Patent Application
20250092386
A computer readable form of the Sequence Listing XML containing the file named “UMCO-H563US-17193-00128.xml,” which is 211,000 bytes in size and was created on Aug. 14, 2024, is provided herein and is herein incorporated by reference. This Sequence Listing consists of SEQ ID NOs: 1-236.
The present disclosure provides an artificial exonic barcode system that can be delivered with genetic constructs to differentiate between genome copies and transcript copies of the genetic construct in downstream evaluation methods such as real-time PCR, high throughput sequencing, conventional PCR, Southern blotting, Northern blotting, and in situ hybridization. For example, this can be used to evaluate the transduction and/or induction efficiency of AAV capsids in various tissue types. The present disclosure also provides a method of generating the artificial exonic barcode system.
The treatment effect of gene therapy is achieved by delivering a beneficial DNA expression cassette to patients using a viral or nonviral vector. Vector selection is a major determining factor on whether gene therapy will ameliorate disease without inducing side effects. Often, there are a dozen candidate vectors to select from. The traditional approach compares these vectors side-by-side in a relevant animal model. This approach was tested by comparing 8 AAV capsids in a canine model for systemic muscle gene delivery. Great animal-to-animal and muscle-to-muscle differences were found, suggesting the traditional approach is unreliable. The short nucleotide (3 to 15 nucleotides) barcode system was developed in the last few years. Several groups have used this system to compare the transduction and expression of various AAV capsids using high-throughput sequencing and bioinformatic analysis. However, the short barcode system has many limitations, including (1) the data cannot be validated by a different method, (2) it is not suitable for in situ evaluation of the transduction and expression at the single-cell level in tissues, (3) the cDNA sequence and the gene sequence are identical, making it impossible to completely rule out DNA contamination in the cDNA preparation completely, (4) the bioinformatic tools influence the results, and (5) different algorithms may yield different outcomes. To overcome these limitations, an artificial exonic barcode system was developed.
The present disclosure provides an exonic barcode comprising a nucleotide sequence comprising, from 5′ to 3′, a 5′ barcode, an intron, and a 3′ barcode,
The present disclosure further provides a library of exonic barcodes comprising two or more exonic barcodes as described elsewhere herein, wherein there are no duplicated fragments longer than eight nucleotides shared among any 5′ barcode, any 3′ barcode, and any 5′ barcode and 3′ barcode.
The present disclosure is also directed to a method of generating an exonic barcode library, the method comprising:
The present disclosure is also directed to a method of screening for efficiency of transformation and/or expression of one or more genetic constructs in a subject, the method comprising:
The present disclosure is further directed to a primer comprising a nucleotide sequence of any one of SEQ ID NO: 146-159, 174-201, and 216-229; a real-time PCR primer comprising a nucleotide sequence of any one of SEQ ID NO: 146-159, 174-201, and 216-229, a fluorophore, and a quencher; and an in situ hybridization probe comprising a nucleotide sequence of any one of SEQ ID NO: 160-173 and 202-215 and a label.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.
This disclosure describes an exonic barcode comprising a nucleotide sequence comprising, from 5′ to 3′, a 5′ barcode, an intron, and a 3′ barcode,
The intron can be any intron known in the art. The intron can be a pCI intron. In particular, the intron can be a pCI intron of SEQ ID NO: 236.
The 5′ barcode can have a maximum aligned identical sequence length with the human and/or dog genome of equal to or less than 21. The 3′ barcode can have a maximum aligned identical sequence length with the human and/or dog genome of equal to or less than 18. The 5′ barcode and 3′ barcode can have no identical sequence fragments equal to or greater than 8 nucleotides. The nucleotide sequence of the exonic barcode can be at least 300 nucleotides long. The nucleotide sequence can comprise any one of SEQ ID NO: 31 AND 33-45.
The human genome can be a Homo sapiens genome. The monkey genome can be a Macaca mulatta genome. The pig genome can be a Sus scrofa genome. The dog genome can be a Canis lupus familiaris genome. The rabbit genome can be a Oryctolagus cuniculus genome. The mouse genome can be a Mus musculus genome. The rat genome can be a Rattus norvegicus genome.
The present disclosure is further directed to a synthetic reporter gene comprising a nucleotide sequence comprising a reporter coding sequence and an exonic barcode as described elsewhere herein. The reporter can be GFP, EGFP, RFP, BFP, YFP, Luciferase, or any other reporter known in the art.
The present disclosure is also directed to a library of exonic barcodes comprising two or more exonic barcodes as described elsewhere herein, wherein there are no duplicated fragments longer than eight nucleotides shared among any 5′ barcode, any 3′ barcode, and any 5′ barcode and 3′ barcode.
The present disclosure is further directed to a method of generating an exonic barcode library, the method comprising:
The exonic barcode can have a GC content of about 50% to about 60%. The 5′ barcode and 3′ barcode can each not contain “TTAATTAA,” “GCTAGC,” or any sequence identical to “TTAATTAA” or “GCTAGC” except for one different nucleotide. Each barcode from the 5′ exonic barcode library and the refined 3′ exonic barcode library can be used at most once in generating the exonic barcodes of the exonic barcode library in step e). Step d) can comprise removing any barcode in the 5′ exonic barcode library that has a maximum aligned identical sequence length with the human and/or dog genome of greater than 21. Step d) can comprise removing any barcode in the 3′ exonic barcode library that has a maximum aligned identical sequence length with the human and/or dog genome of greater than 18.
The human genome can be a Homo sapiens genome. The monkey genome can be a Macaca mulatta genome. The pig genome can be a Sus scrofa genome. The dog genome can be a Canis lupus familiaris genome. The rabbit genome can be a Oryctolagus cuniculus genome. The mouse genome can be a Mus musculus genome. The rat genome can be a Rattus norvegicus genome.
The present disclosure is also directed to a method of screening for efficiency of transformation and/or expression of one or more genetic constructs in a subject, the method comprising:
The transformation can be any transformation method known in the art. The transformation can be a stable integration or via transfection or a virus. The virus can be AAV or any virus used in the art for transformation. The protein of interest of the one or more genetic constructs can each comprise a different AAV capsid. The subject can be a human, a non-human primate, pig, canine, rabbit, mouse, rat, or a cell line thereof. The one or more genetic constructs comprise up to 14 genetic constructs.
The method of screening for efficiency of transformation and/or expression of one or more genetic constructs in a subject can further comprise harvesting cells from more than one tissue of the subject in step b) and performing steps c) and d) separately on the cells from each tissue to screen for efficiency of transformation and/or expression separately in each tissue. The more than one tissue can comprise at least two tissues selected from the list consisting of heart, retina, brain, spinal cord, kidney, lung, muscle, and liver tissue. More specifically, the more than one tissue can comprise muscle tissue and liver tissue.
The present disclosure is further directed to a primer comprising a nucleotide sequence of any one of SEQ ID NO: 146-159, 174-201, and 216-229; a real-time PCR primer comprising a nucleotide sequence of any one of SEQ ID NO: 146-159, 174-201, and 216-229, a fluorophore, and a quencher; and an in situ hybridization probe comprising a nucleotide sequence of any one of SEQ ID NO: 160-173 and 202-215 and a label.
As used in this application, including the appended claims, the singular forms “a,” “an,” and “the” include plural references unless the content clearly dictates otherwise, and are used interchangeably with “at least one” and “one or more.”
The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the preceding description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
To overcome the limitations of previous methods to compare transduction and expression of various AAV capsids, an artificial exonic barcode system was developed. This system is based on 14 pairs of carefully designed artificial exons distinctive from the genome sequence of commonly studied species including humans, non-human primates, dogs, pigs, mice, rats, and rabbits. Exonic barcode-specific TaqMan™ qPCR assays for quantifying the vector genome and the transcript copy number were also designed and validated. 11 AAV capsids were screened using this system in a mouse model of Duchenne muscular dystrophy and in canines. These results are highly consistent with the literature. The exonic barcode system described in this disclosure is highly advantageous for identifying the best viral or nonviral vectors for gene therapy. This is detailed in the examples below.
Traditionally, comparing the tissue tropism of different AAV serotypes was performed by delivering individual serotype AAV vector to the target tissue and then quantifying transgene expression. This approach was used in this first study. Specifically, 8 different AAV capsids (AAV8, AAV9, AAV.B1, AAV.KP1, AAV.NP22, AAV.NP66, AAV.S1P1, and AAV.S10P1) were tested in four 4-month-old normal dogs by local injection in various muscles [right and left extensor carpi ulnaris (ECU,) right and left flexor carpi ulnaris (FCU), right and left cranial tibialis (CT), and right and left semitendinosus (ST)] at the dose of 1×1011 vg/muscle/AAV in a volume of 500 μl/muscle/AAV (
Two weeks after injection, animals were euthanized, and muscles were harvested. AAV-mediated expression was examined by histochemical staining for AP activity. Intriguingly, significant differences were found among different dogs and different muscles. This made it impossible to reach a solid conclusion on the transduction efficiency of various AAV capsids that were studied. It is suspected that this outcome was likely attributed to the differences in fiber type composition of different muscles and minor differences in injection techniques in each muscle, and individual variance of the experimental animals.
The dog study suggests that the traditional AAV tropism comparison method cannot meet the need of large animal studies. To overcome this hurdle, the transduction efficiency of different AAV capsids must be compared in the same muscle of the same animal. This has been achieved by many groups in the last couple of years with barcoded AAV vectors. Specifically, a 3 to 15-nucleotide-long barcode is included in the AAV genome. Each barcoded AAV genome is packaged in a specific AAV variant. Barcode-tagged AAV vectors were mixed and delivered to the target tissue. AAV biodistribution and expression were then determined using high throughput sequencing of DNA and cDNA extracted from the target tissue, followed by bioinformatic analysis. Despite its widespread use, this method has many inherent limitations. First, DNA and cDNA share an identical barcode. Any contamination of DNA in the cDNA preparation may alter expression data. Second, this approach heavily depends on bioinformatic analysis. Differences in the analytic algorithm may yield different results. Third, the results cannot be validated by a different method. Fourth, it cannot reveal subcellular localization (spatial information) of vector transduction and transgene expression.
To overcome these limitations, an artificial exonic barcode system was developed. Specifically, a series of unique intron-containing synthetic EGFP genes were engineered. Each synthetic EGFP gene carries a ˜300 bp unique DNA fragment as the barcode. This system allows one to readily distinguish the cDNA from the genomic DNA because the intron is spliced out in the cDNA (
In this study, the length of the 5′-exonic barcode was defined as 150 bp, and the length of the 3′-exonic barcode was defined as 50 bp. The synthetic intron from pCI (Promega, Madison, WI) was used as the intron in the synthetic EGFP gene. It is a β-globin/IgG chimeric intron of small size. The synthetic intron pCI has the sequence:
There are many challenges in designing exonic barcodes. First is the size of the exonic barcode. The conventional barcode is 3 to 15 nucleotides. For the exonic barcode, it is envisioned to be at least 50 bp on either side of the intron to meet the needs of various applications. One side of the barcode is also envisioned to be at least 100 bp to facilitate subsequent TaqMan™ PCR analysis. Second, the barcode sequence should have minimum overlap with the human genome sequence and the genome sequences of commonly used animal models (such as monkey, pig, dog, rabbit, mouse, and rat). In other words, there should be minimum homology between the barcode and the genome sequence. Third, the barcode sequence should not overlap with each other. Fourth, the barcode sequences should have similar GC content. Fifth, the 5′-barcode should not contain the conserved splicing donor signal (GGT), and the 3′-barcode should not contain the conserved splicing acceptor signal (AGG) (
To generate robust 5′ and 3′-exonic barcodes, a stepwise approach was taken (
A custom-made algorithm (programmed with Python) was used to generate two random DNA fragment libraries called the 5′-fragment library and the 3′-fragment library.
The 5′-fragment library was used to build the 5′-exonic barcode library, and the 3′-fragment library was used to build the 3′-exonic barcode library. The programming parameters include (1) Each fragment has 20 nucleotides; (2) There are no repeated subfragments longer than 6 nucleotides in each fragment; (3) The GC content ranges from 55% to 65% in each fragment; (4) The fragment does not contain “TTAATTAA”, “GCTAGC”, and their one-miss-match counterparts. “TTAATTAA” and “GCTAGC” are two restriction sites used in AAV vector cloning. “TTAATTAA” is for PacI and “GCTAGC” is for NheI; (5) The fragment does not contain four identical nucleotides in a row, including “AAAA”, “GGGG”, “TTTT”, and “CCCC”; (6) The 5′-fragment library does not contain “Ggt” which is the conserved splicing donor signal (the capital letter is the conserved nucleotide in the exon and the small letters are the conserved nucleotides in the intron) (
In total, the 5′-fragment library contains 500,000 DNA fragments, and the 3′-fragment library contains 200,000 DNA fragments.
Next, DNA fragments were removed that share high homology with the genome. Since the exonic barcode system was originally planned to be used in human and canine muscles, the random DNA fragment libraries were filtered with pairwise sequence alignment to reduce their sequence identity with the human genome (Homo sapiens, GRCh38) and the dog genome (Canis lupus familiaris, GCF_000002285.3_CanFam3.1). The sequence alignment was performed with the software BLAST 2.9.0 using the following commands. Specifically:
Below is an example of the alignment result:
The BLAST alignment results were analyzed based on the aligned identical sequence length between a query fragment sequence and an object genome sequence (L). L is calculated as the product of the aligned sequence length and the identity (in percentage).
L=(the aligned sequence length)×(the identity)÷100
For a query fragment sequence, there are many Ls corresponding to different aligned regions in the same genome sequence or regions in different genome sequences. Hence, the maximum aligned identical sequence length (maxL) was used to filter the DNA fragment libraries. Specifically, the fragments with a maxL greater than 16 were removed to make the filtered fragments as dissimilar to the genomes as possible.
After refinement, the 5′-fragment library contained 96,223 DNA fragments and the 3′-fragment library contained 137,070 DNA fragments.
The length of the 5′-exonic barcode was set to 150 nucleotides. To generate the 5′-exonic barcode library, eight fragments were randomly combined from the filtered 5′-fragment library and then the last 10 nucleotides were removed.
The length of the 3′-exonic barcode was set to 50 nucleotides. To generate the 3′-exonic barcode library, three fragments were randomly combined from the filtered 3′-fragment library and then the last 10 nucleotides were removed.
The exonic barcode libraries were further refined with the following parameters including (1) There are no repeated fragments longer than 6 nucleotides in each exonic barcode. In other words, the maximum length of repeated fragments within a single barcode cannot be equal to or longer than 6 nucleotides; (2) The 5′-barcodes must end with “CAG” (the conserved exonic splicing donor signal) (
In total, 500,000 5′-barcodes and 500,000 3′-barcodes were generated.
To reduce the homology of the exonic barcodes with the human genome (Homo sapiens, GRCh38) and the dog genome (Canis lupus familiaris, GCF_000002285.3_CanFam3.1), the barcode libraries were filtered with pairwise sequence alignment using the software BLAST 2.9.0 as was done in the refinement of the DNA fragment libraries.
For the 5′-barcode libraries, the barcodes with a maximum aligned identical sequence length (maxL) greater than 21 were removed. This means there were no identical sequence fragments of lengths greater than 21 nucleotides between the filtered 5′-barcodes and the human/dog genomes. For the 3′-barcode libraries, the barcodes with a maxL greater than 18 were removed. This means there were no identical sequence fragments of lengths greater than 18 nucleotides between the filtered 3′-barcodes and the human/dog genomes.
The candidate barcodes were further refined by removing the ones that contained repeated fragments (≤8 nucleotides) between different barcodes. In other words, the maximum length of repeated fragments among barcodes (5′-barcodes versus 5′-barcodes, 3′-barcodes versus 3′-barcodes, and 5′-barcodes versus 3′-barcodes) cannot be equal to or longer than 8 nucleotides.
In the end, 15 5′-exonic barcodes and 15 3′-exonic barcodes were obtained. The sequences of the 15 5′-exonic barcodes are shown in Table 1, and the sequences of the 15 3′-exonic barcodes are shown in Table 2.
Next, the 30 exonic barcodes were analyzed with the software BLAST 2.9.0 to confirm that these barcodes indeed have low sequence identity with the human and dog genomes. The Blast search results of the 5′-exonic barcodes and the Blast search results of the 3′-exonic barcodes were conducted separately. The Blast search summary is shown in Table 3.
In the human genome, (i) the maxL values of the 5′- and 3′-exonic barcodes are 18 to 21 and 15 to 18, respectively, suggesting minimum homology; (ii) the E-values of the 5′- and 3′-exonic barcodes are 13 to 571 and 101 to 741, respectively, suggesting they are not good hits for homology matches. In the dog genome, (i) the maxL values of the 5′- and 3′-exonic barcodes are 18 to 21 and 16 to 18, respectively, suggesting minimum homology; (ii) the E-values of the 5′- and 3′-exonic barcodes are 13 to 571 and 101 to 352, respectively, suggesting they are not good hits for homology matches.
Examination of 30 Refined Exonic Barcodes for the Sequence Identity with the Genomes of Other Five Commonly Used Mammalian Experimental Models
During the bioinformatic design of the exonic barcodes, sequence identity with the human genome and the dog genome was considered (Table 3). To expand the utility of the exonic barcodes in preclinical studies, the sequence similarities were examined between the finalized exonic barcodes and the genomes of the other five species, including rat (Rattus norvegicus, GCF_015227675.2_mRatBN7.2), mouse (Mus musculus, GCF_000001635.27_GRCm39), monkey (Macaca mulatta, GCF_003339765.1_Mmul_10), pig (Sus scrofa, GCF_000003025.6_Sscrofa11.1), and rabbit (Oryctolagus cuniculus, GCF_000003625.3_OryCun2.0). The Blast search results of the exonic barcodes with these genomes were conducted separately. Overall, bioinformatic analysis suggests that the customer-designed exonic barcodes share minimum homology to the genomic sequences in rats, mice, monkeys, pigs, and rabbits. Hence, this barcode system can also be used in these 5 species.
The Blast search results for all 7 species are summarized in Tables 4 and 5.
To further refine the exonic barcodes, potential alternative splice sites in the intact barcodes were examined with the alternative splice site predictor software (ASSP) (Wang & Marin, 2006). The intact barcode was generated by joining the sequence of 5′-exonic barcode with the sequence of the synthetic intron and the sequence of the corresponding 3′-exonic barcode in the order of: (from 5′ to 3′) 5′-exonic barcode, synthetic intron, and 3′-exonic barcode. The sequences of the 15 intact barcodes are shown in Table 6. Capital letters indicate exonic sequence, and small letters indicate intronic sequence.
The results of ASSP analysis are shown in Table 7.
In 14 exonic barcodes, the splice strength of the expected splice donor and accepter had the highest score in each respective barcode (all >10). However, in barcode #2, two accepter signals were found with a splice strength higher than 10, indicating potential multiple splicing events. For this reason, this barcode was excluded. In the end, a total of 14 exonic barcodes were obtained. These are the same barcodes reported in Table 6, with exonic barcode #2 excluded (SEQ ID NOs: 31 and 33-45).
The GC content of the exonic barcodes was also calculated. The results are shown in Table 8 below.
To accurately quantify the transduction and expression of barcoded AAV vectors in animals, 28 sets of unique primers and probes were designed. 14 sets were designed to evaluate transduction efficiency by quantifying the vector genome copy number. These primers/probes should generate an ˜60 bp amplicon targeting the 5′-exonic barcodes (
14 separate sets were designed to evaluate exonic barcode expression (transcript copy number). These primers/probes should generate an ˜60 bp amplicon targeting the junction region between the 5′- and 3′-exonic barcodes (
To determine whether the primers and probes designed for TaqMan™ PCR are unique for the customer-designed exonic barcodes, sequence alignment was performed with the genomes of 7 species (human, dog, mouse, rat, monkey, pig, and rabbit) using the BLAST program. The Blast searches for vector genome TaqMan™ PCR primers/probes and the Blast searches for transcript TaqMan™ PCR primers/probes were conducted separately.
In example B of
In example C of
Bioinformatic Analysis of TaqMan™ PCR Primers and Probes that Match with the Genome Sequence
A primer (or probe) sequence and the corresponding genome sequence are considered a match if they have no more than two different nucleotides. These primers (or probes) may bind DNA sequences in the genome of experimental animals. For vector genome and transcript TaqMan™ PCR, the matched primers/probes were determined via Blast search.
To determine whether these matched primers and probes can create noise signals in TaqMan™ PCR, primers and probes were identified that recognized the same gene and measured the distance between the 5′-primer and 3′-primer or between the primer (either 5′ or 3′) and the probe. The shortest distance is ˜20 kb. The amplicon size of the TaqMan™ PCR is ˜60 bp. This suggests that the primer/probe sets used in the vector genome PCR and vector transcript PCR will not generate any signal from the host genome. The results of the bioinformatic analysis suggest that the barcode TaqMan™ PCR reactions are highly specific for the barcode.
To determine whether the primer/probe set designed for one specific barcode can detect other barcodes, multiple approaches were used. In the first method, all 14 barcodes were cloned into one plasmid, and the plasmid was named the ‘all-in-one plasmid’ (XP249) (
The specificity of the primer/probe sets designed to quantify the vector genome copy number was first evaluated (
To further confirm the specificity of the primers and probes designed to quantify the vector genome copy number, PCR reactions were performed with an individual barcode plasmid as the template but using the primer/probe set designed for every barcode one by one.
To compare the amplification efficiency of the TaqMan™ PCR reactions, a linear regression analysis was performed for PCR reactions that used the all-in-one plasmid as the template, but a barcode-specific primer/probe set in each PCR (
Specificity of primers and probes designed to quantify the transcript copy number was next evaluated. A series of plasmids was first made to mimic the cDNA sequence of each barcode (
A similar study as in
In this study, 11 different AAV capsids were compared in the mdx4cv model of Duchenne muscular dystrophy. These include AAV2, AAV8, AAV9, AAVrh74, AAV-B1, AAVNP22, AAV-NP66, AAV-S1P1, AAV-S10P1, and AAVMYO. AAV2 is the first and most studied AAV serotype. AAV2 did not support systemic muscle delivery and was used as a control. AAV8, AAV9, and AAVrh74 are currently used in systemic gene therapy for inherited neuromuscular diseases. AAV-B1 is engineered by the Miguel Sena-Esteves lab. It previously showed superior transduction in mouse muscle and central nervous system. AAV-NP22 and AAV-NP66 are developed by the Mark Kay lab. These two capsids previously showed significantly increased transduction in human and rhesus skeletal muscle fiber. AAV-S1P1 and AAV-S10P1 are generated in the Dirk Grimm lab. These capsids previously showed increased potency and specificity for systemic delivery to muscle and de-targeting from the liver. AAVMYO is developed in the Dirk Grimm lab, too. AAVMYO exceeded AAV-S1P1 and AAV-S10P1 in muscle targeting and liver detargeting. AAV-KP1 is generated in the Mark Kay lab. This capsid transduced mouse and human liver at very high levels and was used as an additional control.
The exonic barcode system was packaged with the above-listed 11 AAV capsids, and the barcoded AAV viruses were purified. The cross-reactivity of the primer/probe sets designed to quantify the vector genome copy number was first checked. It was shown that these primer/probe sets were highly specific to their corresponding barcodes when plasmids were used as the template (
In Vivo Study in mdx4cv Mice
The study was performed in 4-m-old male mdx4cv mice by tail vein injection. The barcoded virus mixture was delivered at a dose of either 3×1012 vg/kg/AAV capsid (3.3×1013 vg/kg total AAV) or 1×1013 vg/kg/AAV capsid (1.1×1014 vg/kg total AAV) (n=3 mice/dose). Tissues were harvested one month later.
In summary, this pilot mouse study highlighted the importance of evaluating both the vg copy number (for transduction) and transcript copy number (for expression). While most times, these were consistent, there are many exceptions. Further, AAV-mediated gene transfer could be greatly influenced by the target tissue or organ. For example, AAV8 resulted in good transduction but the poor expression in skeletal muscle. However, transduction and expression were consistent in the liver for AAV8.
The same 11 capsids investigated in mdx4cv mice were used in the dog study. AAV mixture was delivered by intravenous injection to one 1-week-old puppy at the dose of 3.6×1012 vg/kg/AAV (4×1013 vg/kg total AAV) and one 1-month-old dog at the dose of 5.5×1012 vg/kg/AAV (6.1×1013 vg/kg total AAV). Both were carrier dogs (they did not have muscular dystrophy). Tissues were harvested at 3 weeks after injection. The vector genome copy number and the transcript copy number were quantified from five skeletal muscles (diaphragm, triceps, biceps femoris, extensor digitorum longus, and vastus lateralis), heart, and liver.
The correlation between AAV transduction and AAV expression was compared for both dogs (
In the heart, AAV8 and AAVrh74 showed the highest vector genome copy number (the highest transduction efficiency) but only moderate expression (transcript copy number). In contrast, AAVMYO had a moderate transduction efficiency but the highest expression. AAVB1, AAV2, AAV9, and AAV-S1P1 showed moderate transduction and moderate expression. AAV-S10P1 had very low transduction but a moderate expression. AAV-NP22, AAV-NP66, and AAV-KP1 have minimal transduction and minimal expression.
In the liver, AAV8 showed the highest vector genome copy number but only moderate expression. AAVrh74 had a high copy number, but the high expression was only found in the 1-m-old dog. AAVrh74 expression was similar to AAV8 in the 1-week-old puppy. AAV-NP22, AAV-NP66, and AAV-KP1 showed good (in 1-week-old puppy) and moderate (in 1-m-old dog) transduction. However, only AAV-KP1 showed high expression. AAV-NP-66 had a nominal expression.
AAV8, AAV9, and AAVrh74 are currently used in clinical trials to treat inherited neuromuscular diseases. They showed good performance in muscle tissues, but they also had strong liver targeting (especially AAVrh74 and AAV8). This is consistent with the liver toxicity observed in human trials.
This invention claims priority to U.S. Provisional Application Ser. No. 63/583,005, filed Sep. 15, 2023, which is incorporated by reference in its entirety.
This invention was made with government support under NS090634 and NS131416 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63583005 | Sep 2023 | US |
