subsequence, modification, or variant thereof.
Embodiment 88: The rAAV vector of any one of embodiments 11-48, 50-81 , or 87 or rAAV vector plasmid of any one of embodiments 49-87, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 14.
Embodiment 89: The rAAV vector of any one of embodiments 11-48, 50-81 , 87, or 88 or rAAV vector plasmid of any one of claims 49-88, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 15, or a functional subsequence, modification, or variant thereof.
Embodiment 90: The rAAV vector of any one of embodiments 11-48, 50-81 , or 87-89 or rAAV vector plasmid of any one of claims 49-89, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 15.
Embodiment 91 : The rAAV vector of any one of embodiments 11-48, 50-81 , or 87-90, wherein the entire length of the nucleic acid of the rAAV vector is equal to or less than approximately 5 kilobases in length or is equal to or less than 4.7 kilobases in length.
Embodiment 92: The rAAV vector plasmid of any one of embodiments 49-90, wherein the entire length of the rAAV vector plasmid is equal to or less than approximately 12 kilobases in length or is equal to or less than 4.7 kilobases in length.
Embodiment 93: A pharmaceutical composition comprising the nucleic acid molecule of any one of embodiments 1-10, or the rAAV vector of any one of embodiments 11-48, 50-81 , or 87-91 , and at least one pharmaceutically acceptable salt. Embodiment 94: The pharmaceutical composition of embodiment 93, wherein the at least one pharmaceutically acceptable salt is present in an amount ranging from about 1 mM to about 450 mM.
Embodiment 95: The pharmaceutical composition of either embodiment 93 or embodiment 94, wherein the at least one pharmaceutically acceptable salt is present in an amount ranging from about 2 mM to about 350 mM.
Embodiment 96: The pharmaceutical composition of any one of embodiments 93-95, wherein the at least one pharmaceutically acceptable salt is sodium chloride, magnesium chloride, potassium chloride, calcium chloride, or calcium phosphate.
Embodiment 97: The pharmaceutical composition of embodiment 96, wherein the at least one pharmaceutically acceptable salt comprises sodium chloride and magnesium chloride. Embodiment 98: The pharmaceutical composition of embodiment 96, wherein the at least one pharmaceutically acceptable salt comprises sodium chloride and potassium chloride. Embodiment 99: The pharmaceutical composition of any one of embodiments 93-98, further comprising at least one buffer.
Embodiment 100: The pharmaceutical composition of embodiment 99, wherein the buffer is citrate, histidine, acetate, phosphate, tris hydrochloride, or tromethamine.
Embodiment 101 : The pharmaceutical composition of embodiment 100, wherein the buffer is phosphate.
Embodiment 102: The pharmaceutical composition of embodiment 100, wherein the buffer is tris hydrochloride and tromethamine.
Embodiment 103: The pharmaceutical composition of any one of embodiments 99-102, wherein the at least one buffer is present in an amount ranging from about 10 mM to about 40 mM.
Embodiment 104: The pharmaceutical composition of embodiment 103, wherein the at least one buffer is present in an amount of about 20 mM.
Embodiment 105: The pharmaceutical composition of any one of embodiments 93-104, further comprising at least one cryoprotectant.
Embodiment 106: The pharmaceutical composition of embodiment 105, wherein the at least one cryoprotectant is a sugar or a sugar alcohol.
Embodiment 107: The pharmaceutical composition of embodiment 105, wherein the at least one cryoprotectant is trehalose, sucrose, sorbitol, or mannitol.
Embodiment 108: The pharmaceutical composition of embodiment 107, wherein the at least one cryoprotectant is sucrose.
Embodiment 109: The pharmaceutical composition of embodiment 107, wherein the at least one cryoprotectant is sorbitol. Embodiment 110: The pharmaceutical composition of any one of embodiments 105-109, wherein the at least one cryoprotectant is present in an amount of up to about 20%.
Embodiment 111 : The pharmaceutical composition of embodiment 110, wherein the at least one cryoprotectant is present in an amount ranging from about 3% to about 15%.
Embodiment 112: The pharmaceutical composition of embodiment 112, wherein the at least one cryoprotectant is present in an amount of about 4% or about 5%.
Embodiment 113: The pharmaceutical composition of any one of embodiments 93-112, further comprising at least one surfactant.
Embodiment 114: The pharmaceutical composition of embodiment 113, wherein the at least one surfactant is a polaxamer or a polysorbate.
Embodiment 115: The pharmaceutical composition of embodiment 1114, wherein the at least one surfactant is polaxamer 188, polysorbate 20, or polysorbate 80.
Embodiment 116: The pharmaceutical composition of any one of embodiments 113-115, wherein the at least one surfactant is present in an amount ranging from about 0.0001% to about 1 %.
Embodiment 117: The pharmaceutical composition of embodiment 116, wherein the at least one surfactant is present in an amount of about 0.02%.
Embodiment 118: The pharmaceutical composition of embodiment 116, wherein the at least one surfactant is present in an amount of about 0.002%.
Embodiment 119: The pharmaceutical composition of any one of embodiments 93-118, wherein the pharmaceutical composition has a pH ranging from about 6 to about 8. Embodiment 120: The pharmaceutical composition of embodiment 119, wherein the pharmaceutical composition has a pH ranging from about 7 to about 8.
Embodiment 121 : The pharmaceutical composition of embodiment 120, wherein the pharmaceutical composition has a pH of about 7.6.
Embodiment 122: The pharmaceutical composition of embodiment 120, wherein the pharmaceutical composition has a pH of about 7.4.
Embodiment 123: A method for treating a cardiac-related disease or disorder in a subject, the method comprising administering to the subject a therapeutically effective amount of:
(a) the nucleic acid molecule of any one of embodiments 1-10; or
(b) the rAAV vector of any one of embodiments 11-48, 50-81 , or 87-91 ; or
(c) the pharmaceutical composition of any one of embodiments 93-122.
Embodiment 124: The method of embodiment 123, wherein the cardiac-related disease or disorder is associated with a deficiency or dysfunction of BAG3.
Embodiment 125: The method of either embodiment 123 or embodiment 124, wherein the subject has a BAG3 mutation. Embodiment 126: The method of any one of embodiments 123-125, wherein the cardiac- related disease or disorder is BAG3-related dilated cardiomyopathy (DCM).
Embodiment 127: The method of any one of embodiments 123-125, wherein the cardiac- related disease or disorder is BAG3-related heart failure.
Embodiment 128: The method of embodiment 123, wherein the cardiac-related disease or disorder is not associated with a deficiency or dysfunction of BAG3.
Embodiment 129: The method of either embodiment 123 or embodiment 128, wherein the subject does not have a BAG mutation.
Embodiment 130: The method of any one of embodiments 123, 128, or 129, wherein the cardiac-related disease or disorder is heart failure unrelated to BAG3 expression.
Embodiment 131 : A method for reducing the frequency or severity of at least one symptom associated with a cardiac-related disease or disorder in a subject, the method comprising administering to the subject:
(a) the nucleic acid molecule of any one of embodiments 1-10; or
(b) the rAAV vector of any one of embodiments 11-48, 50-81 , or 87-91 ; or
(c) the pharmaceutical composition of any one of embodiments 93-122; in an amount effective to reduce the frequency or severity of the at least one symptom.
Embodiment 132: The method of embodiment 131 , wherein the cardiac-related disease or disorder is associated with a deficiency or dysfunction of BAG3.
Embodiment 133: The method of either embodiment 131 or embodiment 132, wherein the subject has a BAG3 mutation.
Embodiment 134: The method of any one of embodiments 131-133, wherein the cardiac- related disease or disorder is BAG3-related dilated cardiomyopathy (DCM).
Embodiment 135: The method of any one of embodiments 131-133, wherein the cardiac- related disease or disorder is BAG3-related heart failure.
Embodiment 136: The method of embodiment 131 , wherein the cardiac-related disease or disorder is not associated with a deficiency or dysfunction of BAG3.
Embodiment 137: The method of either embodiment 131 or embodiment 136, wherein the subject does not have a BAG mutation.
Embodiment 138: The method of any one of embodiments 131 , 136, or 137, wherein the cardiac-related disease or disorder is heart failure unrelated to BAG3 expression.
Embodiment 139: The method of any one of embodiments 131-134, wherein the at least one symptom is characteristic of BAG3-related DCM.
Embodiment 140: The method of any one of embodiments 131-133 or 135, wherein the at least one symptom is characteristic of BAG3-related heart failure.
Embodiment 141 : The method of any one of embodiments 131 or 136-138, wherein the at least one symptom is characteristic of heart failure unrelated to BAG3 expression. Embodiment 142: The method of any one of embodiments 123-141 , wherein the effective amount of the rAAV vector ranges from about 1 E10 to about 1 E17 vector genomes per kilogram (vg/kg) of subject body weight.
Embodiment 143: The method of embodiment 142, wherein the effective amount of the rAAV vector ranges from about 3E13 to about 1 E14 vector genomes per kilogram (vg/kg) of subject body weight.
Embodiment 144: The method of either embodiment 142 or embodiment 143, wherein the effective amount of the rAAV vector is about 3E13 vector genomes per kilogram (vg/kg) of subject body weight.
Embodiment 145: The method of either embodiment 142 or embodiment 143, wherein the effective amount of the rAAV vector is about 7E13 vector genomes per kilogram (vg/kg) of subject body weight.
Embodiment 146: The method of either embodiment 142 or embodiment 143, wherein the effective amount of the rAAV vector is 1 E14 vector genomes per kilogram (vg/kg) of subject body weight.
Embodiment 147: Use of the nucleic acid molecule of any one of embodiments 1-10 in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject. Embodiment 148: Use of the rAAV vector of any one of embodiments 11-48, 50-81 , or 87- 91 in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
Embodiment 149: Use of the pharmaceutical composition of any one of embodiments 93- 122 in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
Embodiment 150: A plasmid comprising the nucleic acid molecule of any one of embodiments 1-10.
Embodiment 151 : A plasmid comprising the rAAV vector sequence of any one of embodiments 11 -48, 50-81 , or 87-91 .
Embodiment 152: A host cell for rAAV vector production comprising the plasmid of embodiment 150.
Embodiment 153: A host cell for rAAV vector production comprising the plasmid of embodiment 151 .
Embodiment 154: A host cell for rAAV vector production comprising the rAAV vector plasmid of any one of embodiments 49-90.
Embodiment 155: The host cell of any one of embodiments 152-154, wherein the host cell is an HEK293 cell or derivative thereof. Embodiment 156: The host cell of any one of embodiments 152-155, wherein the host cell further comprises a nucleic acid molecule comprising a nucleotide sequence encoding an AAV Rep protein.
Embodiment 157: The host cell of any one of embodiments 152-156, wherein the host cell further comprises a nucleic acid molecule comprising a nucleotide sequence encoding an AAV9 capsid protein.
Embodiment 158: The host cell of any one of embodiments 152-157, wherein the host cell further comprises a nucleic acid molecule comprising a nucleotide sequence encoding a viral helper factor. Embodiment 159: A method of making an rAAV vector comprising:
(a) incubating the host cell of any one of embodiments 152-158 under conditions sufficient to allow the production of rAAV vectors; and
(b) purifying the rAAV vectors produced thereby.
Embodiment 160: An rAAV vector produced by the method of embodiment 159.
Table 1. Sequences
Figure imgf000059_0001
Figure imgf000060_0001
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Figure imgf000064_0001
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0002
Figure imgf000068_0003
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
EXAMPLES
The following examples are intended as illustration only and are not meant to limit the disclosure in any way.
Example 1 : AAV Vector Production
HEK 293 cells were grown in suspension culture and transfected with 3 plasmids to produce a rAAV vector using standard methods known in the art. One of the plasmids comprised Compound A. The HEK 293 cells were harvested, lysed, flocculated, and the resulting lysate was filtered to produce a clarified lysate. The rAAV vector comprising the BAG3 transgene was purified by a series of chromatography and filtration steps and suspended in a formulation comprising: 10 mM Phosphate pH 7.4 with 350 mM NaCI, 2.7 mM KCI, 5% Sorbitol and 0.002% Pluronic.
Table 2. Vector Productivity
Figure imgf000074_0001
Table. 3. Stability
Figure imgf000074_0002
Figure imgf000074_0003
Figure imgf000074_0007
Figure imgf000074_0004
Figure imgf000074_0005
Figure imgf000074_0006
Figure imgf000075_0001
Table 4. Summary of batch attributes
Figure imgf000075_0002
Figure imgf000075_0003
Example 2: Pharmacology
Compound A pharmacology was evaluated in vitro and in vivo. Cell-based assay data indicated that Compound A effectively transduced and induced the synthesis of functional BAG3 protein in wild-type human induced pluripotent stem cell-derived cardiomyocytes (HiPSC-CM). Human BAG3 protein expression was detected in the hearts of wild-type (WT) mice and WT non-human primates (NHPs) following administration of Compound A. Administration of Compound A in the mouse disease model prevented further deterioration of the disease process. Specifically, it stabilized cardiac structure and function and this correlated with the dose level and amount of human BAG3 protein expression in the heart. Compound A vector transduction and human BAG3 protein expression were evaluated in NHPs. Compound A -treated NHPs had sustained human BAG3 expression in their hearts at the predicted efficacious therapeutic target levels.
Table 5.
Figure imgf000076_0001
Primary Pharmacology In Vitro
Compound A was tested in wild-type human induced pluripotent stem cell derived cardiomyocytes (HiPSC-CM, CDI iCell Cardiomyocyte) to demonstrate transduction (viral genome counts, VGC) and transgene expression (mRNA, protein) as well as stabilization of a BAG3 partner protein (HSPB8). HiPSC-CM were used with the goal of implementing a potency assay in a cell type in which the cardiac troponin promoter element is active, thus allowing expression of the transgene. HSPB8 is a BAG3 partner protein whose stability is dependent on the presence of functional BAG3 and is being used as a surrogate for BAG3 activity (Fang et al., JCI Insight 4(4): e126464 (2019); Fang et al., J. Clin. Invest. 127(8): 3189-200 (2017); Judge et al., JCI Insight 2(14): e94623 (2017)).
HiPSC-CMs were transduced with Compound A and 4 days post transduction transgene mRNA was readily detected (FIG.1). Total BAG3 protein (human endogenous + human transgene) was measured using the Protein Simple WES platform. Total BAG3 protein levels demonstrated a dose responsive increase with increasing vector multiplicity of infection (MOI).
HiPSC-CMs were first transfected with an siRNA targeting endogenous BAG3 expression, which resulted in significant knockdown of endogenous BAG3 protein expression and HSPB8 destabilization (FIG. 2). Subsequently the HiPSC-CMs were transduced with Compound A , resulting in a robust upregulation of total BAG3 protein (human endogenous plus human transgene) and stabilization of HSPB8 partner protein. Primary Pharmacology In Vivo
Primary pharmacology in vivo was investigated in wild-type mice (biodistribution & expression), in a mouse model of disease (characterization of model and evaluation of dose response associated efficacy) and in non-human primates (biodistribution and expression).
Evaluation of biodistribution & expression in wild-type mice
Wild type mice (n:12, age: 8 weeks) were dosed with Compound A (3E13 vg/kg) with a planned necropsy at 3- and 8-weeks post dosing. No significant differences in body weight were detected during the study between Compound A-treated mice and vehicle-treated control mice (FIG. 3A).
Viral genome copies were readily detected in the hearts of Compound A-treated mice at 3 and 8 weeks post-dose (FIG. 3B). At the 8-week timepoint, liver viral genome levels were approximately 175x higher than in the heart. Transgene mRNA expression was highest in the heart with a similar level at both timepoints. In the liver, transgene mRNA expression was approximately 40-50% of the signal in the heart (FIG. 3C). Transgene protein expression (assayed using an antibody specific for human BAG3 protein) was readily detected in the hearts of Compound A-treated mice while no signal was detected in the skeletal muscle and a low signal was detected in the liver (FIG. 3D). When quantifying total BAG3 protein in the heart a similar level of BAG3 expression was detected in hearts of Compound A-treated mice as that detected in control vehicle-treated mice.
Cardiac function (left ventricular ejection fraction) and structure (left ventricular end diastolic volume) were measured by echocardiography at 4- and 7-weeks post dosing. No significant differences were detected in dosed compared to vehicle-treated control mice (FIG. 3E). Finally, the proportion of area in the heart expressing the human transgene was assayed using BAG3 immunohistochemistry showing similar biodistribution at 3- and 8-weeks (74% and 56%, respectively) (FIG. 3F).
Example 3: Characterization of the cKO mouse model of disease:
Mice with cardiac specific knockdown of BAG3 (BAG3 cKO, n:20, male and female) (Fang et al., J. Clin. Invest. 127(8): 3189-200 (2017)) and wild-type control mice (BAG3 cWT, n:20, male and female) were characterized longitudinally using cardiac echocardiography between the ages of 7- and 21- weeks (FIG. 4A-4B). A small but significant deficit in ejection fraction was detected as early as 7-8 weeks of age (BAG3 cKO: 64.2 ± 6.0% vs. BAG3 cWT: 70.5 ± 3.9%) which became larger by 18-21 weeks of age (BAG3 cKO: 31 .9 ± 8.7% vs. BAG3 cWT: 72.2 ± 3.6%). Similarly, a significant increase in left ventricular end diastolic volume was observed in BAG3 cKO mice as compared to wildtype control at 18-21 weeks of age (BAG3 cKO: 93.4 ± 30.4% vs. BAG3 cWT: 61 .5 ± 9.0%). No significant difference in body weight was detected between the two cohorts between 11- 15 and 21-23 weeks of age (FIG. 4C).
As expected, BAG3 protein (measured by Protein Simple WES assay) was absent from the hearts of cKO mice whereas it was readily detected in hearts of control wild-type mice (FIG. 4D). A significant decrease in HSPB8 protein was observed in the hearts of BAG3 cKO mice with the signal being approximately 20% of that measured in wild-type control mice (FIG. 4E). BAG3 protein levels in liver and skeletal muscle tissue of BAG3 cKO mice were the same as in wild-type mice.
Expression levels (mRNA) of heart failure (Nppa, Nppb, Myh7/Myh6 ratio) and fibrosis (Col1a1 , Col1a2, Fn1 , Postn, Timpl) biomarkers were significantly upregulated in the hearts of BAG3 cKO mice compared to wild-type control mice (FIG. 4F-4G). Finally, based on the histological assessment (PicroSirius red staining) of heart tissue, a significantly higher percentage of fibrosis was observed in the hearts of BAG3 cKO as compared to control wildtype mice (FIG. 4H).
Example 4: Evaluation of dose response associated efficacy in mouse model of disease:
To determine whether restoration of BAG3 expression in the heart via AAV gene delivery results in a therapeutic effect, a dose response efficacy study in the cKO mouse model of disease was pursued. BAG3 cKO mice were administered (age: 12 weeks, IV) Compound A at 1 E13 vg/kg (n:15), 3E13 vg/kg (n:15), 9E13 vg/kg (n:15). The study also included two control groups: BAG3 cKO untreated mice (n:20), wild-type untreated mice (n:20). Two weeks prior to treatment, mice were characterized using echocardiography to determine baseline cardiac function and structure. Mice were randomized into groups based on echocardiography readouts (ejection fraction, left ventricular end diastolic volume), body weight, and gender.
Cardiac function (ejection fraction) and structure (left ventricular end diastolic volume) were measured longitudinally using echocardiography (FIG. 5A-B) at 4-, 8-, and 12- weeks post dosing. At week 12, a significant improvement in ejection fraction was detected in mice treated with Compound A at 3E13 vg/kg (42.5 ± 11 .4%) and 9E13 vg/kg (47.9 ± 7.3%) as compared to untreated BAG3 cKO mice (28.2 ± 10.0%). At week 12, a significant improvement in left ventricular end diastolic volume was detected in mice treated with Compound A at 3E13 vg/kg (78.5 ± 12.2uL) and 9E13 vg/kg (71.7 ± 9.0%) as compared to untreated BAG3 cKO mice (97.2 ± 32.5uL). No significant differences in body weight were detected in these mouse groups (FIG. 5C).
Viral genome biodistribution was examined in heart, liver and skeletal muscle tissue collected at necropsy from mice treated with Compound A at 1 E13 vg/kg, 3E13 vg/kg, and 9E13 vg/kg (FIG. 5D). A clear dose response in biodistribution was detected in the heart: 1 E13 vg/kg (0.03 ± 0.01 vg/mTFRC), 3E13 vg/kg (0.19 ± 0.1 vg/mTFRC), 9E13 vg/kg (0.6 ± 0.2 vg/mTFRC). The highest viral genomes were detected in liver (40-45x higher than the heart), with lower vector genomes observed in skeletal muscle (0.2x of the heart level). Transgene mRNA expression was highest in the heart, compared to other tissues examined, with the liver having approximately O.lx the heart level and skeletal muscle having approximately 0.01 x the heart level (FIG. 5E).
Total BAG3 protein expression (human plus mouse) was determined using a Protein Simple WES assay. BAG3 protein was not detected in the hearts of untreated control cKO mice. A dose-responsive increase in BAG3 protein levels was observed in cKO mouse hearts after treatment with Compound A. At the highest dose, approximately 80% (0.78 ± 0.45) of the WT level of BAG3 was detected and at the mid-dose, approximately 20% (0.20 ± 0.11%) of WT BAG3 levels was observed (FIG. 5F). Compound A also induced a dose- responsive increase in HSPB8 protein expression in the same heart tissue samples: approximately 70% (0.68 ± 0.20) at the highest dose, and approximately 35% (0.34 ± 0.06%) of wild-type levels at the mid-dose (FIG. 5G).
Human BAG3 protein expression was quantified using an LC/MS assay specific for the human sequence: at 9E13 vg/kg, the expression was approximately 70% of the level in wild-type mouse heart and, at 3E13 vg/kg, it was approximately 20% of the level expressed in the wild-type mouse heart (FIG. 5H). Transgene spatial expression was determined using in situ hybridization (human BAG3 mRNA) and immunohistochemistry (BAG3 protein, antibody specific for human protein) (FIG. 5I-5J). At a dose of 9E13 vg/kg, 52 ± 18% of cardiomyocytes were positive for human BAG3 mRNA and 52 ± 14% of the heart region was positive for BAG3 protein. At a dose of 3E13 vg/kg, 39 ± 26% of card io myocytes were positive for transgene mRNA and 29 ± 15% of the heart region was positive for transgene protein.
Biomarkers of heart failure and fibrosis were examined using RT-PCR (FIG. 5K). When comparing to untreated control mice, treatment with Compound A at 9E13 and 3E13 vg/kg resulted in a significant decrease in Nppa, Nppb, and the Myh7/Myh6 ratio. A significant decrease was also detected in the levels of Col1 a1 and Postn expression although no significant change was detected in Col1a2, Fn, and Timpl levels. No significant difference following treatment was detected in NT-proBNP levels measured in serum.
Example 5: Evaluation of biodistribution & expression in non-human primates:
To determine the degree of viral genome biodistribution in non-human primates, a cohort of animals was treated with Compound A at 3E13 and 1 E14. Repeated titering after administration led to a more accurate titer of the administered vector and the actual dose levels are 4E13 and 1 .3E14 vg/kg. Actual dose levels were used for modeling and dose projection in Example 8. Each dose level was administered to 1 male and 1 female adult animal. The study also included a pair of vehicle-treated animals. Vehicle consisted of 0.002% pluronic F68 in 10 mM phosphate, 350 mM NaCI, 2.7 mM KCI, and 5% sorbitol in sterile water for injection (pH 7.4). The in-life component of the study was 6 weeks long.
The number of viral genomes detected in the heart increased with vector dose: 0.86 ± 0.15 vg/MfTFRC (4E13 vg/kg) and 2.72 vg/MfTFRC (1 .3E14 vg/kg) (FIG. 6A). Viral genomes in the liver were about 167-243x higher than those in the heart. Viral genomes were also detected in the dorsal root ganglia (0.12-0.35x heart levels), the spinal cord (0.06x heart levels), skeletal muscle (0.2-0.35x heart levels) and testis or ovary (0.04-0.08x heart levels). One female animal administered with the 1 .3E14 vg/kg dose exhibited very low biodistribution and it was determined that this animal had seroconverted prior to dosing and carried neutralizing antibodies against AAV9.
Transgene mRNA expression levels were quantified and normalized either to endogenous HPRT or endogenous BAG3 (FIG. 6B-6C). Expression levels achieved in the heart were approximately 6-8x higher in animals treated with 1 .3E14 vg/kg, compared to the 4E13 vg/kg dose. Transgene mRNA expression in the liver was higher than that detected in the heart: 1 ,8x at the 4E13 vg/kg dose and 6.4x at the 1 .3E14 vg/kg dose. T ransgene expression in the dorsal root ganglia was approximately 0.44x compared to the signal detected in the heart at the 1 .3E14 vg/kg dose. A much lower signal was detected in the spinal cord and skeletal muscle. Upon normalization of transgenic BAG3 mRNA levels to endogenous BAG3 levels, it was found that in the heart, at the 4E13 vg/kg dose level, the transgene mRNA levels were approximately 0.1x that of endogenous BAG3, and 0.8x at the 1 .3E14 vg/kg dose level. In the liver, the signal was higher: 3x endogenous at the 4E13 vg/kg and 25x endogenous at the 1 .3E14 vg/kg.
Human BAG3 protein expression was measured using LC/MS (FIG. 6E-6F). A peptide with a sequence conserved in both human and cyno BAG3 protein was used to measure total protein, whereas a peptide with a sequence specific for the human protein was used to quantify human protein. When comparing BAG3 levels in the heart, 369 ng/mg of protein at the 1.3E14 vg/kg dose, 248 ng/mg of protein at the 4E13 vg/kg dose, and 189 ng/mg of protein in vehicle-dosed animals was detected.
In non-cardiac tissues of vehicle-dosed animals, endogenous BAG3 levels were highest in the spinal cord (157 ng/mg) and lowest in the liver (7 ng/mg). Human transgene protein was only detected in Compound A-dosed animals. At the 4E13 vg/kg dose, approximately 13.9 ng/mg (male animal) and 4.6 ng/mg (female animal) of BAG3 protein was detected in the heart while no transgene protein was detected in liver, dorsal root ganglia, spinal cord, or skeletal muscle. At the 1.3E14 vg/kg dose, approximately 70 ng/mg of BAG3 protein was detected in the heart while no transgene protein was detected in dorsal root ganglia, spinal cord, or skeletal muscle. A small signal (approximately 3 ng/mg) was detected in the liver. When comparing to total BAG3 levels, the human BAG3 protein level detected in the heart was approximately 4% of the total BAG3 level at the 4E13 vg/kg dose level and approximately 30% of total BAG3 at 1 .3E14 vg/kg.
Spatial BAG3 expression was evaluated in the heart using in situ hybridization (FIG. 6D). At the 4E13 vg/kg dose30 ± 11 % (female) and 64 ± 19% (male) of cardiomyocytes stained positive by ISH. At the 1 .3E14 vg/kg dose 89 ± 5% of cardiomyocytes stained positive by ISH (male animal; seroconverted female animal was excluded from this analysis).
Example 6: Toxicology and Safety Pharmacology Brief Summary
The nonclinical safety of Compound A was evaluated in studies in both WT and cKO mice (pharmacology) with biodistribution and toxicology endpoints. In addition, a 6-week exploratory toxicology and biodistribution study (ETS) in cynomolgus monkeys was completed. Safety pharmacology endpoints or the potential for insertional mutagenesis were not evaluated in these early studies.
In the WT mouse study, animals were administered 3E13 vg/kg Compound A by IV bolus with a limited biodistribution, clinical pathology, and histopathology endpoint list evaluated at 3 and/or 8 weeks post dose administration. There was target expression in the WT mouse at 3E13 vg/kg with no toxicity findings.
In the cKO mouse study (1 E13, 3E13, and 9E13 vg/kg Compound A), histopathology findings were limited to animals at the high dose evaluated 12 weeks following dose administration. The Compound A-related findings at the high dose (9E13 vg/kg) consisted of mild cardiomyocyte degeneration/necrosis, however, they were not associated with any changes in cardiac biomarker endpoints of toxicity and occurred in the presence of functional efficacy (/.e., echocardiographic improvement). Functional improvement in the disease mouse model was identified at >3E13 vg/kg identifying the mouse efficacious range.
In the 6-week monkey ETS, Compound A was tolerated at both dose levels evaluated (3E13 and 1 E14 vg/kg) with no Compound A-related microscopic findings. Repeated titering after administration led to a more accurate titer of the administered vector and the actual dose levels are 4E13 and 1.3E14 vg/kg. Based on transient clinical pathology changes while in the presence of a daily immunosuppression regimen (increases in ALT and GLDH, >4E13 vg/kg; increase troponin at 4E13 vg/kg), cytokine increase (TNF at 1 .3E14 vg/kg), the heart, liver, and immune system may be potential target organs with higher dose and/or longer duration.
In summary, the early nonclinical toxicology assessment in mice (WT and cKO) and monkeys provided an adequate safety profile for continued development and supported dosage selection for evaluation in regulatory toxicology.
Toxicology Species Selection
Cynomolgus monkeys (cyno) were selected as a relevant toxicology species for Compound A evaluation. The cynomolgus monkey was selected based on the following weight of evidence: (i) high target homology, (ii) ability to support transgene expression, (iii) demonstrated transgene protein localization at site of action, and (iv) species sensitivity for gene therapy-related toxicity assessment such as acute liver toxicity and microscopic changes in the dorsal root ganglia.
BAG3 has approximately 97% identity across the full-length protein sequence for cynomolgus monkey and human. Moreover, the substantial similarity between cyno and human BAG3 indicates that it is likely to maintain all of the relevant binding partners and interactions. BAG3 binds partner proteins mainly through its WW1 , WW2, IPV1 , IPV2, PXXP, and BAG domains. Comparing cyno and human BAG3 protein sequences, the WW1 , IPV1 , IPV2, and BAG domains have identical sequences while the WW2 and PXXP domains have 97% and 92% identity. Further support comes from the cyno ETS study results that showed significant and dose responsive human BAG3 expression by in situ hybridization (BAG3 mRNA) in heart tissue with digital imaging analysis. Importantly, the human BAG3 expression in the cyno translated to detectable and dose responsive human BAG3 protein levels in the heart.
Furthermore, LCMS evaluation of purified sarcomeres isolated from the cyno ETS hearts (3 heart sections/animal) identified the single peptide unique to the human isoform. This peptide displayed a dose-dependent increase in signal across the two dose levels of the administered human BAG3 transgene (FIG. 7) and supports localization of human BAG3 at the site of sarcomere action. Finally, the human BAG3 transgene was found to rescue the cardiac function deficit in BAG3 cKO mice despite the sequence differences between human and mouse BAG3 (84% identity). Taken together, BAG3 homology, expression, localization, along with species sensitivity for gene therapy-related toxicity assessment support relevance of the cyno as a toxicology species.
Three exploratory toxicity (eTox) studies performed
1. Exploratory WT mouse biodistribution and tolerability study at 3 and 8 weeks following single IV bolus of3E13 vg/kg Compound A.
A biodistribution and toxicology study used male WT mice (BL6/J; 8 weeks old) that were administered 3E13 vg/kg Compound A intravenously via tail vein injection and necropsied following 3- or 8-weeks post injection. A separate control group received a single saline administration. Endpoint evaluations for heart, liver, and skeletal muscle included molecular biology (VGC, RNA, protein; as shown in FIG. 3B-3D), clinical pathology, histopathology, in addition to IHC (protein; FIG. 3F; FIG. 8) and ISH (RNA; FIG.9). The targeted panel of clinical pathology parameters consisted of liver, cardiac and skeletal muscle biomarkers (ALT, AST, ALP, total bilirubin, GLDH, Cardiac Troponin (cTNI), Fatty acid binding protein 3 (FABP3), Myosin light chain 3 (Myl3), and Skeletal troponin I (sTnl)). Animals were evaluated for potential Compound A-related microscopic tissue effects at 8- weeks post dose administration (heart, liver, skeletal muscle, brain, adrenal gland, kidney, lung, spinal cord, and dorsal root ganglia [DRG]).
Table 6
Figure imgf000083_0001
All mice survived to the scheduled sacrifice at 3 or 8 weeks with no Compound A- related changes in body weight (FIG. 3A), clinical pathology markers of heart (cTnl, Myl3, FABP3), liver (ALT, AST, ALP, total bilirubin, GLDH) or skeletal muscle injury (sTNI, Myl3, FABP3) compared to controls. There were no Compound A-related histopathology findings noted at 8-weeks.
Human BAG3 protein immunoreactivity was evaluated by IHC in the heart, liver, and skeletal muscle. IHC revealed a widespread expression pattern that varied in intensity across animals dosed with 3E13 vg/kg Compound A. The BAG3 heart expression pattern and intensity was generally similar at 3- or 8-weeks with heart area staining (FIG 3F; FIG. 8). The left ventricular free wall and interventricular septum of the heart showed slightly greater intensity compared with other locations. Very low expression of BAG3 protein via IHC was noted in liver of all animals in the centrilobular zones as well as marginal expression in the DRG. No BAG3 expression was observed in the skeletal muscle.
Human BAG3 ISH (mRNA) was completed on heart, liver, skeletal muscle from select animals and DRGs from all animals at 8-week time point. Representative images are shown in FIG. 9. ISH labeling in the heart was nuclear and cytoplasmic, variable and labeled fewer card io myocytes than IHC. In the liver, ISH labeling was mostly nuclear and frequently observed in hepatocytes. There was minimal human BAG3 RNA expression in the DRG. Skeletal muscle was BAG3 negative.
In summary, 3E13 vg/kg Compound A administered by the intended route of administration in the clinic, was tolerated in WT mice at 3- and 8-weeks post IV administration. There were no Compound A-related clinical pathology changes in markers of heart, liver, or skeletal muscle injury or microscopic findings. Evaluation by IHC revealed a widespread variable pattern of BAG3 human protein expression in heart of all animals, while there was very low level expression in liver and DRG, and no expression observed in skeletal muscle.
2. Exploratory cKO mouse biodistribution and tolerability study (12 weeks) following single IV bolus of 1E13, 3E13 and 9E13 vg/kg Compound A. An exploratory pharmacology/toxicology study was performed in 12-week old BAG3 cKO dilated cardiomyopathy disease model (DCM) mice treated with a single intravenous tail vein administration of saline or Compound A. The single dose administration of 1 E13, 3E13, or 9E13 vg/kg Compound A was followed by necropsy at 12-weeks post dose. A cohort of cKO mice and a cohort of WT mice were included to establish a baseline for comparison at study start.
Table. 7.
Figure imgf000084_0001
Table 8: Individual animal mortality summary
Figure imgf000084_0002
Figure imgf000085_0001
Mortality occurred across treatment groups including cKO saline control animals (Table 8 above), which was attributed to DCM disease and not related to Compound A treatment. Necropsy was performed at approximately 12-weeks post dosing and serum was collected. No Compound A-related differences in a targeted panel of clinical pathology parameters were observed across any groups (ALT, AST, ALP, GLDH, TBIL, cTNI, MYL3, sTNI, and FABP3). A marker of cardiac toxicity, NT-proBNP (indicative of myocyte stretch) was found to be elevated at 12-weeks post dose in the cKO mouse control group compared to WT mice and indicated the pathological progression of the disease model. There were no Compound A-related changes in NT-proBNP at 12-weeks post dose.
Tissues collected at 12-weeks post dosing included heart, liver, skeletal muscle, spinal cord/DRG, lung, kidney, adrenal gland and brain; however, only heart, liver and skeletal muscle were evaluated for potential histopathology findings. Microscopic heart evaluation of the untreated control cKO mice at baseline (11-12 weeks of age) showed microscopic changes of minimal severity consistent with the DCM disease model (Table 9; severity score compared to WT mice). The saline control cKO hearts at study end (23-25 weeks of age) were similar to the baseline cohort of cKO mouse hearts, except for findings of mild to moderate ventricular dilatation and mild cardiomyocyte atrophy.
In the cKO group treated with 3E13 vg/kg Compound A, signs of efficacy were seen by functional assessment (echocardiography, FIG. 5A and 5B) and by microscopic evaluations (decreases in mean severity of ventricular dilatation and cardiomyocyte atrophy). This dose level (3E13 vg/kg) did not have Compound A-related toxicity findings, although rare highly-expressing karyocytomegalic cardiomyocytes with cytoplasmic basophilia were observed. The cKO group treated with the high-dose (9E13 vg/kg) of Compound A also showed functional improvement (FIG. 5A and 5B) and microscopic signs of efficacy in the heart. While efficacy was still evident at the high dose, there was mild Compound A-related cardiomyocyte degeneration/necrosis with karyocytomegaly, cytoplasmic basophilia and occasionally vacuolation. These microscopic findings in the high dose animals occurred without changes in biomarkers of cardiotoxicity and in the presence of functional (efficacy) indicating continued improvement. As such, clinical doses into this range (/.e., 9E13 vg/kg) would not be precluded.
Immunohistochemistry (IHC) and in situ hybridization (ISH) were used to evaluate the biodistribution of transgene expression in the heart, liver, and skeletal muscle (other tissues including spinal cord/DRG were not evaluated). Human BAG3 protein immunoreactivity by IHC generally increased with dose of Compound A, with variable distribution of signal observed within treatment groups and within individual heart samples (FIG. 10). Digital image analysis indicated that up to a mean of 52% of the heart was positive for BAG3 protein (Table 9; FIG. 5J). Human BAG3 mRNA was detected by ISH and signal was also observed to increase with the dose of Compound A. Digital image analysis indicated up to 52% of the card io myocytes were positive for human BAG3 expression across dose groups (Table 9; FIG. 10; FIG. 5I).
Table 9: Summary of heart microscopic findings, mean human BAG3 percent positive cardiomyocyte protein levels by immunohistochemistry, and mean human BAG3 RNA by in situ hybridization in the hearts of cKO mice.
Figure imgf000086_0001
In summary, evaluation of Compound A in BAG3 cKO mice (1 E13, 3E13, 9E13 vg/kg), administered by the intended route of clinical administration, indicated functional improvement at >3E13 vg/kg as well as dose-dependent expression by ISH (RNA) and IHC (protein) in cardiomyocytes. Evaluation of a targeted set of safety endpoints at 12-weeks post dose did not reveal any Compound A-related clinical pathology changes in markers of liver, heart or skeletal muscle toxicity. At the high dose of 9E13 vg/kg (approximately 3-fold higher than the efficacious dose of 3E13 vg/kg in this study), Compound A-related mild cardiomyocyte degeneration/necrosis was observed. These microscopic findings occurred without changes in biomarkers of cardiotoxicity and in the presence of continued functional (efficacy) improvement.
3. Single dose IV exploratory toxicity and biodistribution study (6-weeks) in cynomologus monkeys at 4E13 and 1.3E14 vg/kg Compound A.
Male and female cynomolgus monkeys, approximately 3-4 years old at initiation of dosing, were administered either a single dose of vehicle or Compound A by IV injection. The objective of this study was to investigate the potential toxicological effects as well as biodistribution in cynomolgus monkeys following a single IV dose of Compound A at 3E13 and 1 E14 vg/kg. Important to note that based on re-titer analysis of the lot completed after the study, the stock concentration was revised from 5.02E13 vg/mL to 6.7E13 vg/mL so that the intended doses of 3E13 and 1 E14 vg/kg were actually 4E13 vg/kg and 1.3E14 vg/kg. All groups were administered methylprednisolone once daily at 5 mg/kg by IM injection starting the day prior to and continuing through to the day prior to necropsy.
Table 10.
Figure imgf000087_0001
Animals were prescreened for anti-AAV9 neutralizing antibodies (nAb) prior to dosing and negative animals selected on study. The nAb evaluation used cell-based transduction inhibition assay. The nAb titers were reported as the lowest reciprocal serum dilution (5, 10, 20, 40) that had > 50% transduction inhibition. Samples with titers <5 were considered as nAb negative for AAV9. However, upon re-check post dosing, the high dose female (1 .3E14 vg/kg) was confirmed to have seroconverted with a high AAV9 nAb titer which accounts for the lack of target protein expression observed in this animal and impacted immune endpoint evaluation.
All animals survived to scheduled necropsy with no Compound A-related clinical observations. There were no Compound A-related macroscopic or microscopic findings.
There were Compound A-related increases in ALT, AST, GLDH, CK, cardiac troponin I, neutrophils, monocytes at > 4E13 vg/kg.
At 4E13 vg/kg, ALT was increased on Days 3 (female) and 8 (male, female) and returned to baseline by Day 15 (FIG. 11 A). At 1.3E14 vg/kg, ALT was increased on Day 15 (peak) and remained above baseline through Day 43 in the male only. AST was increased on Day 3 (female) at 4E13 vg/kg or Day 8 (male) at 1 .3E14 vg/kg and returned to baseline by Day 15. GLDH was also transiently increased on Days 8 (peak) and 15 in the male at 1 .3E14 vg/kg and on Days 3 (peak) and 8 in the female at 4E13 vg/kg. The ALT and GLDH increases are indicative of hepatocellular injury, however there was no microscopic correlate from histopathology evaluation performed on liver samples (necropsy Day 44 or 47). In the male only, at 1.3E14 vg/kg, CK was increased on Days 3 (peak) and 15, and returned to baseline by Day 29. Cardiac troponin I was elevated in the female animal only at 4E13 vg/kg on Day 43 consistent with a rising trend at study end. In the male only at 1 .3E14 vg/kg, neutrophils, monocytes and LUC were increased on Days 3, 8, and/or 43.
Evaluation of cytokines and complement factors revealed Compound A-related changes at the high dose. There were no Compound A-related changes in cytokines or complement activation products in animals dosed with 4E13 vg/kg Compound A. At 1.3E14 vg/kg, increased TNF (FIG. 11B) was observed in the male (7.6x baseline; Day 15) and female (4.8-9.4x baseline; peak on Day 15), as well as an increase in SC5b-9 (53x baseline; Day 1 at 6 HPD) in the female. The complement activation (SC5b-9) in the high dose female (1 .3E14 vg/kg) was likely initiated by AAV9 nAbs and not considered directly related to Compound A administration. The AAV9 nAbs along with complement activation likely potentiated the earlier onset and greater magnitude of TNF increase observed in the high dose female compared to the high dose male. The nAb response from pre-dose samples revealed that this animal seroconverted prior to dosing, thus indicating the animal was no longer immunologically naive and potentially impacting subsequent immune endpoint evaluations. A positive AAV9 capsid ELISpot response was noted in this high dose animal and was likely a recall I memory cell mediated response as a result of prior AAV9 exposure as evidenced by seroconversion prior to Compound A administration. There were smaller, uncertain, ELISpot signals noted in the males at both dose levels that were not considered related to Compound A administration.
The biodistribution (VGC, RNA, BAG3 protein) of Compound A at 4E13 vg/kg and 1 .3E14 vg/kg was evaluated with select tissues shown in Table 11 below (see also FIG. 6A- F). Heart expression was observed at >4E13 vg/kg with protein translation in all animals except the high dose female due to seroconversion. Evidence of expression was observed in the liver (protein in male only) and DRG neurons (no protein observed) without histopathology findings.
Table 11 . Compound A VGC, RNA, and BAG3 protein in select cyno tissues
Figure imgf000088_0001
Figure imgf000089_0001
In situ hybridization for BAG3 RNA was performed on heart sections from males and females from all groups. The positive signal, present as punctate red dots (FIG. 12), was present in the nucleus and cytoplasm of cardiomyocytes for all Compound A-dosed animals, except for the high dose female. The intensity and extent of positive ISH labelling in cardiomyocytes varied across heart samples and individual animals. In general, labelling was higher (number of red dots per cardiomyocytes and/or number of cardiomyocytes with red dots) with increasing dose in the males and higher in the male than the female at 4E13 vg/kg. In addition to semi-quantitative evaluation of percent positive cardiomyocytes by a pathologist, digital image analysis was performed to quantify the percent of positive cardiomyocytes (FIG. 6D). There were moderate variations in the positive labeling between the heart sections from a given animal within a group. Percent of BAG3 ISH positive cardiomyocytes in each section in the male and female administered 4E13 vg/kg ranged from 45 to 92% and 20 to 56%, respectively. In the male administered 1 .3E14 vg/kg, these values ranged from 79 to 95%.
In summary, 4E13 and 1.3E14 vg/kg Compound A, administered by the intended route of clinical administration, was tolerated in monkeys at 6-weeks post IV infusion and in the presence of a daily IS regimen. There were no Compound A-related histopathology findings. Clinical pathology results indicated Compound A-related increases in ALT, AST, CK, cardiac troponin I, neutrophils, monocytes at > 4E13 vg/kg. In addition, at the high dose (1.3E14 vg/kg), there were changes in immune endpoints (cytokine, complement, ELISpot) and one high dose animal that had seroconverted prior to dosing. Heart in situ hybridization for BAG3 RNA revealed a high percentage of BAG3-positive cardiomyocytes at 4E13 vg/kg ranging from 20 to 92% and at 1 .3E14 vg/kg ranging from 79% to 95% across heart sections in the high dose male.
Example 7: Tissue distribution / Tropism
BAG3 biodistribution was evaluated following IV administration of Compound A up to 1.3E14 vg/kg (approximately 3.3xthe efficacious dose demonstrated in cKO mice) in the cyno ETS (see cyno ETS Table 11 and FIG. 6A-F). Viral genome copies (VGC) were present and generally increased dose-dependently in the heart, liver, skeletal muscle, gonads, spinal cord, and DRG (FIG. 6A). While there was evidence of VGC in these tissues, there were no histopathology findings. AAV9 vector-mediated BAG3 expression (RNA) was detected primarily in the liver and heart (FIG. 6C), while expression was also noted in skeletal muscle, spinal cord, and DRG (gonads were not evaluated for RNA). ISH demonstrated significant and dose-dependent BAG3 expression across cyno cardiomyocytes (FIG. 6D). While total BAG3 (conserved) protein was noted in the cyno heart, liver, skeletal muscle, spinal cord, and DRG, the human specific peptide confirmed that human BAG3 protein was primarily localized to the heart at both dose levels evaluated. Marginal human BAG3 protein was detected at the high dose in the liver and no protein in spinal cord or DRG (FIG. 6E-6F).
Example 8: Pharmacokinetics-Pharmacodynamics Relationship and Prediction of Efficacious Human Dose.
The dose-translation plan for Compound A involved two steps: First the efficacious levels of target (BAG3) expression and heart coverage were determined using data from disease model mouse (BAG3-cKO) dose-response studies. Second, the dose necessary to achieve the mouse-based efficacious BAG3 expression was determined using data from a cynomolgus monkey study that tested Compound A at two different dose levels to evaluate BAG3 expression dose-response in monkey heart.
This translational plan assumed that the BAG3 expression (mRNA and proteinefficacy relationship in the BAG3 cKO mouse disease model is representative of the same relationship in BAG3 DCM patients. In addition, it was assumed that the dose-BAG3 expression relationship in humans can be based on the observed dose-BAG3 relationship in cynomolgus monkeys. These assumptions and the data from BAG3 cKO mouse and cynomolgus monkey studies were integrated into a quantitative systems pharmacology model for AAV gene therapy (developed and validated using available literature and inhouse data) to produce the efficacious dose and dose-dependent BAG3 expression predictions as described below. It should be noted that since the number of animals in the cynomolgus monkey ETS study used to project clinical dose was small (n = 2 at 4E13 and n = 1 at 1 .3E14 vg/kg) the dose-predictions may be updated when data based on future studies.
Nonclinical Pharmacology and Therapeutic Level of BAG3 Expression
The target therapeutic level of BAG3 expression in heart was determined based on results from a dose-response efficacy study in the BAG3 cKO mouse model of disease as described above. The echocardiography-based changes in cardiac structure and function post-treatment in individual animals observed in this study were correlated with the corresponding BAG3 mRNA and protein expression measured in heart tissue at necropsy to determine the BAG3 expression-efficacy relationship (FIG. 13A-13D).
Specifically, human BAG3 protein expression in BAG3 cKO mouse heart (quantified using LC/MS assay specific for the human BAG3 protein) which increased from 0 (control) to 70% (9E13 vg/kg) of wild-type mouse heart BAG3 expression with Compound A treatment was related to an increase in ejection fraction from 29% to 49%. The same improvement in ejection fraction also correlated with an increase in human BAG3 transgene heart tissue spatial coverage determined using in situ hybridization (human BAG3 mRNA; 52% cardiomyocytes hBAG3 positive at 9E13 vg/kg) and immunohistochemistry (BAG3 protein; 52% heart region hBAG3 positive at 9E13 vg/kg). All measures of protein and mRNA expression were also correlated with each other across dose groups.
Notably the relationship between human BAG3 mRNA/protein expression and improvement in cardiac function tended to saturation above approximately 20% wild-type mouse heart BAG3 protein expression and approximately 20% human BAG3 mRNA+ cardiomyocytes as determined by ISH (FIG. 13A-13B). Comparison of efficacy in individual mice binned by hBAG3 protein or ISH expression showed that mice that had >20% expression level by either measurement had a better ejection fraction change than mice that had <20% expression but were comparable to mice that had >40% expression (FIG. 13C- 13D). These results suggested that cardiac function improvement saturates around approximately 20% BAG3 expression level as measured by LC/MS-based bulk protein level and ISH-based cardiomyocyte coverage and therefore this level of expression was selected as the target therapeutic level of BAG3 expression.
Human Dosing
To determine the human dose necessary to achieve the target therapeutic levels of BAG3 expression data from the dose-response study of Compound A in cynomolgus monkeys together with a quantitative systems pharmacology (QSP) model developed was used and validated using available literature and in-house data for cross-species translation of AAV gene therapies.
In the cynomolgus monkey ETS, BAG3 biodistribution was evaluated following IV administration of Compound A at 4E13 and 1.3E14 vg/kg (doses based on final viral titer determined post-study - updated from original study design of 3E13 and 1 E14 vg/kg). The observed heart transduction of Compound A, measured as viral genome copy number per diploid genome equivalent (VCN/dge), increased dose-linearly in cynomolgus monkeys (FIG. 14A). The observed transduction was consistent with the model-predicted heart transduction for AAV9 as well as historical literature and in-house data for this capsid. This enabled use of this model to predict heart transduction for Compound A in humans. Note that the model predictions and available clinical data for AAV9 gene therapies indicated that heart transduction dose-dependence for Compound A can be expected to be very similar between non-human primates and humans.
The observed heart cardiomyocyte coverage of Compound A, measured using ISH for hBAG3 mRNA, also increased dose-dependently in cynomolgus monkeys (FIG. 14B). Heart tissue coverage exceeded the target level of >20% card io myocytes at both 4E13 and 1.3E14 vg/kg doses in monkeys and was anticipated to be translatable between monkeys and humans. Therefore any Compound A dose equal to or greater than 4E13 vg/kg was anticipated to be sufficient for achieving this therapeutic target level.
A Compound A-dose-dependent increase was also observed for hBAG3 protein level (measured using LC/MS) in the cynomolgus monkey hearts (FIG. 14C). The increase in protein level was greater than dose-linear (7x increase from 4E13 to 1 .3E14 vg/kg) although data was only available for one monkey at the high dose. This data was modeled using a power-law and included in the QSP model allowed us to project the Compound A dosedependent BAG3 protein expression in monkeys as shown in FIG. 14C.
To extend projections to humans, endogenous BAG3 protein expression was measured in untreated healthy cynomolgus monkey and healthy human heart samples. These measurements indicated an approximately 1.7-fold lower BAG3 protein level in human heart relative to monkey hearts (human:110 ng BAG3/mg protein vs cyno:190 ng BAG3/mg protein). A similar 1 ,7x lower protein expression efficiency for the human protein projection model was accordingly assumed. Based on these assumptions the model- predicted BAG3 protein dose-dependence in humans is shown in FIG. 14C. Using this predicted dose-dependence the clinical dose necessary to achieve the target level of BAG3 protein expression in human heart (22 ng BAG3/mg protein based on 20% of 110 ng BAG3/mg protein in normal healthy human heart) is projected to be about 1 E14 vg/kg of Compound A delivered intravenously. Note that if the monkey to human correction factor of 1 ,7x was not used and instead human protein expression was assumed to follow the cynomolgus monkey dose-dependence the projected clinical dose would be about 7E13 vg/kg of Compound A delivered intravenously.
A smaller effect than maximal efficacy could still be beneficial to patients, however. For example, a difference from placebo in ejection fraction of 5% would be both measureable and clinically meaningful. At 3E13 vg/kg, the ejection fraction change is estimated to be about 5 - 10%. Thus, an estimated dose of approximately 3E13 vg/kg could define the lower end of the clinical dose range.
In sum, about 3E13-1 E14 vg/kg of Compound A is projected to be the minimum efficacious dose range that is predicted to achieve the target levels BAG3 protein expression and cardiomyocyte coverage necessary for therapeutic benefit in patients. There are three key sources of uncertainty in this dose projection. In some embodiments, a pharmaceutically effective amount of the rAAV vector ranges from about 1 E10 to about 1 E17 vector genomes per kilogram (vg/kg) of subject body weight.
Example 9: In Vivo Efficacy Study of Compound A in A BAG3 Cardiac Heterozygous Mouse Model
Primary pharmacology of Compound A in vivo was interrogated in a mouse model of disease to evaluate the dose response associated efficacy. The mouse model of disease was generated by cardiac specific knockout of one or both BAG3 alleles resulting in partial (BAG3 cHET mice) or complete (BAG3 cKO mice) knockdown of BAG3 expression in the heart. These mice either have partial BAG3 expression (approximately 50%, BAG3 cHET) or completely lack BAG3 expression (BAG3 cKO) in cardiomyocytes, develop cardiac dysfunction and dilatation, develop cardiac fibrosis, and express biomarkers of heart failure and fibrosis in the heart (Fang et al., J. Clin. Invest. 127(8): 3189-200 (2017)). BAG3 cKO mice develop the disease phenotype at a faster rate when compared to the BAG3 cHET mice.
To determine whether restoration of BAG3 expression in the heart via AAV gene delivery results in improvement of cardiac structure and function or improvement in survival, a dose-response efficacy study in the BAG3 cHET mouse model of disease was pursued. BAG3 cHET mice were administered Compound A at 3E13 vg/kg, and 1 E14 vg/Kg. Cardiac structure and function and survival were assessed longitudinally. At necropsy AAV biodistribution and transgene expression (mRNA, protein) were assessed in the heart. HSPB8 stabilization (a surrogate of BAG3 expression) and biomarkers of heart failure (Nppa, Nppb, Myh6, Myh7) and apoptosis (Col1 a1 , Col1a2, Postn, Fn1 , Timpl) were also assessed in the heart.
Methods for Dose-response Efficacy and Survival Study
BAG3 cHET mice at age 27-28 weeks were administered Compound A intravenously at 3E13 vg/kg (n:14), and 1 E14 vg/Kg (n:14). The study also included a no-treatment control cohort of BAG3 cHET mice (n:14) and a no-treatment control cohort of BAG3 cWT mice (n:15). Cardiac structure and function were assessed using echocardiography at 25-26 weeks (baseline, 2-weeks prior to treatment) and at 30-31 weeks (3-weeks post treatment), at 35-36 weeks (8-weeks post treatment), and at 40-41 weeks (13-weeks post treatment). Survival was monitored approximately 14-weeks post-treatment.
At necropsy, heart tissue was collected for molecular biology analysis: AAV biodistribution, and transgene expression (mRNA, protein). Prior to treatment mice were randomized into groups based on echocardiography readouts (ejection fraction, left ventricular end diastolic volume), body weight and gender.
Echocardiography Assessment
For echocardiography imaging, mice were induced to anesthetic state using isoflurane (3%) or sevoflurane (5 to 6%) in an induction chamber, and then anesthetic status was maintained at approximately 2% isoflurane or approximately 4 to 4.5% sevoflurane during animal preparation and image acquisition. While anesthetized, an animal was transferred onto a water-circulating heated blanket to remove hair around the left lateral and ventral thoracic area using a chemical hair removal agent. After hair removal, each animal was transferred onto a heated (approximately 34 to 35° C) platform for echocardiography. Transthoracic parasternal long axis B-mode and parasternal short axis M-mode images of the heart were acquired using 18-38 MHz transducer (VisualSonics MS400®) in Vevo 2100® or Vevo 3100® ultrasound machine to assess left ventricular (LV) structure and function. Anesthesia level was adjusted to maintain heart rate between 450 to 550 bpm during image acquisition. After image acquisition, mice were transferred to a warm cage for recovery. Post image acquisition, images were analyzed using Vevo lab® analysis software, or automated analysis tool. The following parameters were collected from image analysis: LV ejection fraction, fractional shortening, LV end diastolic and systolic volume, LV end diastolic and systolic area, LV posterior and anterior wall.
Survival Monitoring Assessment
General animal well-being was monitored once daily. In addition, general signs and symptoms of heart failure such as abnormal breathing, poor body condition (< 2 out 5), poor activity/not moving around the cage etc. was monitored 1 to 2 times per week. Echocardiography was performed once in 3 to 5 weeks to assess cardiac function and structure. During monitoring for signs of heart failure, all animals were scored using an inhouse heart failure scoring chart to grade level of disease burden:
Table 12. Survival monitoring
Figure imgf000094_0001
Figure imgf000095_0001
Tissue Analysis
Frozen tissue samples were used for DNA isolation using phenol/chloroform DNA extraction methods. The DNA pellet was washed with ice cold 70% ethanol and resuspended in nuclease free water. DNA concentration was measured with Qiaxpert.
RNA isolation from frozen tissue was prepared by homogenization of approximately 20 mg of tissue sample in 1 mL Trizol with the presence of a 5 mm stainless steel bead using a Tissuelyzer II set at frequency 25 Hz for 5 minutes. Lysates were transferred to phasemaker tubes and 200 mL chloroform was added. Samples were vortexed for 15 seconds, incubated at room temperature for 5 minutes, and centrifuged at 14,000 g for 5 min at 4°C. The clear supernatant was transfer to a new tube and processed with the RNeasy RNA mini kit per manufacturer instructions. DNAse treatment was performed on column for 20 min before elution with nuclease free water. RNA concentration was measured using Nanodrop spectrophotometer
Protein isolated from frozen tissue was prepared by homogenization of approximately 20 mg of tissue sample in 100 pL RIPA buffer containing 1x protease inhibitor with the presence of a 5 mm stainless steel bead using a Tissuelyzer II set at frequency 25 Hz or 5 minutes. Lysates were incubated in wet ice for 30 minutes, and centrifuged at full speed for 30 minutes at 4°C. The clear supernatant was transferred to a new tube. Protein concentration was measured using BOA assay Kit.
Vector Genome Quantification (VGC)
VGC quantification was performed using ddPCR using the primer and probe sequences to amplify BAG3 transgene in all samples. The forward primer sequence was: GGCTGGCCCTTCTTCGT (SEQ ID NO: 16). The reverse primer sequence was GCCCTCAGAAGGCACTCT (SEQ ID NO: 17). The probe sequence was CCACAATAGCAGAACCAC (SEQ ID NO: 18).
Quantification of Transgene mRNA (BAG3) Expression
Isolated RNA samples were reverse transcribed to generate a cDNA library using the Superscript IV First-Stand Synthesis System following manufacturer’s protocol. 100 or 400 ng of total RNA was used in a 20 pL reaction. Reverse transcription was performed at 23°C for 10 minutes, 55°C for 10 minutes, then inactivate the reaction at 80°C for 10 minutes for 5 minutes. cDNA samples were stored at -20° C until RT-PCR analysis. cDNA was diluted using nuclease-free H2O by 1 :10 or 1 :40 to make the final 2.5 ng RNA amount in each ddPCR reaction. Quantification of BAG3 transgene mRNA expression was determined using ddPCR with the same BAG3 primers and probes as described in above section and housekeeping gene mTBP primer probes. PCR reaction mixture containing ddPCR Supermix (no dUTP) and above primer probes was prepared in an Airclean 600 PCR workstation and added to a ddPCR 96-well plate. Droplet generation, PCR programs, and data acquisition were performed as described in above section of VGC assessment. The mRNA expression was calculated by the ratio of FAM to VIC channel.
Assessment Total BAG3/HSPB8 Protein Expression
Protein expression of total BAG3 (human and mouse), human BAG3, and HSPB8 was detected using Wes/Jess from ProteinSimple with optimized conditions (protein amount and antibody dilution) following the manufacturer’s instruction. GAPDH was detected as the loading control. The chemiluminescent intensity of each detected protein was generated automatically by the instrument software. The protein expression of total BAG3, human BAG3, and HSPB8 was quantified by the ratio of each protein to GAPDH.
Quantification of Biomarkers of Heart Failure and Fibrosis
A total of 400 ng of RNA was used to prepare cDNA with the kit Superscript IV Vilo RT with ezDNase by following manufacturer instructions resulting in a final concentration of 20 ng/pL cDNA. For each RT reaction and no RT control reaction 10 pL of gDNA reaction mix was prepared by combining 1 pL of 10x ezDNase buffer, 1 pL of ezDNase enzyme, RNA (400 ng), and nuclease free water. Samples were incubated at 37°C for 2 min and returned to ice. The RT and No RT reactions were then prepared; for each RT reaction 4 pL of SSIV Vilo Master Mix was combined with 6 pL of nuclease free water, and for each no RT control reaction 4 pL of SSIV Vilo No RT Control Master Mix was combined with 6 pL of nuclease free water. 10 pL of master mix (RT or No RT respectively) was mixed with the 10 uL gRNA reaction to bring the reaction to a 20 pL final volume. RT was performed at 25°C for 10 min, 50°C for 10 min, and 85°C for 5 min. Samples were stored at -20 until RT-qPCR analysis. cDNA was prepared in a 96-well PCR plate. qPCR master mixes were then prepared with the cDNA template. cDNA was diluted using nuclease-free H2O by 1 :10 or 1 :40 to make the final 2.5 ng RNA amount in each ddPCR reaction. For each sample the following was mixed: 55 pL of TaqMan Fast Advanced Master Mix (2x), 2.5 pL of 20 ng/uL cDNA, and 52.5 pL of nuclease free water. 100 pL of prepared PCR mix was then loaded into each reservoir on the array card. A total of 7 samples and one no reverse transcription (RT) control was added to each plate (8 reservoirs total/plate). The array card was centrifuged to ensure all the liquid was at the bottom on the tubes. The array card was removed from the centrifuge and sealed using the TaqMan Array Card Sealer. After sealing, the fill reservoir strip was cut from the card using scissors. The Array Card was the run on a ViiA 7 qPCR instrument using the standard cycling protocol (50°C for 2 minutes, 95°C for 20 seconds, [95°C for 1 second, 60°C for 20 seconds] x 40) for an Array Card and TaqMan Fast Advanced Master Mix. Results were analyzed using relative quantification to the housekeeping gene HPRT.
Table 13: Primers.
Figure imgf000097_0001
Results and Discussion
BAG3 cHET mice (mixed gender) were treated with Compound A at 3E13 vg/Kg and 1 E14 vg/Kg (age: 27-28 weeks). The study also included a no-treatment control cohort of cHET mice and a no-treatment control cohort of cWT mice.
Cardiac function (ejection fraction) and structure (left ventricular end-diastolic & end- systolic volume) were assessed longitudinally using echocardiography (FIG. 15A-15C) at an age of 25-26 weeks (baseline, 2-weeks prior to treatment), at an age of 30-31 weeks (3- weeks post treatment), at an age of 35-36 weeks (8-weeks post treatment), and at and age of 40-41 weeks (13-weeks post treatment). When measuring cardiac ejection fraction at all three timepoints post-treatment, no significant differences were detected when comparing treated mice (3E13 vg/Kg or 1 E14 vg/Kg) and the non-treated BAG3 cHET control cohort. A significant decrease was detected within all cHET groups when comparing values collected at baseline and at 8- or 13-weeks post treatment. When measuring LVEDV at all three timepoints post-treatment, no significant differences were detected when comparing treated mice (3E13 vg/Kg or 1 E14 vg/Kg) and the non-treated BAG3 cHET control cohort. A significant increase was detected in the non-treated control group when comparing values collected at baseline and at 8- or 13-weeks post treatment. When measuring LVESV at all three timepoints post-treatment, no significant differences were detected when comparing treated mice (3E13 vg/Kg or 1 E14 vg/Kg) and the non-treated BAG3 cHET control cohort. A significant increase was detected in the non-treated BAG3 cHET control group when comparing values collected at baseline and at 8- or 13-weeks post treatment.
Survival was assessed longitudinally up to 42 weeks (approximately 14-weeks post treatment) based on a pre-defined set of criteria described above. No significant differences in survival were detected when comparing treated mice (3E13 vg/Kg or 1 E14 vg/Kg) and the non-treated BAG3 cHET control cohort (FIG. 16A). No significant differences in body weight were detected in these mouse groups (FIG. 16B).
Viral genome biodistribution was examined in heart tissue collected at necropsy from BAG3 cHET mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 17A). A dose response in biodistribution was detected in the heart: 3E13 vg/kg (0.131 ±0.066 vg/mTFRC), 1 E14 vg/kg (0.371±0.107 vg/mTFRC).
Transgene mRNA expression was examined in heart tissue collected at necropsy from mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 17B). A dose response in expression was detected in the heart: 3E13 vg/kg (10.81±6.18 vg/mTBP), 1 E14 vg/kg (50.889±14.607 vg/mTBP).
BAG3 protein expression was examined in heart tissue collected at necropsy from mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 17C). Protein expression was normalized to the levels of BAG3 expression detected in the hearts of a cohort of wild type mice. A dose-responsive increase in BAG3 protein levels was observed in BAG3 cHET mouse hearts after treatment with Compound A. At the high dose level (1 E14 vg/Kg), approximately 90% (0.912±0.196) of the WT level of BAG3 was detected and at the low dose (3E13 vg/Kg), approximately 60% (0.607±0.134) of WT BAG3 levels was observed, approximately 40% (0.392±0.096) of the WT level of BAG3 was detected in notreated cHET BAG3 mice.
HSPB8 protein expression was examined in heart tissue collected at necropsy from mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 17D). Protein expression was normalized to the levels of BAG3 expression detected in the hearts of a cohort of wild type mice. A dose-responsive increase in HSPB8 protein levels was observed in BAG3 cHET mouse hearts after treatment with Compound A. At the high dose level (1 E14 vg/Kg), approximately 85% (0.855±0.155) of the WT level of BAG3 was detected and at the low dose (3E13 vg/Kg), approximately 63% (0.637±0.117) of WT BAG3 levels was observed, approximately 46% (0.460±0.071) of the WT level of BAG3 was detected in notreated cHET BAG3 mice.
Biomarkers of fibrosis (Col1a1 , Col1 a2, Fn1 , Postn, Timpl) and heart failure (Nppa, Nppb, Myh7, Myh6) were assessed (RNA expression) in the heart of treated and untreated mice. When measuring biomarkers of fibrosis, no significant differences were detected when comparing treated mice (3E13 vg/Kg or 1 E14 vg/Kg) and the non-treated BAG3 cHET control cohort (FIG. 18A-18E). When measuring biomarkers of heart failure, no significant differences were detected when comparing treated mice (3E13 vg/Kg or 1 E14 vg/Kg) and the non-treated BAG3 cHET control cohort (FIG. 18F-18H).
Conclusion
Treatment of BAG3 cHET mice at 27-28 weeks with Compound A did not result in improvement of cardiac structure, cardiac function, or survival when compared to nontreated control BAG3 cHET mice. A dose dependent increase of viral genomes in the heart correlated with a dose-dependent increase in transgene mRNA and protein expression and restoration of HSPB8 protein expression. No significant improvement was detected in biomarkers of heart failure or fibrosis.
Example 10: In vivo survival and efficacy study of Compound A in a BAG3 cardiac knockout mouse model
Primary pharmacology of Compound A in vivo was interrogated in wild type mice to evaluate the dose response associated efficacy. The mouse model of disease was generated by cardiac specific knockout of BAG3 expression (BAG3 cKO mice). These mice lack BAG3 expression in cardiomyocytes, develop cardiac dysfunction and dilatation, develop cardiac fibrosis, and express biomarkers of heart failure and fibrosis in the heart (Fang et al., J. Clin. Invest. 127(8): 3189-200 (2017)).
To determine whether restoration of BAG3 expression in the heart via AAV gene delivery results in improved survival, a dose-response efficacy study in the cKO mouse model of disease was pursued. BAG3 cKO mice were administered Compound A at 3E13 vg/kg, and 1 E14 vg/kg. Survival, cardiac structure and function were assessed longitudinally, using echocardiography. At necropsy AAV biodistribution and transgene expression (mRNA, protein) were assessed in the heart. Methods for Dose-Response Survival Study
BAG3 cKO mice at age 14-15 weeks were administered Compound A intravenously at 3E13 vg/kg (n:16), and 1 E14 vg/kg (n:15). The study also included a control cohort of cKO mice which was administered vehicle (n:13). Survival was monitored approximately 21 weeks post-treatment. Cardiac structure and function were assessed using echocardiography at baseline (1-week prior to treatment) and at 2-, 5-, 9- and 13-weeks post treatment. At necropsy, heart tissue was collected for molecular biology analysis: AAV biodistribution, and transgene expression (mRNA, protein). Prior to treatment mice were randomized into groups based on echocardiography readouts (ejection fraction, left ventricular end diastolic volume), body weight and gender.
General methods
The following methods were performed as described in Example 9: DNA isolation, RNA isolation, protein preparation, VGC quantification, quantification of BAG3 transgene RNA expression, quantification of total BAG3 protein expression, echocardiography assessment and survival monitoring assessment.
Results and Discussion
BAG3 cKO mice (mixed gender) were treated with either vehicle or Compound A at 3E13 vg/Kg and 1 E14 vg/Kg (age: 14-15 weeks). Survival (FIG. 19A) was assessed longitudinally (up to approximately! 6 weeks post treatment) based on a pre-defined set of criteria (see Example 9). It was determined that vehicle-treated mice (Group 1) had a significantly lower survival rate than mice treated with Compound A at either 3E13 vg/Kg (Group 2) or 1 E14 vg/Kg (Group 3). No significant differences in body weight were detected in these mouse groups (FIG. 19B).
Cardiac function (ejection fraction) and structure (left ventricular end-diastolic & end- systolic volume) were assessed longitudinally using echocardiography (FIG. 20A-20C) at baseline and at 2-, 5-, 9-, and 13-weeks post treatment. At week 13 post treatment, a significant improvement in ejection fraction was detected in mice treated with Compound A at 3E13 vg/kg (41 ,0±17.1 %) and 1 E14 vg/kg (51 ,2±16.6%) as compared to vehicle-treated BAG3 cKO mice (27.0±15.8%). At week 13, a significant improvement in left ventricular end diastolic volume and left ventricular end systolic volume was also detected in mice treated with Compound A at 1 E14 vg/kg (LVEDV: 54.7±23.7 uL, LVESV: 29.8±26.5 uL) as compared to vehicle-treated BAG3 cKO mice (LVEDV: 75.6±25.1 uL, LVESV: 57.6±28.3 uL).
Viral genome biodistribution was examined in heart tissue collected at necropsy from mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 21 A). A dose response in biodistribution was detected in the heart: 3E13 vg/kg (0.080±0.039 vg/mTFRC), 1 E14 vg/kg (0.32±0.13 vg/mTFRC).
Transgene mRNA expression was examined in heart tissue collected at necropsy from mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 21 B). A dose response in expression was detected in the heart: 3E13 vg/kg (8.21 ±5.59 vg/mTFRC), 1 E14 vg/kg (43.91 ±15.99 vg/mTFRC).
BAG3 protein expression was also examined in heart tissue collected at necropsy from mice treated with Compound A at 3E13 vg/kg and 1 E14 vg/kg (FIG. 21 C). Protein expression was normalized to the levels of BAG3 expression detected in the hearts of a cohort of wild type mice. A dose-responsive increase in BAG3 protein levels was observed in cKO mouse hearts after treatment with Compound A. At the high dose level (1 E14 vg/Kg), approximately 50% (0.49±0.16) of the WT level of BAG3 was detected and at the low dose (3E13 vg/Kg), approximately 8% (0.08±0.04) of WT BAG3 levels was observed.
Conclusion
Treatment of BAG3 cKO mice with Compound A resulted in improvement in survival and a dose-dependent improvement of both cardiac structure and function that correlated with expression of human BAG3 protein in the heart.
Example 11 : Clinical Study
BAG3 is implicated in diverse cellular function including but not limited to excitation contraction coupling, maintenance of sarcomere integrity and regulation of autophagy. Comprehensive assessments of the manifestations of disease caused by BAG3 mutations in the general population are complicated by the rarity of the disease and the single center nature of most case reports of BAG3 associated disease. Precise characterization BAG3 DCM with imaging and circulating biomarkers at presentation as well as its clinical progression remains to be elucidated. The development of novel transformational therapies for BAG3 DCM requires clear understanding of circulating, imaging, and clinical biomarkers of disease status at baseline and overtime. As such, a longitudinal natural history study in patients diagnosed with dilated cardiomyopathy due to likely pathogenic or pathologic BAG3 mutations is being conducted to clarify these measures.
Eligible subjects from this longitudinal study may be enrolled in a 2-Part, Phase 1 b, Interventional, Open-Label, Dose-Ascending Study, Followed by a Phase 2, Placebo- Controlled, Double Blinded Study to Investigate the Safety, Tolerability, and Efficacy of a Single Dose of ALXN2350 in Participants with BAG3 Mutation Associated Dilated Cardiomyopathy.
This prospective, open-label, dose-evaluation Phase 1 b followed by blinded, placebo-controlled Phase 2 study is a first-in-human (FIH)/first-in-patient (FIP) study with adeno-associated virus, serotype 9 (AAV9)-based gene therapy Compound A. This study aims to evaluate safety, tolerability, and efficacy following a single dose of Compound A in participants with dilated cardiomyopathy attributable to likely pathogenic or pathogenic BAG3 mutations. Other objectives include exploratory assessments relevant to long-term safety, dose selection, quality of life, and functional capacity to support future clinical development.
A two-part design with sequential conduct of Phase 1 b and Phase 2, with each part conducted in distinct/separate cohorts of participants, is proposed. The Phase 1 b portion of the study aims to explore safety, tolerability and immunogenicity across the dose range from the starting projected minimally active dose of approximately 3E13 vg/kg to the maximum feasible dose of approximately 1 E14 vg/kg. To allow for a blinded assessment of efficacy, the Phase 2 portion of the study will compare the proposed clinical dose level discovered in the Phase 1 b to a matching placebo in a randomized double-blinded study design. After an initial 12 months of efficacy and safety follow up, all eligible participants in the Phase 2 portion that received placebo will be given the opportunity to cross over to intervention with Compound A to allow for expanded investigation of safety and efficacy (employing a delayed start analysis to further evaluate the impact of therapy on disease progression). The doubleblinded nature of the study will remain in place until all participants have completed at least 12-months of follow-up and an independent data monitoring committee has determined the suitability of open label extension.
The Phase 1 b/2 study will be followed by a phase 3 double blinded randomized placebo-controlled study with the primary efficacy endpoint of improvements in functional capacity and symptoms. In this pivotal phase 3 registrational study, an interim analysis will be conducted to examine the effect of the investigational medicinal product on positive cardiac remodeling. At this interim analysis, both futility as well as overwhelming success criteria will be leveraged. If the level of positive (restorative) remodeling achieves prespecified levels of success compared to placebo, this data will be leveraged for an early accelerated approval strategy.
Table 14. First in patient clinical plan
Figure imgf000102_0001
Figure imgf000103_0002
Table 15. Clinical biomarker plan
Figure imgf000103_0001
Selection of subjects Subjects included in the protocol must meet specific inclusion criteria that include but is not limited to the following: Males/Females; Known BAG-3 mutation (likely pathologic/pathologic); Age >18 years; LVEF <50%; Stage B (NYHA l/IV)
Subjects will be excluded if they have: CKD > I lib; Non BAG3 related Heart Disease; Transaminase >2 x ULN; T. Bili > 1 ,5x ULN.

Claims

WHAT IS CLAIMED IS:
1 . A nucleic acid molecule comprising a nucleotide sequence encoding a Bcl2- associated athanogene 3 (BAG3) polypeptide, or variant thereof.
2. The nucleic acid molecule of claim 1 , wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is a codon-optimized nucleotide sequence.
3. The nucleic acid molecule of either claim 1 or claim 2, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to the nucleotide sequence of SEQ ID NO: 4 or 19- 24.
4. The nucleic acid molecule of any one of claims 1-3, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
5. The nucleic acid molecule of any one of claims 1-4, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 85% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
6. The nucleic acid molecule of any one of claims 1-5, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 90% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
7. The nucleic acid molecule of any one of claims 1-6, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 95% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
8. The nucleic acid molecule of any one of claims 1-7, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 98% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
9. The nucleic acid molecule of any one of claims 1-8, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 99% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
10. The nucleic acid molecule of any one of claims 1-9, wherein the nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is the nucleotide sequence of SEQ ID NO: 4 or 19-24.
11. A recombinant adeno-associated virus (rAAV) vector comprising the nucleic acid molecule of any one of claims 1-10.
12. The rAAV vector of claim 11 , wherein the rAAV vector comprises serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype 9 (AAV9), serotype 10 (AAV10), serotype 11 (AAV11), or serotype 12 (AAV12) capsid protein.
13. The rAAV vector of either claim 11 or claim 12, wherein the rAAV vector comprises AAV9 capsid protein.
14. The rAAV vector of claim 13, wherein the AAV9 capsid protein is a VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, a VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, or a VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
15. The rAAV vector of either claim 13 or claim 14, wherein the AAV9 capsid protein comprises the VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, the VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, and the VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
16. The rAAV vector of any one of claims 11-15, wherein the rAAV vector further comprises at least one cardiac promoter operably linked to the nucleic acid molecule comprising the nucleotide sequence encoding a BAG3 polypeptide, or variant thereof.
17. The rAAV vector of claim 16, wherein the at least one cardiac promoter is chicken troponin T (cTNT), CAG, MHCK7, CK7, endogenous BAG promoter, desmin (Des), alphamyosin heavy chain (a-MHC), myosin light chain 2 (MLC-2), cardiac troponin C (TNNC1 or cTnC), human cardiac troponin T (TNNT2) promoter, or a functional subsequence, modification, or variant respectively thereof.
18. The rAAV vector of either claim 16 or claim 17, wherein the at least one cardiac promoter is cTNT promoter or a functional subsequence, modification, or variant thereof.
19. The rAAV vector of either claim 17 or claim 18, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5, or a functional subsequence, modification, or variant thereof.
20. The rAAV vector of either claim 17 or claim 18, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5.
21 . The rAAV vector of any one of claims 11-20, wherein the rAAV vector further comprises at least one intron.
22. The rAAV vector of claim 21 , wherein the intron comprises the nucleotide sequence of SEQ ID NO: 6, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31 , or a functional subsequence, modification, or variant thereof.
23. The rAAV vector of either claim 21 or claim 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 6.
24. The rAAV vector of either claim 21 or claim 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 29.
25. The rAAV vector of either claim 21 or claim 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 30.
26. The rAAV vector of either claim 21 or claim 22, wherein the intron comprises the nucleotide sequence of SEQ ID NO: 31 .
27. The rAAV vector of any one of claims 11-26, wherein the rAAV vector further comprises at least one 5’ inverted terminal repeat (ITR) sequence.
28. The rAAV vector of claim 27, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8, or a functional subsequence, modification, or variant thereof.
29. The rAAV vector of either claim 27 or claim 28, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8.
30. The rAAV vector of any one of claims 11-29, wherein the rAAV vector further comprises at least one 3’ ITR sequence.
31 . The rAAV vector of claim 30, wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9, or a functional subsequence, modification, or variant thereof.
32. The rAAV vector of either claim 30 or claim 31 , wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9.
33. The rAAV vector of any one of claims 11-32, wherein the rAAV vector further comprises at least one transcription terminator sequence.
34. The rAAV vector of claim 33, wherein the at least one transcription terminator sequence is an SV40 polyA sequence, a bovine growth hormone (BGH) polyA sequence, a rabbit b-globin (rPg) polyA sequence, or a functional subsequence, modification, or variant thereof.
35. The rAAV vector of either claim 33 or claim 34, wherein the at least one transcription terminator sequence is an SV40 polyA sequence.
36. The rAAV vector of any one of claims 33-35, wherein the at least one transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7, or a functional subsequence, modification, or variant thereof.
37. The rAAV vector of any one of claims 33-36, wherein the at least transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7.
38. The rAAV vector of any one of claims 11-37, wherein the rAAV vector further comprises at least one stuffer or filler sequence, preferably wherein the at least one stuffer of filler sequence increases the entire length of the nucleic acid molecule of the rAAV vector, inclusive of the ITR sequences, to approximately 4.2 to 4.7 kilobases.
39. The rAAV vector of claim 38, wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 , or a functional subsequence, modification, or variant thereof.
40. The rAAV vector of either claim 38 or claim 39, wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 .
41 . An rAAV vector comprising, in 5’ to 3’ order:
(a) at least one 5’ ITR sequence;
(b) at least one cardiac promoter;
(c) at least one intron;
(d) at least one nucleotide sequence encoding a Bcl2-associated athanogene 3 (BAG3) polypeptide, or variant thereof, operably linked to the at least one cardiac promoter;
(e) at least one transcription terminator sequence;
(f) at least one stuffer or filler sequence; and
(g) at least one 3’ ITR sequence.
42. The rAAV vector of claim 41 , wherein the rAAV vector comprises serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype 9 (AAV9), serotype 10 (AAV10), serotype 11 (AAV11), or serotype 12 (AAV12) capsid protein.
43. The rAAV vector of either claim 41 or claim 42, wherein the rAAV vector comprises AAV9 capsid protein.
44. The rAAV vector of claim 43, wherein the AAV9 capsid protein is a VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, a VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, or a VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
45. The rAAV vector of either claim 43 or claim 44, wherein the AAV9 capsid protein comprises the VP1 protein comprising the amino acid sequence of SEQ ID NO: 1 or a functional subsequence, modification, or variant thereof, the VP2 protein comprising the amino acid sequence of SEQ ID NO: 2 or a functional subsequence, modification, or variant thereof, and the VP3 protein comprising the amino acid sequence of SEQ ID NO: 3 or a functional subsequence, modification, or variant thereof.
46. An rAAV vector plasmid comprising, in 5’ to 3’ order:
(a) at least one left spacer sequence;
(b) the at least one 5’ ITR sequence;
(c) the at least one cardiac promoter;
(d) the at least one intron;
(e) the at least one nucleotide sequence encoding a Bcl2-associated athanogene 3 (BAG3) polypeptide, or variant thereof, operably linked to the at least one cardiac promoter;
(f) the at least one transcription terminator sequence;
(g) the at least one stuffer or filler sequence;
(h) the at least one 3’ ITR sequence; and
(i) at least one right spacer sequence.
47. The rAAV vector of any one of claims 41 -45 or rAAV vector plasmid of claim 46, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is a codon-optimized nucleotide sequence.
48. The rAAV vector of any one of claims 41-45 or 47 or rAAV vector plasmid of any one of claims 46 or 47, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
49. The rAAV vector of any one of claims 41 -45, 47, or 48 or rAAV vector plasmid of any one of claims 46-48, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 80% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
50. The rAAV vector of any one of claims 41 -45 or 47-49 or rAAV vector plasmid of any one of claims 46-49, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 85% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
51 . The rAAV vector of any one of claims 41 -45 or 47-50 or rAAV vector plasmid of any one of claims 46-50, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 90% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
52. The rAAV vector of any one of claims 41 -45 or 47-51 or rAAV vector plasmid of any one of claims 46-51 , wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 95% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
53. The rAAV vector of any one of claims 41 -45 or 47-52 or rAAV vector plasmid of any one of claims 46-52, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 98% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
54. The rAAV vector of any one of claims 41 -45 or 47-53 or rAAV vector plasmid of any one of claims 46-53, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is at least about 99% identical to the nucleotide sequence of SEQ ID NO: 4 or 19-24.
55. The rAAV vector of any one of claims 41 -45 or 47-54 or rAAV vector plasmid of any one of claims 46-54, wherein the at least one nucleotide sequence encoding the BAG3 polypeptide, or variant thereof, is the nucleotide sequence of SEQ ID NO: 4 or 19-24.
56. The rAAV vector of any one of claims 41 -45 or 47-55 or rAAV vector plasmid of any one of claims 46-55, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8, or a functional subsequence, modification, or variant thereof.
57. The rAAV vector of any one of claims 41 -45 or 47-56 or rAAV vector plasmid of any one of claims 46-56, wherein the at least one 5’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 8.
58. The rAAV vector of any one of claims 41 -45 or 47-57 or rAAV vector plasmid of any one of claims 46-57, wherein the at least one cardiac promoter is chicken troponin T (cTNT), CAG, MHCK7, CK7, endogenous BAG promoter, desmin (Des), alpha-myosin heavy chain (a-MHC), myosin light chain 2 (MLC-2), cardiac troponin C (TNNC1 or cTnC), human cardiac troponin T (TNNT2) promoter, or a functional subsequence, modification, or variant thereof.
59. The rAAV vector or rAAV vector plasmid of claim 58, wherein the at least one cardiac promoter is cTNT promoter or a functional subsequence, modification, or variant thereof.
60. The rAAV vector or rAAV vector plasmid of either claim 58 or claim 59, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5, or a functional subsequence, modification, or variant thereof.
61 . The rAAV vector or rAAV vector plasmid of any one of claims 58-60, wherein the cTNT promoter comprises the nucleotide sequence of SEQ ID NO: 5.
62. The rAAV vector of any one of claims 41 -45 or 47-61 or rAAV vector plasmid of any one of claims 46-61 , wherein the at least one intron comprises the nucleotide sequence of SEQ ID NO: 6, or a functional subsequence, modification, or variant thereof.
63. The rAAV vector of any one of claims 41 -45 or 47-62 or rAAV vector plasmid of any one of claims 46-62, wherein the at least one intron comprises the nucleotide sequence of SEQ ID NO: 6.
64. The rAAV vector of any one of claims 41 -45 or 47-63 or rAAV vector plasmid of any one of claims 46-63, wherein the intron comprises the nucleotide sequence of SEQ ID NO:
29.
65. The rAAV vector of any one of claims 41 -45 or 47-64 or rAAV vector plasmid of any one of claims 46-64, wherein the intron comprises the nucleotide sequence of SEQ ID NO:
30.
66. The rAAV vector of any one of claims 41 -45 or 47-65 or rAAV vector plasmid of any one of claims 46-65, wherein the intron comprises the nucleotide sequence of SEQ ID NO:
31.
67. The rAAV vector of any one of claims 41 -45 or 47-66 or rAAV vector plasmid of any one of claims 46-66, wherein the at least one transcription terminator sequence is an SV40 polyA sequence, a bovine growth hormone (BGH) polyA sequence, a rabbit b-globin (rPg) polyA sequence, or a functional subsequence, modification, or variant thereof.
68. The rAAV vector of any one of claims 41 -45 or 47-67 or rAAV vector plasmid of any one of claims 46-67, wherein the at least one transcription terminator sequence is an SV40 polyA sequence.
69. The rAAV vector of any one of claims 41 -45 or 47-68 or rAAV vector plasmid of any one of claims 46-68, wherein the at least one transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7, or a functional subsequence, modification, or variant thereof.
70. The rAAV vector of any one of claims 41 -45 or 47-69 or rAAV vector plasmid of any one of claims 46-69, wherein the at least transcription terminator sequence comprises the nucleotide sequence of SEQ ID NO: 7.
71 . The rAAV vector of any one of claims 41-45 or 47-70 or rAAV vector plasmid of any one of claims 46-70, wherein at least one stuffer or filler sequence increases the entire length of the nucleic acid molecule of the rAAV vector or rAAV vector plasmid, inclusive of the ITR sequences and excluding the spacer sequences, to approximately 4.2 to 4.7 kilobases.
72. The rAAV vector of any one of claims 41-45 or 47-71 or rAAV vector plasmid of any one of claims 46-71 , wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 , or a functional subsequence, modification, or variant thereof.
73. The rAAV vector of any one of claims 41 -45 or 47-72 or rAAV vector plasmid of any one of claims 46-72, wherein the at least one stuffer or filler sequence comprises the nucleotide sequence of SEQ ID NO: 11 .
74. The rAAV vector of any one of claims 41 -45 or 47-73 or rAAV vector plasmid of any one of claims 46-73, wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9, or a functional subsequence, modification, or variant thereof.
75. The rAAV vector of any one of claims 41 -45 or 47-74 or rAAV vector plasmid of any one of claims 46-74, wherein the at least one 3’ ITR sequence comprises the nucleotide sequence of SEQ ID NO: 9. Ill
76. The rAAV vector plasmid of any one of claims 46-75, wherein the at least one left spacer sequence comprises the nucleotide sequence of SEQ ID NO: 12, or a functional subsequence, modification, or variant thereof.
77. The rAAV vector plasmid of any one of claims 46-76, wherein the at least one left spacer sequence comprises the nucleotide sequence of SEQ ID NO: 12.
78. The rAAV vector plasmid of any one of claims 46-77, wherein the at least one right spacer sequence comprises the nucleotide sequence of SEQ ID NO: 13, or a functional subsequence, modification, or variant thereof.
79. The rAAV vector plasmid of any one of claims 46-78, wherein the at least one right spacer sequence comprises the nucleotide sequence of SEQ ID NO: 13.
80. The rAAV vector plasmid of any one of claims 46-79, wherein the rAAV vector plasmid further comprises at least one left spacer and/or at least one right spacer, preferably wherein the at least one left spacer and/or at least one right spacer increases the entire length of the rAAV vector plasmid to approximately 4.7 to 12 kilobases, preferably to approximately 9 to 10 kilobases.
81 . The rAAV vector of any one of claims 11 -45 or 47-75 or rAAV vector plasmid of any one of claims 46-80, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 14, or a functional subsequence, modification, or variant thereof.
82. The rAAV vector of any one of claims 11 -45, 47-75, or 81 or rAAV vector plasmid of any one of claims 46-81 , wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 14.
83. The rAAV vector of any one of claims 11 -45, 47-75, 81 , or 82 or rAAV vector plasmid of any one of claims 46-82, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 15, or a functional subsequence, modification, or variant thereof.
84. The rAAV vector of any one of claims 11-45, 47-75, or 81-83 or rAAV vector plasmid of any one of claims 46-83, wherein the rAAV vector or rAAV vector plasmid comprises the nucleotide sequence of SEQ ID NO: 15.
85. The rAAV vector of any one of claims 11-45, 47-75, or 81-84, wherein the entire length of the nucleic acid molecule of the rAAV vector is equal to or less than approximately 5 kilobases in length or is equal to or less than 4.7 kilobases in length.
86. The rAAV vector plasmid of any one of claims 46-84, wherein the entire length of the rAAV vector plasmid is equal to or less than approximately 12 kilobases in length or is equal to or less than 4.7 kilobases in length.
87. A pharmaceutical composition comprising the nucleic acid molecule of any one of claims 1-10, or the rAAV vector of any one of claims 11-45, 47-75, or 81-85, and at least one pharmaceutically acceptable salt.
88. The pharmaceutical composition of claim 87, wherein the at least one pharmaceutically acceptable salt is present in an amount ranging from about 1 mM to about 450 mM.
89. The pharmaceutical composition of either claim 87 or claim 88, wherein the at least one pharmaceutically acceptable salt is present in an amount ranging from about 2 mM to about 350 mM.
90. The pharmaceutical composition of any one of claims 87-89, wherein the at least one pharmaceutically acceptable salt is sodium chloride, magnesium chloride, potassium chloride, calcium chloride, or calcium phosphate.
91 . The pharmaceutical composition of claim 90, wherein the at least one pharmaceutically acceptable salt comprises sodium chloride and magnesium chloride.
92. The pharmaceutical composition of claim 90, wherein the at least one pharmaceutically acceptable salt comprises sodium chloride and potassium chloride.
93. The pharmaceutical composition of any one of claims 87-92, further comprising at least one buffer.
94. The pharmaceutical composition of claim 93, wherein the buffer is citrate, histidine, acetate, phosphate, tris hydrochloride, or tromethamine.
95. The pharmaceutical composition of claim 94, wherein the buffer is phosphate.
96. The pharmaceutical composition of claim 94, wherein the buffer is tris hydrochloride and tromethamine.
97. The pharmaceutical composition of any one of claims 93-96, wherein the at least one buffer is present in an amount ranging from about 10 mM to about 40 mM.
98. The pharmaceutical composition of claim 97, wherein the at least one buffer is present in an amount of about 20 mM.
99. The pharmaceutical composition of any one of claims 87-98, further comprising at least one cryoprotectant.
100. The pharmaceutical composition of claim 99, wherein the at least one cryoprotectant is a sugar or a sugar alcohol.
101 . The pharmaceutical composition of claim 99, wherein the at least one cryoprotectant is trehalose, sucrose, sorbitol, or mannitol.
102. The pharmaceutical composition of claim 101 , wherein the at least one cryoprotectant is sucrose.
103. The pharmaceutical composition of claim 101 , wherein the at least one cryoprotectant is sorbitol.
104. The pharmaceutical composition of any one of claims 99-103, wherein the at least one cryoprotectant is present in an amount of up to about 20%.
105. The pharmaceutical composition of claim 104, wherein the at least one cryoprotectant is present in an amount ranging from about 3% to about 15%.
106. The pharmaceutical composition of claim 105, wherein the at least one cryoprotectant is present in an amount of about 4% or about 5%.
107. The pharmaceutical composition of any one of claims 87-106, further comprising at least one surfactant.
108. The pharmaceutical composition of claim 107, wherein the at least one surfactant is a polaxamer or a polysorbate.
109. The pharmaceutical composition of claim 108, wherein the at least one surfactant is polaxamer 188, polysorbate 20, or polysorbate 80.
110. The pharmaceutical composition of any one of claims 107-109, wherein the at least one surfactant is present in an amount ranging from about 0.0001% to about 1 %.
111. The pharmaceutical composition of claim 110, wherein the at least one surfactant is present in an amount of about 0.02%.
112. The pharmaceutical composition of claim 110, wherein the at least one surfactant is present in an amount of about 0.002%.
113. The pharmaceutical composition of any one of claims 87-112, wherein the pharmaceutical composition has a pH ranging from about 6 to about 8.
114. The pharmaceutical composition of claim 113, wherein the pharmaceutical composition has a pH ranging from about 7 to about 8.
115. The pharmaceutical composition of claim 114, wherein the pharmaceutical composition has a pH of about 7.6.
116. The pharmaceutical composition of claim 114, wherein the pharmaceutical composition has a pH of about 7.4.
117. A method for treating a cardiac-related disease or disorder in a subject, the method comprising administering to the subject a therapeutically effective amount of:
(a) the nucleic acid molecule of any one of claims 1-10; or
(b) the rAAV vector of any one of claims 11 -45, 47-75, or 81-85; or
(c) the pharmaceutical composition of any one of claims 87-116.
118. The method of claim 117, wherein the cardiac-related disease or disorder is associated with a deficiency or dysfunction of BAG3.
119. The method of either claim 117 or claim 118, wherein the subject has a BAG3 mutation.
120. The method of any one of claims 117-119, wherein the cardiac-related disease or disorder is BAG3-related dilated cardiomyopathy (DCM).
121. The method of any one of claims 117-119, wherein the cardiac-related disease or disorder is BAG3-related heart failure.
122. The method of claim 117, wherein the cardiac-related disease or disorder is not associated with a deficiency or dysfunction of BAG3.
123. The method of either claim 117 or claim 122, wherein the subject does not have a BAG mutation.
124. The method of any one of claims 117, 122, or 123, wherein the cardiac-related disease or disorder is heart failure unrelated to BAG3 expression.
125. A method for reducing the frequency or severity of at least one symptom associated with a cardiac-related disease or disorder in a subject, the method comprising administering to the subject:
(a) the nucleic acid molecule of any one of claims 1-10; or
(b) the rAAV vector of any one of claims 11 -45, 47-75, or 81-85; or
(c) the pharmaceutical composition of any one of claims 87-116; in an amount effective to reduce the frequency or severity of the at least one symptom.
126. The method of claim 125, wherein the cardiac-related disease or disorder is associated with a deficiency or dysfunction of BAG3.
127. The method of either claim 125 or claim 126, wherein the subject has a BAG3 mutation.
128. The method of any one of claims 125-127, wherein the cardiac-related disease or disorder is BAG3-related dilated cardiomyopathy (DCM).
129. The method of any one of claims 125-127, wherein the cardiac-related disease or disorder is BAG3-related heart failure.
130. The method of claim 125, wherein the cardiac-related disease or disorder is not associated with a deficiency or dysfunction of BAG3.
131. The method of either claim 125 or claim 130, wherein the subject does not have a BAG mutation.
132. The method of any one of claims 125, 130, or 131 , wherein the cardiac-related disease or disorder is heart failure unrelated to BAG3 expression.
133. The method of any one of claims 125-128, wherein the at least one symptom is characteristic of BAG3-related DCM.
134. The method of any one of claims 125-127 or 129, wherein the at least one symptom is characteristic of BAG3-related heart failure.
135. The method of any one of claims 125 or 130-132, wherein the at least one symptom is characteristic of heart failure unrelated to BAG3 expression.
136. The method of any one of claims 117-135, wherein the effective amount of the rAAV vector ranges from about 1 E10 to about 1 E17 vector genomes per kilogram (vg/kg) of subject body weight.
137. The method of claim 136, wherein the effective amount of the rAAV vector ranges from about 3E13 to about 1 E14 vector genomes per kilogram (vg/kg) of subject body weight.
138. The method of either claim 136 or claim 137, wherein the effective amount of the rAAV vector is about 3E13 vector genomes per kilogram (vg/kg) of subject body weight.
139. The method of either claim 136 or claim 137, wherein the effective amount of the rAAV vector is about 7E13 vector genomes per kilogram (vg/kg) of subject body weight.
140. The method of either claim 136 or claim 137, wherein the effective amount of the rAAV vector is 1 E14 vector genomes per kilogram (vg/kg) of subject body weight.
141 . Use of the nucleic acid molecule of any one of claims 1-10 in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
142. Use of the rAAV vector of any one of claims 11-45, 47-75, or 81-85 in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
143. Use of the pharmaceutical composition of any one of claims 87-116 in the manufacture of a medicament for treating a cardiac-related disease or disorder in a subject.
144. A plasmid comprising the nucleic acid molecule of any one of claims 1-10.
145. A plasmid comprising the rAAV vector sequence of any one of claims 11-45, 47-75, or 81-85.
146. A host cell for rAAV vector production comprising the plasmid of claim 144.
147. A host cell for rAAV vector production comprising the plasmid of claim 145.
148. A host cell for rAAV vector production comprising the rAAV vector plasmid of any one of claims 46-84.
149. The host cell of any one of claims 146-148, wherein the host cell is an HEK293 cell or derivative thereof.
150. The host cell of any one of claims 146-149, wherein the host cell further comprises a nucleic acid molecule comprising a nucleotide sequence encoding an AAV Rep protein.
151 . The host cell of any one of claims 146-149, wherein the host cell further comprises a nucleic acid molecule comprising a nucleotide sequence encoding an AAV9 capsid protein.
152. The host cell of any one of claims 146-149, wherein the host cell further comprises a nucleic acid molecule comprising a nucleotide sequence encoding a viral helper factor.
153. A method of making an rAAV vector comprising:
(a) incubating the host cell of any one of claims 146-152 under conditions sufficient to allow the production of rAAV vectors; and
(b) purifying the rAAV vectors produced thereby.
154. An rAAV vector produced by the method of claim 152.
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