Patent Application
20210388332
The present description relates generally to the field of gene editing. More particularly, the description relates to systems and methods for constituting functional donor splice sites.
About 10% of ˜80,000 mutations reported in the human gene mutation database (HGMD) affect splice sites (1). In the HGMD, there are 3390 disease-causing mutations that occur at the +1 donor splice site. These mutations affect 2754 exons in 901 genes. The prevalence is even higher for neuromuscular disorders (NMDs) due to the unusually large size and multiexonic structure of genes encoding muscle structural proteins, further highlighting the importance of these mutations in NMDs (2). Therapeutic genome editing can be exploited to correct disease-causing mutations (3).
As an example of one clinical application, merosin-deficient congenital muscular dystrophy type 1A (MDC1A) is an autosomal recessive neuromuscular disease characterized by neonatal onset of muscle weakness, hypotonia, dysmyelinating neuropathy, and minor brain abnormalities (4). Splice site mutations are estimated to affect ˜40% of the MDC1A patient population (5, 6). Causative mutations are located in the LAMA2 gene, which encodes the α2 chain (Lama2) of laminin-211 (or merosin) heterotrimeric protein complex expressed in the basement membrane of muscle and Schwann cells. In MDC1A, laminin-211 loses its proper interactions with receptors such as integrin α7β1 and dystroglycan, resulting in muscle and Schwann cells apoptosis and degeneration, which leads to fibrosis and loss of muscle function.
So far, development of therapeutic strategies for MDC1A have been mainly focused on preventing fibrosis and apoptosis (4). The degree of LAMA2 deficiency highly correlates with the clinical severity in patients and mouse models (5). The lack of a functional Lama2 leads to the development of severe muscle atrophy and hind limb paralysis in mice. Therefore, restoration of LAMA2 expression holds a tremendous potential for the treatment of MDC1A. It has previously been demonstrated that muscle-specific overexpression of Laminin-211 in merosin-deficient mice improved muscle pathology, but not the associated paralysis, indicating that correction of the peripheral neuropathy requires restoration of Lama2 beyond skeletal muscles (7).
Previously (8-10), the correction of point mutations, e.g. splice site mutations, has mainly been accomplished via the homology-directed repair (HDR) pathway, which is extremely inefficient in post-mitotic tissues such as skeletal muscles, hampering its therapeutic utility in NMDs (11). A standard gene therapy approach to reintroduce the LAMA2 coding region into the genome is impeded by its large size. Moreover, a strategy to miniaturize the gene, as in the case of microdystrophin or exon skipping in Duchenne muscular dystrophy, is unlikely to be successful due to the lack of redundant regions within the protein (12).
The ability to correct disease-causing mutations has been improved by the discovery and development of the CRISPR/Cas9 genome editing technology (3, 9). Cas9 endonuclease generates double stranded-break (DSB) in a specific genomic region, which is located adjacent to a protospacer-adjacent motif (PAM) and targeted by a complementary single guide RNA (sgRNA). In the presence of a DNA repair template, a precise genomic modification can take place through homology-directed repair (HDR), whereas non-homologous end-joining (NHEJ) repairs Cas9-induced breaks in the absence of the exogenous template. Moreover, two DSBs can be simultaneously introduced to generate genomic deletions (10-12). The discovery of Cas9 proteins derived from various species which differ in their PAM sequence requirements (3, 13, 35, 36), as well as engineered Cas9 derivatives with purposefully altered PAM specificities (37, 38) offer unprecedented flexibility in genome editing endeavours.
In the context of metabolic liver diseases, injection of CRISPR/Cas9 and a DNA repair template has been shown to correct Fah and Otc mutations in vivo (13-15). However, HDR in post-mitotic tissues, such as skeletal muscle and/or neurons is extremely inefficient.
It is an object of the present disclosure to mitigate and/or obviate one or more of the above deficiencies.
In an aspect, a genome editing system is provided. The system comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner, wherein the genome editing system is configured to form a first and a second blunt-ended double strand break in an intron of a gene, wherein the intron comprises a splice donor site mutation that alters splice site recognition, thereby excising a segment of the intron and simultaneously joining DNA ends flanking the excised segment of the intron to constitute a functional donor splice site.
In an embodiment of the system, the excising of the segment of the intron and simultaneously joining the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site results in restored splice site recognition in the intron.
In an embodiment of the system, the joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through a homology directed repair-independent mechanism.
In an embodiment of the system, the joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through non-homologous end joining.
In an embodiment of the system, the excising occurs at a mutation-eliminating cut site of the intron and at a splice site-generating cut site of the intron of the gene. In an embodiment, the mutation-eliminating cut site and/or the splice generating cut site is at a Cas9 cleavage site occurring in the presence of a PAM nucleotide sequence that is: NGG, NAG, NGA, NGCG, NNGRRT, NNNRRT, NNAGAA, NNNNRYAC, or YG. In an embodiment, the splice site-generating cut site is positioned before a branch splice point for an adjacent exon. In an embodiment, the splice site-generating cut site is positioned at least 25 base pairs from the adjacent exon.
In an embodiment of the system, there is at least one nuclease that generates blunt-ended DNA breaks, which is a Cas9 polypeptide that recognizes a Protospacer Adjacent Motif (PAM) and wherein the system further comprises a mutation-eliminating single guide RNA (sgRNA) and a splice site-generating sgRNA. In an embodiment, the PAM has the nucleotide sequence NNGRRT and the mutation-eliminating cut site of the intron is positioned 3 nucleotides in the 5′ direction of the end of the PAM. In an embodiment, the mutation-eliminating sgRNA and the splice site-generating sgRNA each comprise a CRISPR RNA (crRNA) portion that is 17 to 27 nucleotides in length. In an embodiment, the mutation-eliminating sgRNA comprises the nucleotide sequence aaaacatatatataatacatatGGT (SEQ ID NO: 1).
In an embodiment of the system, there is at least one nuclease that generates blunt-ended DNA breaks, which is a fusion polypeptide comprising a catalytically inactive Cas9 polypeptide that recognizes a PAM and a nuclease that generates blunt-ended DNA breaks. In an embodiment, the polypeptide further comprises a linker between the catalytically inactive Cas9 and the nuclease. In an embodiment, the size of the linker determines the location of the blunt-ended DNA breaks.
In an embodiment of the system, there is at least one nuclease that generates blunt-ended DNA breaks, which is a fusion polypeptide comprising a DNA recognizing protein domain and a nuclease that generates blunt-ended DNA breaks. In an embodiment, the DNA recognizing protein domain comprises a zinc finger, and wherein the system comprises a pair of fusion polypeptides, each comprising a zinc finger and a nuclease that upon dimerization of the nuclease domains generates blunt-ended DNA breaks. In an alternative embodiment, the DNA recognizing protein domain comprises a TALE polypeptide, and wherein the system comprises a pair of fusion polypeptides, each comprising a TALE polypeptide and a nuclease that upon dimerization of the nuclease domains generates blunt-ended DNA breaks. In an embodiment, the nuclease is Mlyl. In an embodiment, the polypeptide further comprises a linker between the DNA recognizing protein domain and the nuclease that generates blunt-ended DNA breaks. In an embodiment, the size of the linker determines the location of the blunt-ended DNA breaks.
In an embodiment of the system, the mutation occurs at the +1 position of the splice donor site. In various embodiments, the mutation occurs at the +2, +3, +4, +5, or +6 position of the splice donor site.
In an embodiment of the system, the system further comprises a delivery vehicle for delivery of the at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner.
In an embodiment of the system, polynucleotides coding for at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner is in a vector. In an embodiment, the nuclease is Cas9 and the vector further comprises a mutation-eliminating single sgRNA or a splice site-generating sgRNA. In an embodiment, the delivery vehicle is an adeno-associated virus (AAV) vector. In various embodiments, the delivery vehicle is an AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8 or AAV9 vector. In an embodiment, the delivery vehicle is an AAV9 vector.
In an embodiment of the system, the delivery vehicle is a liposome or a nanoparticle.
In an embodiment of the system, the mutation is a pathogenic mutation.
In an embodiment of the system, the gene is a gene listed in Table 1.
In an embodiment of the system, the gene is a Lama2 gene. In an embodiment, the mutation is a c.417+1 g→a mutation. In an embodiment, the mutation is in a subject having merosin deficient congenital muscular dystrophy (MDC1A).
In an aspect, the system as described herein is for use in the treatment of merosin deficient congenital muscular dystrophy (MDC1A) in a subject.
In an aspect, a composition is provided. The composition comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner, wherein the composition is configured to form a first and a second blunt-ended double strand break in an intron of a gene, wherein the intron comprises a splice donor site mutation that alters splice site recognition, thereby excising a segment of the intron and simultaneously joining DNA ends flanking the excised segment of the intron to constitute a functional donor splice site.
In an embodiment of the composition, the excising of the segment of the intron and simultaneously joining the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site results in restored splice site recognition in the intron.
In an embodiment of the composition, the joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through a homology directed repair-independent mechanism.
In an embodiment of the composition, the joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through non-homologous end joining.
In an embodiment of the composition, the excising occurs at a mutation-eliminating cut site of the intron and at a splice site-generating cut site of the intron of the gene. In an embodiment, the mutation-eliminating cut site and/or the splice generating cut site is at a Cas9 cleavage site occurring in the presence of a PAM nucleotide sequence that is: NGG, NAG, NGA, NGCG, NNGRRT, NNNRRT, NNAGAA, NNNNRYAC, or YG. In an embodiment, the splice site-generating cut site is positioned before a branch splice point for an adjacent exon. In an embodiment, the splice site-generating cut site is positioned at least 25 base pairs from the adjacent exon.
In an embodiment of the composition, at least one nuclease that generates blunt-ended DNA breaks is a Cas9 polypeptide that recognizes a Protospacer Adjacent Motif (PAM) and wherein the system further comprises a mutation-eliminating single guide RNA (sgRNA) and a splice site-generating sgRNA. In an embodiment, the PAM has the nucleotide sequence NNGRRT and the mutation-eliminating cut site of the intron is positioned 3 nucleotides in the 5′ direction of the end of the PAM. In an embodiment, the mutation-eliminating sgRNA and the splice site-generating sgRNA each comprise a CRISPR RNA (crRNA) portion that is 17 to 27 nucleotides in length. In an embodiment, the mutation-eliminating sgRNA comprises the nucleotide sequence aaaacatatatataatacatatGGT (SEQ ID NO: 1).
In an embodiment of the composition, at least one nuclease that generates blunt-ended DNA breaks is a fusion polypeptide comprising a catalytically inactive Cas9 polypeptide that recognizes a PAM and a nuclease that generates blunt-ended DNA breaks. In an embodiment, the polypeptide further comprises a linker between the catalytically inactive Cas9 and the nuclease. In an embodiment, the size of the linker determines the location of the blunt-ended DNA breaks.
In an embodiment of the composition, at least one nuclease that generates blunt-ended DNA breaks is a fusion polypeptide comprising a DNA recognizing protein domain and a nuclease that generates blunt-ended DNA breaks. In an embodiment, the DNA recognizing protein domain comprises a zinc finger, and wherein the system comprises a pair of fusion polypeptides, each comprising a zinc finger and a nuclease that upon dimerization of the nuclease domains generates blunt-ended DNA breaks. In an alternative embodiment, the DNA recognizing protein domain comprises a TALE polypeptide, and wherein the system comprises a pair of fusion polypeptides, each comprising a TALE polypeptide and a nuclease that upon dimerization of the nuclease domains generates blunt-ended DNA breaks. In an embodiment, the nuclease is Mlyl. In an embodiment, the polypeptide further comprises a linker between the DNA recognizing protein domain and the nuclease that generates blunt-ended DNA breaks. In an embodiment, the size of the linker determines the location of the blunt-ended DNA breaks.
In an embodiment of the composition, the mutation occurs at the +1 position of the splice donor site. In various embodiments, the mutation occurs at the +2, +3, +4, +5, or +6 position of the splice donor site.
In an embodiment of the composition, the composition further comprises a delivery vehicle for delivery of the at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner.
In an embodiment of the composition, polynucleotides coding for at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner is in a vector. In an embodiment, the nuclease is Cas9 and the vector further comprises a mutation-eliminating single sgRNA or a splice site-generating sgRNA. In an embodiment, the delivery vehicle is an adeno-associated virus (AAV) vector. In various embodiments, the delivery vehicle is an AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8 or AAV9 vector. In an embodiment, the delivery vehicle is an AAV9 vector.
In an embodiment of the composition, the delivery vehicle is a liposome or a nanoparticle.
In an embodiment of the composition, the mutation is a pathogenic mutation.
In an embodiment of the composition, the gene is a gene listed in Table 1.
In an embodiment of the composition, the gene is a Lama2 gene. In an embodiment, the mutation is a c.417+1 g→a mutation. In an embodiment, the mutation is in a subject having merosin deficient congenital muscular dystrophy (MDC1A).
In an aspect, the composition as described herein is for use in the treatment of merosin deficient congenital muscular dystrophy (MDC1A) in a subject.
In an aspect, a method of constituting a functional donor splice site in a gene is provided. The gene comprises a mutation in a donor splice site that alters splice site recognition, and the method comprises delivering a genome editing system to the gene, the genome editing system comprising at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner, wherein the genome editing system is configured to form a first and a second blunt-ended double strand break in an intron of a gene, wherein the intron comprises a splice donor site mutation that alters splice site recognition, thereby excising a segment of the intron and simultaneously joining DNA ends flanking the excised segment of the intron to constitute a functional donor splice site.
In an embodiment of the method, the excising of the segment of the intron and simultaneously joining the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site results in restored splice site recognition in the intron.
In an embodiment of the method, the joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through a homology directed repair-independent mechanism.
In an embodiment of the method, the joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through non-homologous end joining.
In an embodiment of the method, the excising occurs at a mutation-eliminating cut site of the intron and at a splice site-generating cut site of the intron of the gene. In an embodiment, the mutation-eliminating cut site and/or the splice generating cut site is at a Cas9 cleavage site occurring in the presence of a PAM nucleotide sequence that is: NGG, NAG, NGA, NGCG, NNGRRT, NNNRRT, NNAGAA, NNNNRYAC, or YG. In an embodiment, the splice site-generating cut site is positioned before a branch splice point for an adjacent exon. In an embodiment, the splice site-generating cut site is positioned at least 25 base pairs from the adjacent exon.
In an embodiment of the method, at least one nuclease that generates blunt-ended DNA breaks is a Cas9 polypeptide that recognizes a Protospacer Adjacent Motif (PAM) and wherein the system further comprises a mutation-eliminating single guide RNA (sgRNA) and a splice site-generating sgRNA. In an embodiment, the PAM has the nucleotide sequence NNGRRT and the mutation-eliminating cut site of the intron is positioned 3 nucleotides in the 5′ direction of the end of the PAM. In an embodiment, the mutation-eliminating sgRNA and the splice site-generating sgRNA each comprise a CRISPR RNA (crRNA) portion that is 17 to 27 nucleotides in length. In an embodiment, the mutation-eliminating sgRNA comprises the nucleotide sequence aaaacatatatataatacatatGGT (SEQ ID NO: 1).
In an embodiment of the method, at least one nuclease that generates blunt-ended DNA breaks is a fusion polypeptide comprising a catalytically inactive Cas9 polypeptide that recognizes a PAM and a nuclease that generates blunt-ended DNA breaks. In an embodiment, the polypeptide further comprises a linker between the catalytically inactive Cas9 and the nuclease. In an embodiment, the size of the linker determines the location of the blunt-ended DNA breaks.
In an embodiment of the method, at least one nuclease that generates blunt-ended DNA breaks is a fusion polypeptide comprising a DNA recognizing protein domain and a nuclease that generates blunt-ended DNA breaks. In an embodiment, the DNA recognizing protein domain comprises a zinc finger, and wherein the system comprises a pair of fusion polypeptides, each comprising a zinc finger and a nuclease that upon dimerization of the nuclease domains generates blunt-ended DNA breaks. In an alternative embodiment, the DNA recognizing protein domain comprises a TALE polypeptide, and wherein the system comprises a pair of fusion polypeptides, each comprising a TALE polypeptide and a nuclease that upon dimerization of the nuclease domains generates blunt-ended DNA breaks. In an embodiment, the nuclease is Mlyl. In an embodiment, the polypeptide further comprises a linker between the DNA recognizing protein domain and the nuclease that generates blunt-ended DNA breaks. In an embodiment, the size of the linker determines the location of the blunt-ended DNA breaks.
In an embodiment of the method, the mutation occurs at the +1 position of the splice donor site. In various embodiments, the mutation occurs at the +2, +3, +4, +5, or +6 position of the splice donor site.
In an embodiment of the method, the system further comprises a delivery vehicle for delivery of the at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner.
In an embodiment of the method, polynucleotides coding for the at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner is in a vector. In an embodiment, the nuclease is Cas9 and the vector further comprises a mutation-eliminating single sgRNA or a splice site-generating sgRNA. In an embodiment, the delivery vehicle is an adeno-associated virus (AAV) vector. In various embodiments, the delivery vehicle is an AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8 or AAV9 vector. In an embodiment, the delivery vehicle is an AAV9 vector.
In an embodiment of the method, the delivery vehicle is a liposome or a nanoparticle.
In an embodiment of the method, the mutation is a pathogenic mutation.
In an embodiment of the method, the gene is a gene listed in Table 1.
In an embodiment of the method, the gene is a Lama2 gene. In an embodiment, the mutation is a c.417+1 g→a mutation. In an embodiment, the mutation is in a subject having merosin deficient congenital muscular dystrophy (MDC1A).
In an aspect, the method as described herein is for use in the treatment of merosin deficient congenital muscular dystrophy (MDC1A) in a subject.
In an aspect, an isolated cell comprising a gene whose mutation at a splice donor site has been repaired according to any of the methods as described herein is provided. In an embodiment, the cell is a postmitotic cell. In an embodiment, the cell is a myocyte, a neuron or a cardiomyocyte.
The details of one or more embodiments are set forth in the accompanying drawings and description below. Other features and advantages will become apparent from the description, the drawings and the claims.
The patent or application file contains at least one drawing in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.
These and other features of the disclosure will become more apparent in the following detailed description in which reference is made to the appended drawings wherein:
Graphical representation of % fibrosis (
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.
As used herein a “genome editing system” means a system that is capable of editing (e.g., modifying or altering) a target gene or DNA sequence. In an embodiment, the target gene or DNA sequence is a gene or DNA sequence that contains a splice site donor mutation (i.e., a mutation in the 5′ splice site (5′ss)). In an embodiment, the splice site donor mutation results in the gene or DNA sequence having a splicing defect. In an embodiment, the genome editing system comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. The genome-editing system may be implemented in a cell or in an in vitro system. In certain embodiments, the genome-editing system is used in a medicament, e.g., a medicament for correcting a splicing defect, or a medicament for treating a disease caused by a splicing defect.
As used herein, a “mutation-eliminating cut” is defined as a cut in DNA generated in a sequence-specific manner by a nuclease. The cut separates a mutation in a donor splice site of a gene from the upstream exons and introns of that gene. In one embodiment, the cut is a blunt ended double strand break. A “mutation-eliminating cut site” is defined as a location in DNA at which a cut is generated in a sequence-specific manner by a nuclease to separate a mutation in a donor splice site of a gene from the upstream exons and introns of that gene. For example, a mutation-eliminating cut may occur at a Cas9 cleavage site occurring in the presence of one of the following Protospacer Adjacent Motif (PAM) sequences: NGG, NAG, NGA, NGCG, NNGRRT, NNNRRT, NNAGAA, NNNNRYAC or YG, when in the presence of a mutation-eliminating sgRNA. As used herein, a “mutation-eliminating sgRNA” is an sgRNA that in concert with a Cas9, creates a blunt ended double strand break at a mutation-eliminating cut site. The mutation-eliminating cut site may be, for example, upstream (i.e., when the DNA is in the 5′ to 3′ direction) of the PAM, for example, at the −3 position.
In other embodiments, the mutation-eliminating cut site may be located as determined by binding by a DNA recognizing protein domain to the DNA and cleavage by a nuclease to which the DNA recognizing protein domain is fused. In another embodiment, the DNA recognizing protein domain and the nuclease are joined by a linker which determines the position of a mutation-eliminating cut site. For example, with a longer linker, the mutation-eliminating cut site is positioned further away from the DNA binding domain.
As used herein, a “splice site-generating cut” is defined as a cut in an intron of a gene that is generated in a sequence-specific manner by a nuclease. The cut, in concert with a mutation-eliminating cut, results in excision of a segment of an intron, the segment containing a mutation in the donor splice site of the gene. In one embodiment, the cut is a blunt ended double strand break. Upon re-ligation with the DNA ends flanking the excised segment of the intron, a functional donor splice site is constituted. This splice site-generating cut and subsequent ligation results in proper splicing of a gene such that all of the exons are expressed in RNA and translated protein. A “splice site-generating cut site” is defined as a location in the intron of a gene at which a cut is generated in a sequence-specific manner by a nuclease and, when used in concert with a mutation-eliminating cut, results in excision of a segment of an intron, the segment containing a mutation in the donor splice site of the gene. For example, a splice site-generating cut may occur at a Cas9 cleavage site occurring in the presence of one of the following Protospacer Adjacent Motif (PAM) sequences: NGG, NAG, NGA, NGCG, NNGRRT, NNNRRT, NNAGAA, NNNNRYAC or YG, when in the presence of a splice site-generating sgRNA. As used herein, a “splice site-generating sgRNA” is an sgRNA that in concert with a Cas9, creates a blunt ended double strand break at a splice site-generating cut site. The mutation-eliminating cut site may be, for example, upstream (i.e., when the DNA is in the 5′ to 3′ direction) of the PAM, for example, at the −3 position.
In other embodiments, the splice site-generating cut may occur at a location as determined by binding by a DNA recognizing protein domain to the DNA and cleavage by a nuclease to which the DNA recognizing protein domain is fused. In another embodiment, the DNA recognizing protein domain and the nuclease are joined by a linker which determines the position of a splice site-generating cut site. For example, with a longer linker, the splice site-generating cut site will be positioned further away from the DNA binding domain.
As used herein, “homology directed repair-independent,” or “HDR-independent” refers to a process of modifying (e.g., repairing) DNA that does not involve homology directed repair (HDR). The homology directed repair-independent process can be, for example, a process that uses non-homologous end-joining to modify the DNA.
As used herein, “non-homologous end-joining” or “NHEJ” refers to ligation mediated modification of DNA (e.g., repair) that does not require a homologous template in the process. HNEJ includes, for example, canonical NHEJ (cNHEJ), alternative NHEJ (altNHEJ), microhomology-mediated end joining (MMEJ), and synthesis-dependent microhomology-mediated end joining (SD-MMEJ).
As used herein “repair” refers to modification of an intron such that proper splicing of the RNA (e.g., pre-mRNA) occurs (i.e., such that splicing occurs as it would in a naturally-occurring RNA, for example, an RNA transcribed from a gene that has no splicing mutations), and such that a polypeptide translated from such an RNA contains all the exons of a naturally-occurring polypeptide. In an embodiment, the mutation causing a splicing defect is a mutation in the donor splice site. As used herein, the repair does not have to be a repair (e.g., correction) of the mutated splice donor site. Instead, for example, the repair may involve excision of an intron fragment containing the mutated donor splice site and ligation of the flanking ends of the DNA to create or constitute a new donor splice site in that gene, resulting in proper splicing of the gene.
As used herein, the first nucleotide of the intron is defined as the “+1” position. The second nucleotide of the intron is defined as the “+2” position. The third nucleotide of the intron is defined as the “+3” position. The fourth nucleotide of the intron is defined as the “+4” position. The fifth nucleotide of the intron is defined as the “+5” position. The sixth nucleotide of the intron is defined as the “+6” position.
As used herein, a “Cas9 molecule” or “Cas9 polypeptide” refers to a molecule or polypeptide, respectively, that can interact with a guide RNA (gRNA) molecule to localize to a site comprising a target domain (e.g., a DNA cut site) and a PAM sequence. Cas9 molecules and Cas9 polypeptides include naturally occurring Cas9 molecules and Cas9 polypeptides and engineered, altered, or modified Cas9 molecules or Cas9 polypeptides that differ, e.g., by at least one amino acid residue, from a reference sequence (e.g., a naturally-occurring Cas9 sequence).
As used herein, a “subject” means a higher eukaryote. The term includes, but is not limited to, mammals (e.g., humans, other primates, pigs, rodents (e.g., mice and rats or hamsters), rabbits, guinea pigs, cows, horses, cats, dogs, sheep, and goats). In certain embodiments, the subject is a human. The human may be a child or an adult.
As used herein, “treat”, “treating” and “treatment”, means the treatment of a disease in a mammal, for example, a human, and includes inhibiting the disease (e.g., decreasing its rate of progression); regressing the disease; relieving or decreasing the severity of one or more symptoms of the disease; and/or curing the disease.
As used herein, “prevent,” “preventing,” and “prevention” means the prevention of a disease in a mammal, and includes inhibiting initiation of the disease; decreasing a predisposition toward the disease; and/or delaying the onset of at least one symptom of the disease.
As used herein, “about” or “approximately” means within an acceptable error range for a particular value as determined by a person skilled in the relevant art. Such an acceptable error range may depend, in part, on how the value is measured or assessed. “About” can mean, for example, within 3 or more than 3 standard deviations. “About” can mean within a percentage range of a given value. For example, the range can be ±1%, ±5%, ±10%, ±20%, ±30%, ±40% or ±50% of a given value. “About” can mean with an order of magnitude of a given value, for example, within 2-fold, 3-fold, 4-fold or 5-fold of a value.
Systems and Compositions
As described herein, the inventors have provided genome editing systems, compositions and methods for constituting a functional donor splice site in a gene. These genome editing systems, compositions and methods for constituting a functional donor splice site in a gene may be used, for example, to correct a splicing defect in a gene or DNA sequence. In an embodiment, the splicing defect is a pathogenic mutation. The mutation may be, for example, in the donor splice site or an intron that results in improper splicing of the RNA molecule transcribed from the gene or DNA sequence.
The disclosed genome editing systems, compositions and methods for constituting a functional donor splice site of a gene harnesses the HDR-independent repair pathway (e.g., via NHEJ) to joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site. In doing so, correction of pathogenic splicing defects occurs.
The disclosed genome editing systems comprise at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. The genome editing system is configured to form a first and a second blunt-ended double strand break in an intron of a gene containing a mutation in the splice donor site, resulting in excision of a segment of the intron containing the mutation. The system simultaneously joins the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site. This results in the creation of a new donor splice site, which allows an RNA (e.g., a pre-mRNA) transcribed from the edited DNA to properly splice (e.g., to splice such that the RNA and the polypeptide translated from the RNA contains all of the exons of a naturally occurring polypeptide, for example, a polypeptide translated from a polynucleotide containing no splicing mutations). In an embodiment, the genome editing system comprises at least two nucleases that generate blunt-ended DNA breaks in a sequence-specific manner.
In an embodiment, the intron comprises a splice donor site mutation that alters splice site recognition, causing a splicing defect. Excising the segment of the intron containing the splice site donor mutation and simultaneously joining the DNA ends flanking the excised segment of the intron results in constitution of a functional donor splice site, thereby restoring splice site recognition in the intron.
In an embodiment, the gene editing system uses a homology directed repair-independent mechanism to join the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site. In a preferred embodiment, the homology directed repair-independent mechanism utilizes non-homologous end joining. This mechanism can be used on all cell types where correction of a splicing defect is desired. This mechanism is particularly useful in post-mitotic (i.e., terminally differentiated) cells, where correction of a splicing defect is desired. Examples of post-mitotic cells, include but are not limited to, myocytes, cardiomyocytes, neurons, adipocytes, and skin cells.
In an embodiment, the excising of the intron occurs at a mutation-eliminating cut site of the intron and at a splice site-generating cut site of the intron. It will be understood that the genome editing system may comprise a nuclease that generates a mutation-eliminating cut site and a splice generating cut site. In an embodiment, the nuclease that generates the mutation-eliminating cut site is the same as the nuclease that generates the splice generating cut site. In another embodiment, the nuclease that generates the mutation-eliminating cut site is different from the nuclease that generates the splice site-generating cut site.
The gene editing system comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. There are a variety of systems that can be used to generate blunt-ended DNA breaks in a sequence-specific manner. For example, the system may be a Cas9 polypeptide or a variant of a Cas9 polypeptide that recognizes a Protospacer Adjacent Motif (PAM) (Cebrian-Serrano and Davies, “CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools”, Mamm Genome, DOI 10.1007/s00335-017-9697-4; and Karvelis et al., “Harnessing the natural diversity and in vitro evolution of Cas9 to expand the genome editing toolbox”, Current Opinion in Microbiology, 2017, 37:88-94). In a system using Cas9, the genome editing system further comprises a mutation-eliminating single guide RNA (sgRNA) and a splice site-generating sgRNA. In this system, the mutation-eliminating sgRNA and a splice site-generating sgRNA each comprise a CRISPR RNA (crRNA) portion as determined appropriate by the person skilled in the art. For example, each of the crRNAs may be about 17 to 27 nucleotides in length.
Methods for designing and making sgRNAs are known to those skilled in the art, and include internet based methods (see also, e.g., Haeussler M. et al., “Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR”, Genome Biol. 2016 Jul. 5; 17(1):148. doi: 10.1186/s13059-016-1012-2). For example, sgRNAs can be designed by finding a PAM motif and considering the preceding 17-27 nucleotides (depending on the Cas9 species to be used) as a target sequence for crRNA. Since it is known that the cleavage will occur at position PAM-3 one can predict where Cas9 is going to cut. Additional scoring for off-target effects can be done by multiple algorithms known to those skilled in the art.
The Cas9 nuclease may be from any species, including but not limited to, S. pyogenes, S. aureus, S. thermophilus, C. jejuni, and F. novicida. In one embodiment, the Cas9 is from S. aureus. Cas9 nucleases generate blunt ended DNA breaks in a PAM-dependent manner, three nucleotides upstream (i.e., when the nucleotides are read in a 5′ to 3′ direction) of a PAM sequence (i.e., PAM-3). In another embodiment, the mutation-eliminating cut site and/or the splice generating cut site is at a Cas9 cleavage site occurring in the presence of one of the following PAM nucleotide sequences: NGG (S. pyogenes, original), NAG (S. pyogenes, original), NGA (S. pyogenes EQR variant), NGCG (S. pyogenes VRER variant), NNGRRT (S. aureus), NNNRRT (S. aureus KKH variant), NNAGAA (S. thermophilus), NNNNRYAC (C. jejuni), YG (F. novicida).
In an embodiment, the genome editing system may comprise a fusion polypeptide comprising a catalytically inactive (i.e., nuclease deficient) Cas9 (dCas9) polypeptide that recognizes a PAM and a nuclease that generates blunt-ended DNA breaks (e.g., such as the PAM sequences described above). dCas9 is commercially available (e.g., Novateinbio). In an embodiment, the catalytically inactive dCas9 is fused to nuclease generating blunt ended DNA breaks. In such an embodiment, the genome editing system comprises a left and right dCas9 that specify binding to DNA in a PAM-dependent manner, followed by a nuclease-dependent cleavage. To excise a segment of an intron containing a splice donor site mutation, two sets of fusion proteins can be used in the system, one that creates blunt-ended double strand breaks at a mutation-eliminating cut site and one that creates blunt-ended double strand breaks at splice site-generating cut site. The excision can them be repaired, for example, by non-homologous end joining.
Specific DNA cleavage (between any desired nucleotides) can be accomplished using other genome-editing systems. Zinc finger nucleases (ZFN) and TALENs are examples of such systems. In general, these systems work as a fusion polypeptide of DNA recognizing protein domains to a nuclease. Precise DNA targeting is accomplished by engineering the zinc finger portion or the TALE portion fused to a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner, and DNA cleavage occurs through the nuclease portion of the fusion polypeptide. Gene editing systems comprising ZFNs and TALENs work as pairs (left and right), so in embodiments in which ZFNs and TALENs are utilized, the genome editing system includes pairs of ZFN or TALENs and the nucleases contained on the ZFNs or TALENs dimerize for the DNA cleavage to occur. In one embodiment, the ZFNs or TALE domains combine with a Mlyl nuclease, which upon dimerization generates blunt ended DNA breaks. To excise a segment of an intron containing a splice donor site mutation, two sets of fusion proteins can be used in the system, one that creates blunt-ended double strand breaks at a mutation-eliminating cut site and one that creates blunt-ended double strand breaks at splice site-generating cut site. The excision can them be repaired, for example, by non-homologous end joining.
In various embodiments, a linker is positioned between the DNA recognizing protein domain (e.g., dCas9, TALE or zinc finger) and a nuclease that generates blunt-ended DNA breaks. The linker may be, for example, a polypeptide linker. The size of the linker may vary based on the distance between the location of the DNA site the DNA recognizing protein domain recognizes and the location at which the nuclease cuts the DNA in a sequence-specific manner.
In other embodiments, the nuclease that cuts the DNA in a sequence-specific manner itself can directly target the DNA sequence of interest (e.g., a mutation-eliminating cut site or a splice site-generating cut site). In other embodiments, the nuclease that cuts the DNA in a sequence-specific manner can be fused to a DNA binding protein or to an oligonucleotide that recognises a DNA sequence in proximity of an intended cut site.
The disclosed genome editing systems may be used to correct various splicing defects. In an embodiment, the splicing site defect is in a splice donor site. The mutation in the splice donor site may occur at the +1 position of the splice donor site. In other various embodiments, the mutation in the splice donor site occurs at the +2, +3, +4, +5, or +6 position of the splice donor site. For example, the splice site donor mutation can be a mutation in a gene provided in Table 1.
In the disclosed genome editing system, the splice site-generating cut site is positioned before a branch splice point for an adjacent exon. Methods for determining branch splice point for an adjacent exon are known to those skilled in the art (see, e.g., Mercer, Genome Research, 2015 PMID: 25561518; Reed, PNAS, 1988 PMID: 3060403). For example, the splice site-generating cut site may be positioned at least, but not limited to, 25, 50, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900 or 1000 base pairs from the mutation-eliminating cut site, provided the splice site-generating cut site is positioned before the branch splice point for an adjacent exon.
In one embodiment, the genome editing system comprises a mutation-eliminating single guide RNA (sgRNA); a splice site-generating sgRNA and a Cas9 molecule that recognizes a PAM having the nucleotide sequence NNGRRT, wherein the mutation-eliminating cut site of the intron is positioned 3 nucleotides in the 5′ direction of the end of the PAM.
In one embodiment, mutation-eliminating cut sites and splice site-generating cut sites are determined by predicting splice sites in a nucleotide sequence. Methods for predicting splices sites are generally known in the art and include the use of tools such as Human Splicing Finder (HSF) (http://www.umd.be/HSF3/), the MaxEntScan donor model and/or the DeepScan donor model. Based on the sequence of the nucleotides at in in proximity to the mutation-eliminating cut sites and splice site-generating cut sites the appropriate nuclease can be selected and the cuts sites can be generated. Excision of the identified intron segment (and the mutation) and simultaneous joining together of the DNA ends flanking the excised intron segment result in constitution of a functional donor splice site, such that the gene can now be properly spliced and a functional protein can be generated upon translation.
In various embodiments, the genome editing system further comprises a delivery vehicle for delivery of the other components of the system (e.g., for delivery of the at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner, and one or more of the sgRNAs, if used in the system). In an embodiment, polynucleotides coding for the at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are in a vector. In another embodiment, when the nuclease is Cas9, the vector further comprises a mutation-eliminating single sgRNA or a splice site-generating sgRNA. The delivery vehicle may be an adeno-associated virus (AAV) vector, for example, an AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8 or AAV9 vector. In a preferred embodiment, the delivery vehicle is an AAV9 vector.
In certain embodiments, a mutation-eliminating sgRNA is present on a first nucleic acid molecule, e.g. a first vector (e.g., a first viral vector, such as a first AAV vector); and a splice generating sgRNA is present on a second nucleic acid molecule e.g., a second vector (e.g., a second vector, for example, a second AAV vector).
In certain embodiments, a mutation-eliminating sgRNA and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are present on one nucleic acid molecule, e.g., one vector (e.g., one viral vector, such as one AAV vector). In certain embodiments, a mutation-eliminating sgRNA and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are present on different vectors. For example, a mutation-eliminating sgRNA is present on a first nucleic acid molecule, e.g. a first vector, (e.g., a first viral vector, for example, a first AAV vector); and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are present on a second nucleic acid molecule, e.g., a second vector (e.g., a second vector, such as a second AAV vector).
In certain embodiments, a splice generating sgRNA and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are present on one nucleic acid molecule, e.g., one vector, (e.g., one viral vector, for example, one AAV vector). In certain embodiments, a splice generating sgRNA and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are present on different vectors. For example, a splice generating sgRNA is present on a first nucleic acid molecule, e.g. a first vector (e.g., a first viral vector, such as, a first AAV vector); and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner are present on a second nucleic acid molecule, e.g., a second vector (e.g., a second vector, for example, a second AAV vector).
The vectors may comprise a promoter operably linked to a mutation-eliminating sgRNA, a splice generating sgRNA or polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. Where a vector contains more than one nucleotide sequence (e.g., a mutation-eliminating sgRNA and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner or a splice generating sgRNA and polynucleotides encoding a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner) the vector may further comprise a second promoter operably linked to the second nucleotide sequence. When two promoters are employed in a vector, the promoter may be the same or they may be different. Promoters for use in expression vectors are known to those skilled in the art.
In addition to AAVs, the vector may comprise plasmid DNA, encoding CRISPR/Cas9 components (Cas9+sgRNA) as a delivery vehicle. Alternatively, the delivery vehicle can comprise RNA, where polynucleotides encoding Cas9 and sgRNAs are comprised of RNA molecules. Alternatively, the delivery vehicle can be in an RNP (ribonucleoprotein) form, where Cas9 is delivered in a complex with sgRNA (RNA form).
In other embodiments, the delivery vehicle is a non-viral delivery vehicle, for example, a liposome, such as a cationic liposome, or polymeric nanoparticles. Methods for delivering the disclosed gene editing system to a cell are known in the art.
In an embodiment, the genome editing system comprises a S. aureus Cas9 molecule that recognizes a PAM, a mutation-eliminating sgRNA and a splice site-generating sgRNA. In an embodiment, the mutation-eliminating sgRNA comprises the nucleotide sequence aaaacatatatataatacatatGGT (SEQ ID NO: 1). The genome editing system targets a pathogenic mutation in the Lama2 gene, wherein the mutation is a c.417+1 g→a mutation. In certain embodiments, the mutation is in a subject having merosin deficient congenital muscular dystrophy (MDC1A).
Compositions comprising one or more components of the gene editing system are also disclosed. The composition may comprise, for example, at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. The composition is configured to form a first and a second blunt-ended double strand break in an intron of a gene, wherein the intron comprises a splice donor site mutation that alters splice site recognition, thereby excising a segment of the intron and simultaneously joining DNA ends flanking the excised segment of the intron to constitute a functional donor splice site.
The nuclease may be in a fusion polypeptide comprising a DNA recognizing protein domain and the nuclease. For example, the fusion polypeptide may comprise a dCas9 molecule that is fused to a nuclease that generates blunt-ended DNA breaks in a sequence-specific manner as described herein. In an embodiment, zinc finger polypeptides are the DNA recognizing protein domain. Similarly, the fusion polypeptide may comprise a TALE polypeptide as the DNA recognizing protein domain. When the nuclease portions of the fusion polypeptides dimerize, the pair of fusion polypeptides generates blunt-ended DNA breaks.
The composition may further comprise a linker between the catalytically inactive Cas9 and the nuclease or between a DNA recognizing protein domain and the nuclease, as described herein.
Where the nuclease is a Cas9 molecule, the composition further comprises a mutation-eliminating sgRNA and a splice site-generating sgRNA. Such compositions may further comprise a delivery vehicle such as a vector (including a viral vector) as described herein or liposomes or nanoparticles. The compositions may be used in the genome editing systems disclosed herein. Each of the mutation-eliminating sgRNA and the splice site-generating sgRNA may comprise a CRISPR RNA (crRNA) portion that is 17 to 27 nucleotides in length.
Methods of Constituting a Functional Donor Splice Site in a Gene
Methods of constituting a functional donor splice site in a gene, where the gene comprises a mutation in a donor splice site that alters splice site recognition are also provided. The method comprises delivering a genome editing system to the gene. The genome editing system comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. The genome editing system is configured to form a first and a second blunt-ended double strand break in an intron of a gene, wherein the intron comprises a splice donor site mutation that alters splice site recognition. This results in excision of a segment of the intron and simultaneously joining of DNA ends flanking the excised segment of the intron to constitute a functional donor splice site. This results in restored splice site recognition in the intron. The joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through a homology directed repair-independent mechanism, for example, through non-homologous end joining.
Other features of the genome editing system for using in a method of constituting a functional donor splice site in a gene are as described herein.
In an embodiment, the gene with the donor splice mutations is a gene listed in Table 1.
Methods of detecting constitution of a functional donor splice site in a gene, where the gene comprises a mutation in a donor splice site that alters splice site recognition are known to those skilled in the art. For example, RT-PCR can be performed on the cDNA flanking the exon affected by the splicing defect and gel electrophoresis can be used to determine if a functional donor splice site has been constituted. Western blot analysis may be performed to determine of a full-length protein has been generated, indicating successful constitution of a function donor splice site. Methods for performing these techniques are known in the art.
Cells
Isolated cells comprising a gene whose mutation at a splice donor site has been repaired according to the method for constituting a functional donor splice site in a gene, where the gene comprises a mutation in a donor splice site that alters splice site recognition are also provided.
The cell may be a post-mitotic cell, for example, a myocyte, cardiomyocyte, neuron, adipocyte, or skin cell.
Components of a genome editing system as described herein are can be delivered by a vector, for example, an AAV vector as described herein. Alternatively, the components can be delivered using non-viral systems, for example, liposomes or nanoparticles. Delivery into cells can occur using techniques known in the art, including, but not limited to microinjection, electroporation, lipid-mediated transfection, RNP-mediated delivery, RNA-mediated delivery, or a combination thereof.
Methods of treating a disease or condition caused by a mutation in a splice donor site in a gene of a subject
Methods for treating a disease or condition caused by a mutation in a splice donor site in a gene of a subject in a subject in need of such treatment are also provided. The method comprises delivering a genome editing system to the intron. The genome editing system comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. The genome editing system is configured to form a first and a second blunt-ended double strand break in an intron of a gene, wherein the intron comprises a splice donor site mutation that alters splice site recognition. This results in excision of a segment of the intron and simultaneously joining of DNA ends flanking the excised segment of the intron to constitute a functional donor splice site. This results in restored splice site recognition in the intron. The joining of the DNA ends flanking the excised segment of the intron to constitute a functional donor splice site occurs through a homology directed repair-independent mechanism, for example, through non-homologous end joining.
Other features of the genome editing system for using in a method of treating a disease or condition caused by a mutation in a splice donor site in an intron in a subject are as described herein.
In an embodiment, the subject has a disease or condition caused by a donor splice mutation in a gene as listed in Table 1.
In certain embodiments, the treatment is initiated prior to onset of the disease. In certain embodiments, the treatment is initiated after onset of the disease. In certain embodiments, the treatment is initiated prior to onset of a symptom of the disease. Alternatively, the treatment is initiated at onset of one or more symptoms of the disease. In certain embodiments, the treatment is initiated after onset one or more symptoms of the disease.
Components of a genome editing system as described herein are can be delivered by a vector, for example, an AAV vector as described herein. Alternatively, the components can be delivered using non-viral systems, for example, liposomes or nanoparticles. Delivery into cells can occur using techniques known in the art, including, but not limited to microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof. The dose(s) of components of the system to use for treating a disease or condition caused by a mutation in a splice donor site of a gene will depend on the mode of delivery and is within the skill of the skilled person to determine.
Components of the genome editing system can be delivered systemically.
Systemic modes of administration include oral and parenteral routes, including but not limited to intravenous, intra-arterial, intramuscular, intradermal, subcutaneous, intranasal, and intraperitoneal routes.
Components of the genome editing system can be delivered locally. Local modes of administration include injection directly into one or more specific tissues. In one embodiment, local delivery occurs by direct injection in a muscle on the subject.
Kits
The present disclosure contemplates kits for carrying out the methods disclosed herein. Such kits typically comprise two or more components required for constituting a functional donor splice site in a gene, where the gene comprises a mutation in a donor splice site that alters splice site recognition. Components of the kit include, but are not limited to, one or more of compounds, reagents, containers, equipment and instructions for using the kit. Accordingly, the methods described herein may be performed by utilizing pre-packaged kits provided herein. In one embodiment, the kit comprises at least one nuclease that generates blunt-ended DNA breaks in a sequence-specific manner. In some embodiments, the instructions comprise one or more protocols for constituting a functional donor splice site in a gene, where the gene comprises a mutation in a donor splice site that alters splice site recognition. In some embodiments, the kit comprises one or more controls.
The following non-limiting examples illustrative of the disclosure are provided.
Cloning and Virus Production
Each sgRNA shown in Table 2, was cloned into pX601 plasmid (Addgene 61591) containing codon optimized S. aureus Cas9 (3).
As control, a GFP plasmid was constructed by replacing the SaCas9 cassette in pX601 with eGFP codon from pEGFP-C1 plasmid (Clontech Takara) using Age1 and EcoR1 directional cloning. 2100 bp stuffer sequence was incorporated into Xba1 site of the vector to maintain AAV genome packaging capacity. The pX601-GFP, -sgRNA1 and -sgRNA2 plasmids were produced as Adeno-associated virus serotype 9 (AAV9), concentrated and quantified by quantitative PCR (Vigene Biosciences). Injection-ready virus solution containing 7.5×1011 viral genome/vector was prepared and brought to 30 μl with 1×PBS (Gibco).
Cell Culture and Guide Screening
Primary myoblasts were isolated from EDL muscle of C57BL/6J wild-type and dy2J/dy2J mice (18) and maintained in DMEM supplemented with 1% Chicken Embryo Extract (Gemini Biosciences), 10% Horse Serum, 1% Penicillin/Streptomycin, 1% L-glutamine (All from Gibco unless indicated otherwise) at 37° C. with 5% CO2. Transfection was performed using Amaxa Basic Nucleofector Kit VPI-1002 (Lonza) in Nucleofector device (Lonza) under program number U-023. Cells were grown for 72 hours and genomic DNA was isolated with Blood and Tissue DNA Isolation Kit based on manufacturer's protocol (Qiagen). The activity of guides combination to remove the intervening region was assessed by PCR using primers in Lama2 exon 2 (RDC 551) and intron 2 (RDC 552) flanking the genomic deletion. The sequences used are shown in Table 3.
AATCCATACC
GTCAAGAATG (SEQ ID NO: 24)
Animal Studies
The dy2J/dy2J and C57BLJ6J mice were purchased from the Jackson Laboratory and maintained in the Toronto Centre for Phenogenomics (TCP). All animal experiments were performed according to Animal Use Protocol number 16-0234H. No statistical methods were used to predetermine sample size. Intramuscular injection was performed on 3-weeks old dy2J/dy2J mice under isofluorane anesthesia. Treatments were randomized among littermates. No blinding was done in the intramuscular treatment. For systemic administration experiments involving neonatal pups, breeding cages were monitored daily for birth and the entire litter of P2 newborns were injected with either GFP- or guide-containing vectors. Mice were genotyped (19) and weaned at the age of 3 weeks old, where randomization occurred and all investigators were subsequently blinded for the different treatment groups throughout the study until the time of necropsy.
Functional Tests
Open field activity test and assessment of in vivo muscle force were performed on 10 weeks-old mice (for both intraperitoneal and temporal vein cohorts) at the Lunenfeld-Tanenbaum Research Institute's Centre for Modeling Human Disease Mouse Phenotyping Facility. For the open field test, mice were placed in the frontal center of a transparent Plexiglas open field (41.25 cm×41.25 cm×31.25 cm) illuminated by 200 lx. Trained operator, who is unaware of the nature of the projects and treatments, performed the experiments. The VersaMax Animal Activity Monitoring System recorded vertical activities and total distance travelled for 20 minutes per animal.
In vivo muscle contraction test was performed using 1300A: 3-in-1 Whole Animal System and analyzed using Dynamic muscle control/analysis (DMC/DMA) High throughput software suite (Aurora Scientific). The mice were anaesthetised with intraperitoneal injection of ketamine/xylazine cocktail at 100 mg/kg and 10 mg/kg of body weight, respectively. Contractile output was measured via percutaneous electrodes that stimulate specific nerves innervating the plantar flexors. Specific tetanic force (200 ms of 0.5-ms pulses at 125 Hz) was recorded and corrected to body weight.
RNA Isolation, RT-PCR, Quantitative PCR (qPCR)
RNA from cultured cells were isolated using Trizol (Invitrogen) according to manufacturer's instruction. For mouse tissues, muscles were sectioned at 10 μm thin, collected in 1.4 mm Zirconium Beads pre-filled tubes (OPS Diagnostics) and homogenized using a MagNA Lyser (Roche Diagnostics) using Trizol (Invitrogen). N6-primed cDNA was synthesized from 1000 ng of RNA using SuperScript III (Invitrogen). PCR amplification to detect exon inclusion was performed using Multiplex PCR mix (Qiagen) and primers in exons 1 and 4 (RDC 449 and 450), with sequences shown in Table 2.
qPCR was performed using Fast SYBR Green Master Mix on Step One Plus Real Time PCR (Applied Biosystems). Control PUC-Lama2 plasmid was generated by directional cloning in our laboratory. Briefly, exon 1-7 Lama2 cDNA was amplified from wild type muscles using primers RDC 1411 and RDC 1479, and cloned into PUC19 plasmid at BamH1 restriction sites. The expression of products with exon 2 inclusion was calculated using primers in exon 2/exon 3 junctions, and normalized to expression of products amplified with exon 4. Copy number of all samples was calculated relative to PUC-Lama2 plasmid control.
Protein Isolation and Western Blot
Sectioned muscles collected in the Zirconium beads tubes were homogenized in 500 μl of RIPA homogenizing buffer (50 mM Tris HCl pH 7.4, 150 nM NaCl, 1 mM EDTA supplemented with protease inhibitor cocktails (Roche)) and lysed with a MagNA Lyser. Subsequently, 500 μl of RIPA double detergents buffer (2% deoxycholate, 2% NP40, 2% Triton X-100 in RIPA homogenizing buffer) was added to the lysates, which were then incubated for 45 minutes at 4° C. with gentle agitation and centrifuged for 10 minutes at 13,000 rpm. The protein concentration was measured using BCA Assay (Thermo Scientific). Protein was separated on 3-8% Tris-Acetate gel and transferred using the Novex system (Invitrogen). The primary antibodies used were rat monoclonal anti-Lama2 (Abcam 11576 4H8-2, 1:500), rabbit polyclonal anti-tubulin (Abcam 4074, 1:5000), and mouse monoclonal anti-HA (Abcam 18181, 1:2500).
Immunofluorescence, H&E and Picrosirius Red Staining
Antibodies used for immunofluorescence stainings were rat monoclonal anti-Lama2 (Abcam 11576 4H8-2, 1:500), mouse monoclonal anti-Neurofilament H (NF-H, Biologend 801601 SMI 31, 1:1000), FITC-conjugated rat anti-mouse Cdllb clone M1/70 (BD Pharmingen 553310, 1:50) and imaged using either Zeiss Axiovert 200M or Nikon TE-2000 epifluorescence microscopes, or Olympus 1X81 quorum spinning disk confocal microscope. Perkin Elmer Volocity software was used for image acquisition.
Hematoxylin and eosin (H&E) staining was performed using standard protocol and Picrosirius Red staining was performed at Pathology Laboratory, the Hospital for Sick Children, Toronto. 300 fibers obtained from 4 different field of views per animal were analyzed using ImageJ 1.51h software for minimum Feret's diameter and cross-sectional area. Fibrosis quantification was performed from Sirius Red-stained (for intraperitoneal cohort) and H&E-stained (for temporal vein cohort) images by image-segmentation using ImageJ 1.51h software.
Off-Target Analysis by T7 Endonuclease Assay
Top 10 predicted off-target sites were computed using Benchling CRISPR Design tool (20). Genomic DNA isolated from treated- and control mice were PCR-amplified using primers targeting loci corresponding to each hit, as listed in Table 2.
Purified PCR products were then digested using T7 Endonuclease I (NEB) based on the manufacturer's instruction.
Deep Sequencing
Genomic DNA extracted from tibialis anterior (TA) muscles from the temporal vein cohorts (Qiagen Blood and Tissue kit) were amplified using oligos RDC 1474 and RDC 1461 as shown in Tables 2 and 4. A second round of PCR was performed to add 5′ and 3′ end barcodes, and sequenced with 125 bp paired-end reads on Illumina HiSeq 2500 at the Toronto Center for Applied Genomics (TCAG). Bioinformatic analyses were done similarly as previously described (21).
Quantitative Droplet Digital PCR (ddPCR)
ddPCR was performed on temporal vein samples using a QX200™ Droplet Digital™ PCR System with QX200™ ddPCR EvaGreen Supermix (BioRad). Three-steps ddPCR was performed with the following conditions: 95° C. (10 mins), 94° C. (30 sec), 62° C. (30 sec), 72° C. (1 min) for 45 cycles, and 98° C. (10 mins) using Lama2 guide screen 1F (RDC 1474) and 1R (RDC 1475). The data were analyzed using QuantaSoft Pro (BioRad).
Mammalian donor splice sites for major U2-type introns have a 9 nucleotides long consensus sequence A/C-A-G-g-t-a/g-a-g-u and are mainly recognized by canonical base pairing to the 5′ end of U1 small nuclear RNA (25). The first two intronic nucleotides (gt) are essentially invariant, whereas certain flexibility is allowed at all other positions. Targeted CRISPR/Cas9-mediated removal of an intronic region containing a pathogenic mutation was used to enable joining of Lama2 exon 2 with a ‘gt’ dinucleotide, leading to reconstitution of a functional donor splice site.
A mouse model of MDC1A, dy2J/dy2J harboring a splice site mutation in intron 2 of Lama2, annotated as c.417+1 g→a, which results in skipping of exon 2 and truncation of the N-terminal domain of the protein (
Approximately 1400 nucleotides in a proximal region of intron 2 were evaluated for SaCas9 targets that would generate genomic deletions in combination with sgRNA1 and, following NHEJ, create potential donor splice sites (splice site-generating cut) (
RT-PCR analysis revealed the presence of an amplicon similar to the wild-type control for sgRNA2, sgRNA3 and sgRNA5, indicating an inclusion of the exon 2 of Lama2 after generation of intronic deletions (
To assess the impact of the full-length Lama2 restoration in skeletal muscle, Cas9 and sgRNAs were delivered into the right tibialis anterior (TA) muscles of 3-week old dy2J/dy2J mice using adeno-associated virus serotype 9 (AAV9) (
RT-PCR analysis successfully identified transcripts with inclusion of exon 2 in all right TA muscles treated with AAV9-Cas9-sgRNA1 and -sgRNA2, but not in contralateral muscles and AAV9-GFP-treated mice (
The expression of Lama2 was analyzed by western blot, and it was observed that in all dy2J/dy2J-isolated muscles, a truncated form of Lama2 was present, whereas a slightly larger full-length protein was expressed in the TA muscles injected with AAV9-Cas9-sgRNA1 and -sgRNA2 combination (
To assess the localization of the restored Lama2, immunofluorescence staining was performed on the treated TA muscles. Lama2 immunoreactivity was detected at the sarcolemma of muscles fibers, similar to the wild-type controls (
This demonstrated the successful inclusion of the previously missing exon 2 and restoration of the full-length Lama2 protein at the sarcolemma of the muscle, which led to overall improvement of muscle histopathology supporting the therapeutic potential of this treatment strategy in the dy2J/dy2J mice.
It was next asked whether the dystrophic pathology, which is already apparent at pre-weaning age (17), could be ameliorated by restoration of Lama2 in neonatal mice. P2 dy2J/dy2J mice were injected with AAV9-Cas9-sgRNA1 and -sgRNA2 via intraperitoneal route and compared to AAV9-GFP-treated controls (
RT-PCR analysis of gastrocnemius muscles isolated 10 weeks post-injection showed successful exon 2 inclusion (
Histological examination using hematoxylin and eosin (H&E) and picrosirius red staining revealed an overall improved morphology of muscles with restored Lama2 expression (
Morphometric analysis showed ˜50% reduction of fibrosis (
RT-PCR and immunofluorescence staining analyses of sciatic nerves showed no restoration of Lama2 transcript and protein (
This finding recapitulated an earlier study demonstrating that muscle-specific overexpression of Laminin-211 in merosin-deficient mice improved muscle pathology, but not the associated paralysis (7), indicating that correction of the peripheral neuropathy requires restoration of Lama2 beyond skeletal muscles. The previously reported feasibility of CMV-driven gene expression mediated by AAV9 into sciatic nerves has been demonstrated mostly via vascular administration routes (26, 27).
To achieve a more robust tissue distribution, AAV9-Cas9-sgRNA1 and -sgRNA2 were injected into the temporal vein of P2 neonatal dy2J/dy2J mice (
At 30 weeks post-injection, the muscles and sciatic nerves were harvested and analyzed for targeted genomic DNA deletion and expression of full-length Lama2 mRNA and protein. The expected ˜493 bp genomic deletion was detected by PCR (
RT-PCR and western blot analyses of the TA muscles indicated expression of full-length Lama2 at transcript and protein levels (
Lama2 restoration was also achieved in sciatic nerve at the transcript (
Consequently, the degree of contracture and paralysis in the hind limbs and overall mobility of the AAV9-Cas9-sgRNA1 and -sgRNA2-treated mice were markedly improved compared to those of control dy2J/dy2J mice. Supporting this finding, open field test demonstrated significantly higher total distance travelled in the AAV9-Cas9-sgRNA1 and -sgRNA2-treated mice compared to the control AAV9-GFP-treated dy2J/dy2J (
In addition to the on-target activity, Cas9 nuclease has been shown to rarely generate DSB at non-intended off-target sites throughout the genome (16). Off-target effects are a safety concern for the eventual translation of gene editing therapies to humans. No off-target mutations at twenty potential off-target sites (ten for each sgRNA) in the mouse genome were observed (
Positions of all exon-intron junctions were obtained from GENCODE gene annotation gtf file (version 19, https://www.gencodegenes.org/releases/19.html) using customized scripts. 5′ splice site (+1) mutations were extracted from the Human Gene Mutation Data database (HGMD, version 20140404). All of these mutations are pathogenic or disease-causing mutations (DM). As used herein, the first nucleotide of the intron is defined as the “+1” position. For each transcript, introns were extracted. For introns that were longer than 1000 base pairs, only the first 1000 base pairs were retained for analysis. For each gene, overlapping introns from different transcripts were merged. If a shorter intron overlaps with a larger one, then the shorter intron was used. For the introns containing a 5′ splice site (+1) mutation, it was first examined if a “mutation-eliminating cut” site could be found. As used herein, a “mutation-eliminating cut” is defined as when any of the available Cas9s cleavage site occurring after the following PAM sequences: NGG, NAG, NGA, NGCG, NNGRRT, NNNRRT, NNAGAA, NNNNRYAC, YG could lead to a cutting that results in the elimination of the mutation. For mutations occurring at the “+1” position, the cut has to be made immediately upstream of the “+1” position (“cut at “+1”). The search for PAM sequences was done on both strands. For the introns where a “mutation-eliminating cut” could be found, the search continued into the introns and it was examined if a″ “splice site-generating cut” site could be found. The first two nucleotides (“gt” at +1 and +2 sites) were required to be restored. Finally, “splice site-generating cut” sites that were at least 50 base pairs away from the next exon were filtered for, to avoid interference with the splicing machinery, although the splice site-generating cut site may be less than 50 base pairs away from the next exon (e.g., at least 25 base pairs away from a downstream (5′ to 3) or adjacent exon).
Splice Site Prediction
Splice sites were scored using (a) the MaxEntScan donor model, receiving in input 3 exonic bp and 6 intronic bp (22) centered at the splice site; (b) the DeepScan donor model, a proprietary predictor developed at Deep Genomics Inc., receiving in input 40 exonic bp and 40 intronic bp centered at the splice site. Both predictors were trained based on human annotated splice sites and genome sequence, and applied to the mouse sequence without further adjustments. MaxEntScan was previously shown to be one of the best performing publicly-available methods also for evaluating the deleteriousness of splice site altering variants (23). DeepScan is based on a deep neural network architecture (24) with convolutional layers and hidden layers consisting of rectified linear units trained using stochastic gradient descent to distinguish sequences of annotated splice sites from decoy splice sites found in introns; it achieved 98% area under the ROC curve for distinguishing held-out donor splice sites from held-out intronic sequences with the core donor dinucleotide GT, achieving a better performance than MaxEntScan as seen in Table 5:
To derive genome wide statistics on donor splice site prediction, all intronic GT sites were extracted for GENCODE Basic version 19 transcripts, using the reverse complement of the hg19/b37 human reference genome sequence for negative strand transcripts; only sites for which the intronic categorization was not ambiguous were retained (i.e. intronic in all transcripts); sites were then categorized as annotated splice site donors or not. Finally, prediction models (MaxEntScan donor model, DeepScan donor model) were used to score these sites, and derive genome wide statistics at different prediction score thresholds. Exon statistics for reconstituted splice site donors (percentage of exons with at least one GT site within 1 kb predicted as donor when deleting the intervening intronic sequence and retaining the exon sequence, average number of such sites per exon) were calculated with respect to the longest transcript isoform of each gene in GENCODE Basic version 19.
A patient has two mutations in the LAMA2 gene, with one of them being +1 mutation (c3037+1G>T) in 5′SS of exon 21 (
Using Human Splicing Finder (HSF) (http://www.umd.be/HSF3/) a “strength” of a non-mutated 5′ss was determined. For that, an exon 21 (181 nt)+50 intronic nucleotides (231 nt total) were analyzed by HSF (
For mutated sequence (c3037+1G>T) HSF and MaxEnt scores dropped to 59.24 and −1.65, respectively, indicating that alteration of 5′ss will likely cause a splicing defect (
By modelling a double stranded break at any position within a sequence, a set of new exon/intron junctions are generated by removing an intervening sequence containing the mutation and linking the end of the exon 21 with intronic sequences starting with ‘gt’ in order to constitute a possible 5′ss. An example is shown in
A set of the generated junctions within the first 505 nucleotides in the intron are scored as described above (Table 6). For the new junction depicted in
Although the disclosure has been described with reference to certain specific embodiments, various modifications thereof will be apparent to those skilled in the art. Any examples provided herein are included solely for the purpose of illustrating the disclosure and are not intended to limit the disclosure in any way. Any drawings provided herein are solely for the purpose of illustrating various aspects of the disclosure and are not intended to be drawn to scale or to limit the disclosure in any way. The scope of the claims appended hereto should not be limited by the preferred embodiments set forth in the above description, but should be given the broadest interpretation consistent with the present specification as a whole. The disclosures of all art recited herein are incorporated herein by reference in their entirety as if each piece of art was specifically and individually indicated to be incorporated by reference.
This application claims priority under the Paris Convention to U.S. Provisional Patent Application Ser. No. 62/530,703, filed Jul. 10, 2017, which is incorporated herein by reference as if set forth in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2017/051152 | 9/29/2017 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62530703 | Jul 2017 | US |
