U.S. patent application number 17/119806 was filed with the patent office on 2021-07-08 for method for efficient exon (44) skipping in duchenne muscular dystrophy and associated means.
The applicant listed for this patent is Academisch Ziekenhuis Leiden, BioMarin Technologies B.V.. Invention is credited to Annemieke Aartsma-Rus, Josephus Johannes De Kimpe, Gerard Johannes Platenburg, Judith Christina Theodora Van Deutekom, Garrit-Jan Boudewijn Van Ommen.
Application Number | 20210207138 17/119806 |
Document ID | / |
Family ID | 1000005462493 |
Filed Date | 2021-07-08 |
United States Patent
Application |
20210207138 |
Kind Code |
A1 |
Platenburg; Gerard Johannes ;
et al. |
July 8, 2021 |
METHOD FOR EFFICIENT EXON (44) SKIPPING IN DUCHENNE MUSCULAR
DYSTROPHY AND ASSOCIATED MEANS
Abstract
The invention relates to a nucleic acid molecule that binds
and/or is complementary to the nucleotide molecule having sequence
5'-GUGGCUAACAGAAGCU (SEQ ID NO:1), 5'-GGGAACAUGCUAAAUAC (SEQ ID
NO:2), 5'-AGACACAAAUUCCUGAGA (SEQ ID NO:3), or 5'-CUGUUGAGAAA (SEQ
ID NO. 4), and to its use in a method for inducing skipping of exon
44 of the DMD gene in a DMD patient.
Inventors: |
Platenburg; Gerard Johannes;
(Voorschoten, NL) ; De Kimpe; Josephus Johannes;
(Utrecht, NL) ; Van Deutekom; Judith Christina
Theodora; (Dordrecht, NL) ; Van Ommen; Garrit-Jan
Boudewijn; (Amsterdam, NL) ; Aartsma-Rus;
Annemieke; (Hoofddorp, NL) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BioMarin Technologies B.V.
Academisch Ziekenhuis Leiden |
Leiden
Leiden |
|
NL
NL |
|
|
Family ID: |
1000005462493 |
Appl. No.: |
17/119806 |
Filed: |
December 11, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16292005 |
Mar 4, 2019 |
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17119806 |
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14859598 |
Sep 21, 2015 |
10246707 |
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16292005 |
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12992218 |
Nov 11, 2010 |
9139828 |
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14859598 |
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PCT/NL2009/050258 |
May 14, 2009 |
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12992218 |
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61128010 |
May 15, 2008 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 48/00 20130101;
C12N 2310/3513 20130101; C12N 15/113 20130101; C12N 2310/315
20130101; C12N 2310/321 20130101; C12N 2310/314 20130101; C12N
2310/3517 20130101; C12N 2310/111 20130101; C12N 2310/346 20130101;
C12N 2310/11 20130101; C12N 2310/3233 20130101; C12N 2320/33
20130101 |
International
Class: |
C12N 15/113 20060101
C12N015/113 |
Foreign Application Data
Date |
Code |
Application Number |
May 14, 2008 |
EP |
08156193.8 |
Claims
1. (canceled)
2. An oligonucleotide 16 to 25 nucleotides in length that comprises
a base sequence selected from SEQ ID NOS: 35-40 and 42-45, wherein
the oligonucleotide induces skipping of exon 44 of human dystrophin
pre-mRNA and comprises a modification.
3. The oligonucleotide of claim 2, which is a 2'-O-alkyl
phosphorothioate oligonucleotide.
4. The oligonucleotide of claim 3, which is a 2'-O-methyl
phosphorothioate oligonucleotide.
5. The oligonucleotide of claim 2, wherein the modification
comprises a modified backbone.
6. The oligonucleotide of claim 5, wherein the modified backbone is
selected from the group consisting of a morpholino backbone, a
carbamate backbone, a siloxane backbone, a sulfide backbone, a
sulfoxide backbone, a sulfone backbone, a formacetyl backbone, a
thioformacetyl backbone, a methyleneformacetyl backbone, a
riboacetyl backbone, an alkene containing backbone, a sulfamate
backbone, a sulfonate backbone, a sulfonamide backbone, a
methyleneimino backbone, a methylenehydrazino backbone and an amide
backbone.
7. The oligonucleotide of claim 2, wherein the modification is
selected from the group consisting of: phosphorodiamidate
morpholino oligomer (PMO), peptide nucleic acid, and locked nucleic
acid.
8. The oligonucleotide of claim 7, wherein the modification is
PMO.
9. A pharmaceutical composition, comprising the oligonucleotide of
claim 2 and a pharmaceutically acceptable carrier.
10. A method of treating Duchenne muscular dystrophy or Becker
muscular dystrophy in a subject, comprising administering to the
subject the oligonucleotide of claim 2.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 16/292,005 filed Mar. 4, 2019, which is a continuation of U.S.
application Ser. No. 14/859,598 filed Sep. 21, 2015, now U.S. Pat.
No. 10,246,707, which is a continuation of U.S. application Ser.
No. 12/992,218 filed Nov. 11, 2010, now U.S. Pat. No. 9,139,828,
which is a continuation of PCT application No. PCT/NL2009/050258
filed May 14, 2009, which claims priority to European application
No. EP 08156193.8 filed May 14, 2008, and to U.S. provisional
application No. 61/128,010 filed May 15, 2008, the contents of each
of which is incorporated by reference in their entirety.
SEQUENCE LISTING
[0002] This application is being filed with a Sequence Listing in
Computer Readable Form (CFR), which is entitled
"0105_05_US1CN4_seq_list.txt" of 41699 bytes in size and was
created Dec. 11, 2020; the content of which is incorporated herein
by reference in its entirety.
FIELD
[0003] The invention relates to the field of genetics, more
specifically human genetics. The invention in particular relates to
the modulation of splicing of the human Duchenne Muscular Dystrophy
gene.
BACKGROUND
[0004] Myopathies are disorders that result in functional
impairment of muscles. Muscular dystrophy (MD) refers to genetic
diseases that are characterized by progressive weakness and
degeneration of skeletal muscles. Duchenne muscular dystrophy (DMD)
and Becker muscular dystrophy (BMD) are the most common childhood
forms of muscular dystrophy. They are recessive disorders and
because the gene responsible for DMD and BMD resides on the
X-chromosome, mutations mainly affect males with an incidence of
about 1 in 3500 boys.
[0005] DMD and BMD are caused by genetic defects in the DMD gene
encoding dystrophin, a muscle protein that is required for
interactions between the cytoskeleton and the extracellular matrix
to maintain muscle fiber stability during contraction. DMD is a
severe, lethal neuromuscular disorder resulting in a dependency on
wheelchair support before the age of 12 and DMD patients often die
before the age of thirty due to respiratory- or heart failure. In
contrast, BMD patients often remain ambulantory until later in
life, and have near normal life expectancies. DMD mutations in the
dystrophin gene are characterized by frame shifting insertions or
deletions or nonsense point mutations, resulting in the absence of
functional dystrophin. BMD mutations in general keep the reading
frame intact, allowing synthesis of a partly functional
dystrophin.
[0006] Several possible treatments have been investigated over the
last 20 years, including myoblast-transplantation, DNA-targeted
gene therapy, and antisense-mediated exon skipping (van Deutekom
and van Ommen, (2003), Nat. Rev. Genet., 4(10):774-83).
Antisense-mediated exon skipping aims at transforming out-of-frame
mutations present in DMD patients into in-frame BMD-like mutations
that result in synthesis of an at least partially functional
dystrophin, which will prolong the viability of the muscles
(Aartsma-Rus and van Ommen, (2007), RNA, 13(10): 1609-24).
[0007] Exon skipping can be induced by antisense oligonucleotides
(AON) directed against the splice donor or splice acceptor site of
a splice junction that are involved in the enzymatic process of
exon joining, or against exon-internal sequences. In general,
splice donor and splice acceptor sites comprise conserved sequences
and targeting these sequences has the inevitable risk of
co-targeting splice sites of additional exons from DMD or other
gene transcripts.
[0008] Exon 44 of the DMD gene consists of 148 base pairs.
Therapeutic skipping of exon 44 would restore the correct reading
frame in DMD patients having deletions including but not limited to
exons 03-43, 05-43, 06-43, 10-43, 13-43, 14-43, 17-43, 19-43,
28-43, 30-43, 31-43, 33-43, 34-43, 35-43, 36-43, 37-43, 38-43,
40-43, 41-43, 42-43, 43, 45, 45-54, and 45-68, or having a
duplication of exon 44. Furthermore, for some DMD patients the
mutations are such that the simultaneous skipping of one or more
exons is required in addition to exon 44 skipping to restore the
reading frame. Non-limiting examples of such mutations are nonsense
point mutations in the flanking exons 43 or 45, requiring exon
43+44 skipping or exon 44+45 skipping respectively. The
aforementioned mutations in total occur in about 6-8% of all DMD
patients. The majority of resulting dystrophin proteins will be
truncated in the central rod domain of the protein, leaving the
essential N-terminal actin-binding domain and the C-terminal domain
binding to dystrobrevin and syntrophin, and the
.beta.-dystroglycan-binding C-terminal cysteine-rich domain,
intact.
DETAILED DESCRIPTION
[0009] The present invention identifies four different regions in
exon 44 that are particularly suited for inducing skipping of exon
44. The invention thus provides a method for modulating splicing of
exon 44 of the DMD gene in a cell, the method comprising providing
said cell with a molecule that binds to a nucleotide sequence
comprising SEQ ID NO. 1: 5'-GUGGCUAACAGAAGCU; SEQ ID NO. 2:
5'-GGGAACAUGCUAAAUAC, SEQ ID NO. 3: 5'-AGACACAAAUUCCUGAGA, or SEQ
ID NO. 4: 5'-CUGUUGAGAAA. This molecule preferably binds or is
complementary to any of SEQ ID NO: 1, 2, 3, or 4 when SEQ ID NO:1,
2, 3, or 4 is present within exon 44 of the DMD pre-mRNA.
[0010] Throughout the application, the expression "inducing
skipping" is synonymous of "modulating splicing".
[0011] It was found that a molecule that binds to a nucleotide
sequence comprising SEQ ID NO. 1: 5'-GUGGCUAACAGAAGCU; SEQ ID NO.
2: 5'-GGGAACAUGCUAAAUAC, SEQ ID NO. 3: 5'-AGACACAAAUUCCUGAGA, or
SEQ ID NO. 4: 5'-CUGUUGAGAAA results in highly efficient skipping
of exon 44 in cells provided with this molecule. Furthermore, none
of the indicated sequences is derived from conserved parts of
splice-junction sites. Therefore, said molecule is not likely to
mediate differential splicing of other exons from the DMD pre-mRNA
or exons from other genes. In addition, other (immuno)toxicity is
preferably avoided by avoiding CpG pairs in the molecule that binds
to a nucleotide sequence as defined herein above.
[0012] Exon skipping refers to the induction in a cell of a mature
mRNA that does not contain a particular exon that is normally
present therein. Exon skipping is achieved by providing a cell
expressing the pre-mRNA of said mRNA, with a molecule capable of
interfering with sequences such as, for example, the splice donor
or splice acceptor sequence required for allowing the enzymatic
process of splicing, or that is capable of interfering with an exon
inclusion signal required for recognition of a stretch of
nucleotides as an exon to be included into the mRNA. The term
pre-mRNA refers to a non-processed or partly processed precursor
mRNA that is synthesized from a DNA template in the cell nucleus by
transcription.
[0013] Certain methods of the invention will alleviate one or more
characteristics of a myogenic cell or muscle cell of a DMD patient
having deletions including, but not limited to, exons 03-43, 05-43,
06-43, 10-43, 13-43, 14-43, 17-43, 19-43, 28-43, 30-43, 31-43,
33-43, 34-43, 35-43, 36-43, 37-43, 38-43, 40-43, 41-43, 42-43, 43,
45, 45-54, and 45-68, or having a duplication of exon 44.
Furthermore, the removal of a flanking exon, such as, for example,
exon 43 or exon 45, because of a nonsense point mutation in the
flanking exon, will result in an out of frame transcript. The
additional skipping of exon 44, in combination with skipping of the
flanking exon, will restore the reading frame of the DMD gene in
myogenic cells or muscle cells of DMD patients. Non-limiting
examples of such mutations are nonsense point mutations in the
flanking exons 43 or 45, requiring exon 43+44 skipping or exon
44+45 skipping respectively.
[0014] In an embodiment, a method of the invention may also
alleviate one or more characteristics of a myogenic cell or muscle
cell of a strong BMD patient, to the characteristics of a mild BMD
patient. The characteristics of a cell of a DMD or BMD patient
include increased calcium uptake by muscle cells, increased
collagen synthesis, altered morphology, altered lipid biosynthesis,
increased oxidative stress, and/or damaged sarcolemma. Preferred
embodiments of a method of the invention are later defined
herein.
[0015] In one embodiment, a molecule as defined herein can be a
compound molecule that binds and/or is complementary to the
specified sequence, or a protein such as an RNA-binding protein or
a non-natural zinc-finger protein that has been modified to be able
to bind to the indicated nucleotide sequence on a RNA molecule.
Methods for screening compound molecules that bind specific
nucleotide sequences are, for example, disclosed in PCT/NL01/00697
and U.S. Pat. No. 6,875,736, which are herein incorporated by
reference. Methods for designing RNA-binding Zinc-finger proteins
that bind specific nucleotide sequences are disclosed by Friesen
and Darby, Nature Structural Biology 5: 543-546 (1998) which is
herein incorporated by reference. Binding to one of the specified
SEQ ID NO: 1, 2, 3, or 4 sequence, preferably in the context of
exon 44 of DMD may be assessed via techniques known to the skilled
person. A preferred technique is gel mobility shift assay as
described in EP 1 619 249. In a preferred embodiment, a molecule is
said to bind to one of the specified sequences as soon as a binding
of said molecule to a labelled sequence SEQ ID NO: 1, 2, 3 or 4 is
detectable in a gel mobility shift assay. Alternatively or in
combination with previous embodiment, a molecule is an
oligonucleotide which is complementary or substantially
complementary to SEQ ID NO:1, 2, 3, or 4 or part thereof as later
defined herein. The term "substantially" complementary used in this
context indicates that one or two or more mismatches may be allowed
as long as the functionality, i.e., inducing skipping of exon 44,
is still acceptable.
[0016] The invention provides a method for designing a molecule,
preferably an oligonucleotide able to induce the skipping of exon
44 of the DMD gene. First said oligonucleotide is selected to bind
to one of SEQ ID NO: 1, 2, 3, or 4 or parts thereof as earlier
defined herein. Subsequently, in a preferred method at least one of
the following aspects has to be taken into account for designing,
improving said molecule any further: [0017] The molecule does not
contain a CpG, [0018] The molecule does not contain a G-quartet
motif, [0019] The molecule has acceptable RNA binding kinetics
and/or thermodynamic properties.
[0020] The presence of a CpG in an oligonucleotide is usually
associated with an increased immunogenicity of said oligonucleotide
(Dorn and Kippenberger, Curr Opin Mol Ther 2008 10(1) 10-20). This
increased immunogenicity is undesired since it may induce the
breakdown of muscle fibers. Immunogenicity may be assessed in an
animal model by assessing the presence of CD4.sup.+ and/or
CD8.sup.+ cells and/or inflammatory mononucleocyte infiltration in
muscle biopsy of said animal. Immunogenicity may also be assessed
in blood of an animal or of a human being treated with an
oligonucleotide of the invention by detecting the presence of a
neutralizing antibody and/or an antibody recognizing said
oligonucleotide using a standard immunoassay known to the skilled
person. An increase in immunogenicity may be assessed by detecting
the presence or an increasing amount of a neutralizing antibody or
an antibody recognizing said oligonucleotide using a standard
immunoassay.
[0021] An oligonucleotide comprising a G-quartet motif has the
tendency to form a quadruplex, a multimer or aggregate formed by
the Hoogsteen base-pairing of four single-stranded oligonucleotides
(Cheng and Van Dyke, Gene. 1997 Sep. 15; 197(1-2):253-60), which is
of course not desired: as a result, the efficiency of the
oligonucleotide is expected to be decreased. Multimerization or
aggregation is preferably assessed by standard polyacrylamide
non-denaturing gel electrophoresis techniques known to the skilled
person. In a preferred embodiment, less than 20% or 15%, 10%, 7%,
5% or less of a total amount of an oligonucleotide of the invention
has the capacity to multimerise or aggregate assessed using the
assay mentioned above.
[0022] The invention allows designing an oligonucleotide with
acceptable RNA binding kinetics and/or thermodynamic properties.
The RNA binding kinetics and/or thermodynamic properties are at
least in part determined by the melting temperature of an
oligonucleotide (Tm; calculated with the oligonucleotide properties
calculator (www.unc.edu/.about.cail/biotool/oligo/index.html) for
single stranded RNA using the basic Tm and the nearest neighbor
model), and/or the free energy of the AON-target exon complex
(using RNA structure version 4.5). If a Tm is too high, the
oligonucleotide is expected to be less specific. An acceptable Tm
and free energy depend on the sequence of the oligonucleotide.
Therefore, it is difficult to give preferred ranges for each of
these parameters. An acceptable Tm may be ranged between 35 and
65.degree. C. and an acceptable free energy may be ranged between
15 and 45 kcal/mol.
[0023] The skilled person may therefore first choose an
oligonucleotide as a potential therapeutic compound as binding
and/or being complementary to SEQ ID NO:1, 2, 3, or 4 of exon 44 or
parts thereof as defined herein. The skilled person may check that
said oligonucleotide is able to bind to said sequences as earlier
defined herein. Optionally in a second step, he may use the
invention to further optimise said oligonucleotide by checking for
the absence of CpG, the absence of a G-quartet motif, and/or by
optimizing its Tm and/or free energy of the AON-target complex. He
may try to design an oligonucleotide wherein no CpG and/or no
G-quartet motif are present and/or wherein a more acceptable Tm
and/or free energy are obtained by choosing a distinct sequence of
exon 44 (for example SEQ ID NO:1, 2, 3, or 4) to which the
oligonucleotide is complementary. Alternatively, if an
oligonucleotide complementary to a given stretch within SEQ ID
NO:1, 2, 3 or 4 of exon 44, comprises a CpG, a G-quartet motif
and/or does not have an acceptable Tm and/or free energy, the
skilled person may improve any of these parameters by decreasing
the length of the oligonucleotide, and/or by choosing a distinct
stretch within any of SEQ ID NO: 1, 2, 3, or 4 to which the
oligonucleotide is complementary and/or by altering the chemistry
of the oligonucleotide.
[0024] As an example, if one chooses SEQ ID NO:1, several
oligonucleotides were designed which were found to bind this
sequence: SEQ ID NO: 5, 41, and 46. The oligonucleotide comprising
SEQ ID NO:5 was found to have the most optimal RNA binding kinetics
and/or thermodynamic properties, such as the most optimal Tm. When
we tested the functionality of these oligonucleotides to induce the
skipping of exon 44, it was confirmed that an oligonucleotide
comprising SEQ ID NO:5 is the most efficient of these four
oligonucleotides. Each of these oligonucleotides is functional in
the sense of the invention. However, an oligonucleotide comprising
SEQ ID NO:5 is the most preferred oligonucleotide identified that
binds and/or is complementary to SEQ ID NO:1.
[0025] At any step of the method, an oligonucleotide of the
invention is preferably an oligonucleotide, which is still able to
exhibit an acceptable level of a functional activity. A functional
activity of said oligonucleotide is preferably to induce the
skipping of exon 44 of the DMD gene to a certain extent, to provide
an individual with a functional dystrophin protein and/or mRNA
and/or at least in part decreasing the production of an aberrant
dystrophin protein and/or mRNA. Each of these features is later
defined herein. Such functional activity may be measured in a
muscular tissue or in a muscular cell of an individual or in vitro
in a cell. The assessment of the functionality may be carried out
at the mRNA level, preferably using RT-PCR. The assessment of the
functionality may be carried out at the protein level, preferably
using western blot analysis or immunofluorescence analysis of
cross-sections. In a preferred embodiment, an oligonucleotide is
said to induce skipping of exon 44 of a DMD gene, when tested in a
muscle cell of a DMD patient, by RT-PCR, the exon 44 skipping
percentage is of at least 30%, or at least 35%, or at least 40%, or
at least 45%, or at least 50%, or at least 55%, or at least 60%, or
at least 65%, or at least 70%, or at least 75%, or at least 80%, or
at least 85%, or at least 90%, or at least 95%, or 100%.
[0026] In a preferred embodiment, such oligonucleotide is
preferably a medicament. More preferably, said medicament is for
preventing or treating Duchenne Muscular Dystrophy or Becker
Muscular Dystrophy in an individual or a patient. As defined herein
a DMD pre-mRNA preferably means the pre-mRNA of a DMD gene of a DMD
or BMD patient. A patient is preferably intended to mean a patient
having DMD or BMD or a patient susceptible to develop DMD or BMD
due to his or her genetic background.
[0027] In the case of a DMD patient, an oligonucleotide used will
preferably correct at least one of the DMD mutations as present in
the DMD gene of said patient and therefore will preferably create a
dystrophin that will look like a BMD dystrophin: said dystrophin
will preferably be a functional dystrophin as later defined
herein.
[0028] In the case of a BMD patient, an oligonucleotide as used
will preferably correct at least one of the BMD mutations as
present in the DMD gene of said patient and therefore will
preferably create a, or more of a, dystrophin, which will be more
functional than the dystrophin which was originally present in said
BMD patient. Even more preferably, said medicament increases the
production of a functional or more functional dystrophin protein
and/or mRNA and/or at least in part decreases the production of an
aberrant or less functional dystrophin protein and/or mRNA in an
individual.
[0029] Preferably, a method of the invention increases production
of a more functional dystrophin protein and/or mRNA and/or
decreases the production of an aberrant or less functional
dystrophin protein and/or mRNA in a patient, by inducing and/or
promoting skipping of at least exon 44 of the DMD pre-mRNA as
identified herein in one or more cells, preferably muscle cells of
said patient.
[0030] Increasing the production of a more functional dystrophin
protein and/or mRNA and/or decreasing the production of an aberrant
dystrophin protein and/or mRNA in a patient is typically applied in
a DMD patient. Increasing the production of a more functional or
functional dystrophin and/or mRNA is typically applied in a BMD
patient.
[0031] Therefore, a preferred method is a method, wherein in a
patient or in one or more cells of said patient, production of a
more functional or functional dystrophin protein and/or mRNA is
increased and/or the production of an aberrant dystrophin protein
and/or mRNA in said patient is decreased, wherein the level of said
aberrant or more functional dystrophin protein and/or mRNA is
assessed by comparison to the level of said dystrophin and/or mRNA
in said patient at the onset of the method.
[0032] As defined herein, a functional dystrophin is preferably a
wild type dystrophin corresponding to a protein having the amino
acid sequence as identified in SEQ ID NO: 47. A functional
dystrophin is preferably a dystrophin, which has an actin binding
domain in its N terminal part (first 240 amino acids at the N
terminus), a cystein-rich domain (amino acid 3361 till 3685) and a
C terminal domain (last 325 amino acids at the C terminus) each of
these domains being present in a wild type dystrophin as known to
the skilled person. The amino acids indicated herein correspond to
amino acids of the wild type dystrophin being represented by SEQ ID
NO: 47. In another embodiment, a functional dystrophin is a
dystrophin, which exhibits at least to some extent an activity of a
wild type dystrophin. "At least to some extent" preferably means at
least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% of a
corresponding activity of a wild type functional dystrophin. In
this context, an activity of a wild type dystrophin is preferably
binding to actin and to the dystrophin-associated glycoprotein
complex (DGC) (Aartsma-Rus A et al, (2006), Entries in the leiden
Duchenne Muscular Dystrophy mutation database: an overview of
mutation types and paradoxical cases that confirm the reading-frame
rule, Muscle Nerve, 34: 135-144.). Binding of dystrophin to actin
and to the DGC complex may be visualized by either
co-immunoprecipitation using total protein extracts or
immunofluorescence analysis of cross-sections, from a biopsy of a
muscle suspected to be dystrophic, as known to the skilled
person.
[0033] Individuals suffering from Duchenne muscular dystrophy
typically have a mutation in the gene encoding dystrophin that
prevents synthesis of the complete protein, i.e., a premature stop
prevents the synthesis of the C-terminus of the protein. In Becker
muscular dystrophy the dystrophin gene also comprises a mutation
compared to the wild type but the mutation does typically not
include a premature stop and the C-terminus of the protein is
typically synthesized. As a result, a functional dystrophin protein
is synthesized that has at least the same activity in kind as a
wild type protein, although not necessarily the same amount of
activity. In a preferred embodiment, a functional dystrophin
protein means an in frame dystrophin gene. The genome of a BMD
individual typically encodes a dystrophin protein comprising the N
terminal part (first 240 amino acids at the N terminus), a
cystein-rich domain (amino acid 3361 till 3685) and a C terminal
domain (last 325 amino acids at the C terminus) but its central rod
shaped domain may be shorter than the one of a wild type dystrophin
(Aartsma-Rus A et al, (2006), Entries in the leiden Duchenne
Muscular Dystrophy mutation database: an overview of mutation types
and paradoxical cases that confirm the reading-frame rule, Muscle
Nerve, 34: 135-144). The amino acids indicated herein correspond to
amino acids of the wild type dystrophin being represented by SEQ ID
NO: 47. Exon-skipping for the treatment of DMD is preferably but
not exclusively directed to overcome a premature stop in the
pre-mRNA by skipping an exon in the rod-domain shaped domain to
correct the reading frame and allow synthesis of remainder of the
dystrophin protein including the C-terminus, albeit that the
protein is somewhat smaller as a result of a smaller rod domain. In
a preferred embodiment, an individual having DMD and being treated
using an oligonucleotide as defined herein will be provided a
dystrophin, which exhibits at least to some extent an activity of a
wild type dystrophin. More preferably, if said individual is a
Duchenne patient or is suspected to be a Duchenne patient, a
functional dystrophin is a dystrophin comparable in functionality
to a dystrophin from an individual having BMD: preferably said
dystrophin is able to interact with both actin and the DGC, but its
central rod shaped domain may be shorter than the one of a wild
type dystrophin (Aartsma-Rus A et al, (2006), Entries in the leiden
Duchenne Muscular Dystrophy mutation database: an overview of
mutation types and paradoxical cases that confirm the reading-frame
rule, Muscle Nerve, 34: 135-144). The central rod domain of wild
type dystrophin comprises 24 spectrin-like repeats (Aartsma-Rus A
et al, (2006), Entries in the leiden Duchenne Muscular Dystrophy
mutation database: an overview of mutation types and paradoxical
cases that confirm the reading-frame rule, Muscle Nerve, 34:
135-144). For example, a central rod shaped domain of a dystrophin
as provided herein may comprise 5 to 23, 10 to 22 or 12 to 18
spectrin-like repeats as long as it can bind to actin and to
DGC.
[0034] Decreasing the production of an aberrant dystrophin in said
patient or in a cell of said patient may be assessed at the mRNA
level and preferably means that 99%, 90%, 80%, 70%, 60%, 50%, 40%,
30%, 20%, 10%, 5% or less of the initial amount of aberrant
dystrophin mRNA, is still detectable by RT PCR. An aberrant
dystrophin mRNA or protein is also referred to herein as a
non-functional or less to non-functional or semi-functional
dystrophin mRNA or protein. A non-functional pre-mRNA dystrophin
preferably leads to an out of frame dystrophin protein, which means
that no dystrophin protein will be produced and/or detected. A non
functional dystrophin protein is preferably a dystrophin protein
which is not able to bind actin and/or members of the DGC protein
complex. A non-functional dystrophin protein or dystrophin mRNA
does typically not have, or does not encode a dystrophin protein
with an intact C-terminus of the protein.
[0035] Increasing the production of a functional dystrophin in a
patient or in a cell of said patient may be assessed at the mRNA
level (by RT-PCR analysis) and preferably means that a detectable
amount of a functional or in frame dystrophin mRNA is detectable by
RT PCR. In another embodiment, 1%, 5%, 10%, 20%, 30%, 40%, 50%,
60%, 70%, 80%, 90% or more of the detectable dystrophin mRNA is a
functional or in frame dystrophin mRNA.
[0036] Increasing the production of a functional dystrophin in a
patient or in a cell of said patient may be assessed at the protein
level (by immunofluorescence and western blot analyses) and
preferably means that a detectable amount of a functional
dystrophin protein is detectable by immunofluorescence or western
blot analysis. In another embodiment, 1%, 5%, 10%, 20%, 30%, 40%,
50%, 60%, 70%, 80%, 90% or more of the detectable dystrophin
protein is a functional dystrophin protein.
[0037] An increase or a decrease is preferably assessed in a
muscular tissue or in a muscular cell of an individual or a patient
by comparison to the amount present in said individual or patient
before treatment with said molecule or composition of the
invention. Alternatively, the comparison can be made with a
muscular tissue or cell of said individual or patient, which has
not yet been treated with said oligonucleotide or composition in
case the treatment is local.
[0038] In a further aspect, there is provided a method for
alleviating one or more symptom(s) of Duchenne Muscular Dystrophy
or Becker Muscular Dystrophy in an individual or alleviate one or
more characteristic(s) of a myogenic or muscle cell of said
individual, the method comprising administering to said individual
an oligonucleotide or a composition as defined herein.
[0039] There is further provided a method for enhancing, inducing
or promoting skipping of an exon from a dystrophin pre-mRNA in a
cell expressing said pre-mRNA in an individual suffering from
Duchenne Muscular Dystrophy or Becker Muscular Dystrophy, the
method comprising administering to said individual an
oligonucleotide or a composition as defined herein. Further
provided is a method for increasing the production of a functional
dystrophin protein and/or decreasing the production of an aberrant
dystrophin protein in a cell, said cell comprising a pre-mRNA of a
dystrophin gene encoding an aberrant dystrophin protein, the method
comprising providing said cell with an oligonucleotide or
composition of the invention and allowing translation of mRNA
produced from splicing of said pre-mRNA. In one embodiment, said
method is performed in vivo, for instance using a cell culture.
Preferably, said method is in vivo in said individual. In this
context, increasing the production of a functional dystrophin
protein has been defined herein.
[0040] Alleviating one or more symptom(s) of Duchenne Muscular
Dystrophy or Becker Muscular Dystrophy in an individual using a
molecule or a composition of the invention may be assessed by any
of the following assays: prolongation of time to loss of walking,
improvement of muscle strength, improvement of the ability to lift
weight, improvement of the time taken to rise from the floor,
improvement in the nine-meter walking time, improvement in the time
taken for four-stairs climbing, improvement of the leg function
grade, improvement of the pulmonary function, improvement of
cardiac function, improvement of the quality of life. Each of these
assays is known to the skilled person. As an example, the
publication of Manzur at al (Manzur A Y et al, (2008),
Glucocorticoid corticosteroids for Duchenne muscular dystrophy
(review), Wiley publishers, The Cochrane collaboration) gives an
extensive explanation of each of these assays. For each of these
assays, as soon as a detectable improvement or prolongation of a
parameter measured in an assay has been found, it will preferably
mean that one or more symptoms of Duchenne Muscular Dystrophy or
Becker Muscular Dystrophy has been alleviated in an individual
using a molecule or composition of the invention. Detectable
improvement or prolongation is preferably a statistically
significant improvement or prolongation as described in Hodgetts et
al (Hodgetts S., et al, (2006), Neuromuscular Disorders, 16:
591-602).
[0041] Alternatively, the alleviation of one or more symptom(s) of
Duchenne Muscular Dystrophy or Becker Muscular Dystrophy may be
assessed by measuring an improvement of a characteristic of a
muscle fiber relating to its function, integrity and/or survival,
said characteristic being assessed on the patient self. Such
characteristics may be assessed at the cellular, tissue level of a
given patient. An alleviation of one or more characteristics may be
assessed by any of the following assays on a myogenic cell or
muscle cell from a patient: reduced calcium uptake by muscle cells,
decreased collagen synthesis, altered morphology, altered lipid
biosynthesis, decreased oxidative stress, and/or improved muscle
fiber function, integrity, and/or survival. These parameters are
usually assessed using immunofluorescence and/or histochemical
analyses of cross sections of muscle biopsies.
[0042] An oligonucleotide as used herein preferably comprises an
antisense oligonucleotide or antisense oligoribonucleotide. In a
preferred embodiment an exon skipping technique is applied. Exon
skipping interferes with the natural splicing processes occurring
within a eukaryotic cell. In higher eukaryotes the genetic
information for proteins in the DNA of the cell is encoded in exons
which are separated from each other by intronic sequences. These
introns are in some cases very long. The transcription machinery of
eukaryotes generates a pre-mRNA which contains both exons and
introns, while the splicing machinery, often already during the
production of the pre-mRNA, generates the actual coding region for
the protein by splicing together the exons present in the
pre-mRNA.
[0043] Exon-skipping results in mature mRNA that lacks at least one
skipped exon. Thus, when said exon codes for amino acids, exon
skipping leads to the expression of an altered product. Technology
for exon-skipping is currently directed towards the use of
antisense oligonucleotides (AONs). Much of this work is done in the
mdx mouse model for Duchenne muscular dystrophy. The mdx mouse
carries a nonsense mutation in exon 23. Despite the mdx mutation,
which should preclude the synthesis of a functional dystrophin
protein, rare, naturally occurring dystrophin positive fibers have
been observed in mdx muscle tissue. These dystrophin-positive
fibers are thought to have arisen from an apparently naturally
occurring exon-skipping mechanism, either due to somatic mutations
or through alternative splicing. AONs directed to, respectively,
the 3' and/or 5' splice sites of introns 22 and 23 in dystrophin
pre-mRNA, have been shown to interfere with factors normally
involved in removal of intron 23 so that also exon 23 was removed
from the mRNA (Alter J, et al. Systemic delivery of morpholino
oligonucleotide restores dystrophin expression bodywide and
improves dystrophic pathology. Nat Med 2006; 12(2):175-7, Lu Q L,
et al. Functional amounts of dystrophin produced by skipping the
mutated exon in the mdx dystrophic mouse. Nat Med 2003; 6:6, Lu Q
L, et al. Systemic delivery of antisense oligoribonucleotide
restores dystrophin expression in body-wide skeletal muscles. Proc
Natl Acad Sci USA 2005; 102(1):198-203, Mann C J, et al, Improved
antisense oligonucleotide induced exon skipping in the mdx mouse
model of muscular dystrophy. J Gene Med 2002; 4(6):644-54 or Graham
I R, et al, Towards a therapeutic inhibition of dystrophin exon 23
splicing in mdx mouse muscle induced by antisense
oligoribonucleotides (splicomers): target sequence optimisation
using oligonucleotide arrays. J Gene Med 2004; 6(10):1149-58).
[0044] By the targeted skipping of a specific exon, a DMD phenotype
is converted into a milder BMD phenotype. The skipping of an exon
is preferably induced by the binding of AONs targeting
exon-internal sequences. An oligonucleotide directed toward an exon
internal sequence typically exhibits no overlap with non-exon
sequences. It preferably does not overlap with the splice sites at
least not insofar, as these are present in the intron. An
oligonucleotide directed toward an exon internal sequence
preferably does not contain a sequence complementary to an adjacent
intron. Further provided is thus an oligonucleotide according to
the invention, wherein said oligonucleotide, or a functional
equivalent thereof, is for inhibiting inclusion of an exon of a
dystrophin pre-mRNA into mRNA produced from splicing of said
pre-mRNA. An exon skipping technique is preferably applied such
that the absence of an exon from mRNA produced from dystrophin
pre-mRNA generates a coding region for a more functional--albeit
shorter--dystrophin protein. In this context, inhibiting inclusion
of an exon preferably means that the detection of the original,
aberrant dystrophin mRNA and/or protein is decreased as earlier
defined herein.
[0045] Within the context of the invention, a functional equivalent
of an oligonucleotide preferably means an oligonucleotide as
defined herein wherein one or more nucleotides have been
substituted and wherein an activity of said functional equivalent
is retained to at least some extent. Preferably, an activity of
said functional equivalent is providing a functional dystrophin
protein. Said activity of said functional equivalent is therefore
preferably assessed by quantifying the amount of a functional
dystrophin protein or by quantifying the amount of a functional
dystrophin mRNA. A functional dystrophin protein (or a functional
dystrophin mRNA) is herein preferably defined as being a dystrophin
protein (or a dystrophin protein encoded by said mRNA) able to bind
actin and members of the DGC protein. The assessment of said
activity of an oligonucleotide is preferably done by RT-PCR (m-RNA)
or by immunofluorescence or Western blot analyses (protein). Said
activity is preferably retained to at least some extent when it
represents at least 50%, or at least 60%, or at least 70% or at
least 80% or at least 90% or at least 95% or more of corresponding
activity of said oligonucleotide the functional equivalent derives
from. Such activity may be measured in a muscular tissue or in a
muscular cell of an individual or in vitro in a cell by comparison
to an activity of a corresponding oligonucleotide of said
oligonucleotide the functional equivalent derives from. Throughout
this application, when the word oligonucleotide is used it may be
replaced by a functional equivalent thereof as defined herein.
[0046] In a preferred embodiment, an oligonucleotide of the
invention, which comprises a sequence that binds and/or is
complementary to a sequence of exon 44 of dystrophin pre-mRNA as
earlier defined herein is such that the complementary part is at
least 50% of the length of the oligonucleotide of the invention,
more preferably at least 60%, even more preferably at least 70%,
even more preferably at least 80%, even more preferably at least
90% or even more preferably at least 95%, or even more preferably
98% or even more preferably at least 99%, or even more preferably
100%. In a most preferred embodiment, an oligonucleotide of the
invention consists of a sequence that is complementary to part of
dystrophin pre-mRNA as defined herein. As an example, an
oligonucleotide may comprise a sequence that is complementary to
part of dystrophin pre-mRNA as defined herein and additional
flanking sequences. In a more preferred embodiment, the length of
said complementary part of said oligonucleotide is of at least 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,
43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
or 60 nucleotides. Preferably, additional flanking sequences are
used to modify the binding of a protein to the oligonucleotide, or
to modify a thermodynamic property of the oligonucleotide, more
preferably to modify target RNA binding affinity.
[0047] It is thus not absolutely required that all the bases in the
region of complementarity are capable of pairing with bases in the
opposing strand. For instance, when designing the oligonucleotide,
one may want to incorporate for instance a residue that does not
base pair with the base on the complementary strand. Mismatches
may, to some extent, be allowed, if under the circumstances in the
cell, the stretch of nucleotides is sufficiently capable of
hybridising to the complementary part. In this context,
"sufficiently" preferably means that using a gel mobility shift
assay as described in example 1 of EP 1 619 249, binding of an
oligonucleotide is detectable. Optionally, said oligonucleotide may
further be tested by transfection into muscle cells of patients.
Skipping of the targeted exon may be assessed by RT-PCR (as
described in EP 1 619 249). The complementary regions are
preferably designed such that, when combined, they are specific for
the exon in the pre-mRNA. Such specificity may be created with
various lengths of complementary regions as this depends on the
actual sequences in other (pre-)mRNA in the system. The risk that
also one or more other pre-mRNA will be able to hybridise to the
oligonucleotide decreases with increasing size of the
oligonucleotide. It is clear that oligonucleotides comprising
mismatches in the region of complementarity but that retain the
capacity to hybridise and/or bind to the targeted region(s) in the
pre-mRNA, can be used in the present invention. However, preferably
at least the complementary parts do not comprise such mismatches as
these typically have a higher efficiency and a higher specificity,
than oligonucleotides having such mismatches in one or more
complementary regions. It is thought that higher hybridisation
strengths, (i.e. increasing number of interactions with the
opposing strand) are favourable in increasing the efficiency of the
process of interfering with the splicing machinery of the system.
Preferably, the complementarity is between 90 and 100%. In general,
this allows for 1 or 2 mismatch(es) in an oligonucleotide of 20
nucleotides or 1, 2, 3 or 4 mismatches in an oligonucleotide of 40
nucleotides, or 1, 2, 3, 4, 5 or 6 mismatches in an oligonucleotide
of 60 nucleotides.
[0048] A preferred molecule of the invention comprises or consists
of a nucleotide-based sequence that is antisense to a sequence
selected from exon 44 of the DMD pre-mRNA. The sequence of the DMD
pre-mRNA is preferably selected from SEQ ID NO 1:
5'-GUGGCUAACAGAAGCU; SEQ ID NO 2: 5'-GGGAACAUGCUAAAUAC, SEQ ID NO
3: 5'-AGACACAAAUUCCUGAGA, and SEQ ID NO 4: 5'-CUGUUGAGAAA.
[0049] A molecule of the invention is preferably an isolated
molecule. A molecule of the invention is preferably a nucleic acid
molecule or a nucleotide-based molecule or an oligonucleotide or an
antisense oligonucleotide which binds and/or is complementary to a
sequence of exon 44 selected from SEQ ID NO:1, 2, 3 or 4.
[0050] A preferred molecule of the invention comprises or consists
of from about 8 to about 60 nucleotides, more preferred from about
10 to about 50 nucleotides, more preferred from about 17 to about
40 nucleotides, more preferred from about 18 to about 30
nucleotides, more preferred from about 18 to about 24 nucleotides,
most preferred about 20 nucleotides, such as 18 nucleotides, 19
nucleotides, 20 nucleotides, 21 nucleotides, 22 nucleotides or 23
nucleotides.
[0051] A preferred molecule of the invention comprises or consists
of from 8 to 60 nucleotides, more preferred from 10 to 50
nucleotides, more preferred from 17 to 40 nucleotides, more
preferred from 18 to 30 nucleotides, more preferred from 21 to 60,
more preferred from 22 to 55, more preferred from 23 to 53, more
preferred from 24 to 50, more preferred from 25 to 45, more
preferred from 26 to 43, more preferred from 27 to 41, more
preferred from 28 to 40, more preferred from 29 to 40, more
preferred from 18 to 24 nucleotides, or preferably comprises or
consists of 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,
42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,
59, or 60 nucleotides.
[0052] In certain embodiments, the invention provides a molecule
comprising or consisting of an antisense nucleotide sequence
selected from the antisense nucleotide sequences depicted in Table
1A.
[0053] A molecule or nucleic acid molecule of the invention that
binds and/or is complementary and/or is antisense to a nucleotide
having nucleotide sequence: SEQ ID NO 1: 5'-GUGGCUAACAGAAGCU
preferably comprises or consists of the antisense nucleotide
sequence of SEQ ID NO 5; SEQ ID NO 6, SEQ ID NO 7, SEQ ID NO 8, SEQ
ID NO 9, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 12, SEQ ID NO 13,
SEQ ID NO 14, SEQ ID NO 15, SEQ ID NO 16, SEQ ID NO 17, SEQ ID NO
18, SEQ ID NO 19, SEQ ID NO 20, SEQ ID NO 21, SEQ ID NO 22, SEQ ID
NO 23, SEQ ID NO 24, SEQ ID NO 25, SEQ ID NO 26, SEQ ID NO 27, SEQ
ID NO 28, SEQ ID NO 29, SEQ ID NO 30, SEQ ID NO 31, SEQ ID NO 32,
SEQ ID NO 33, SEQ ID NO 34, SEQ ID NO:41 or SEQ ID NO: 46. A
preferred molecule that targets this region of the DMD pre-mRNA
comprises or consists of the antisense nucleotide sequence of SEQ
ID NO:5, SEQ ID NO 41, or SEQ ID NO 46. Most preferred
oligonucleotide comprises or consists of the antisense nucleotide
sequence of SEQ ID NO:5.
[0054] In a more preferred embodiment, the invention provides a
molecule comprising or consisting of the antisense nucleotide
sequence SEQ ID NO 5: 5'-UCAGCUUCUGUUAGCCACUG. It was found that
this molecule is very efficient in modulating splicing of exon 44
of the DMD gene in muscle cells. This preferred molecule of the
invention comprising SEQ ID NO:5 comprises from 21 to 60, more
preferred from 22 to 55, more preferred from 23 to 53, more
preferred from 24 to 50, more preferred from 25 to 45, more
preferred from 26 to 43, more preferred from 27 to 41, more
preferred from 28 to 40, more preferred from 29 to 40, or
preferably comprises or consists of 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60
nucleotides.
[0055] In another preferred embodiment, the invention provides a
molecule comprising or consisting of the antisense nucleotide
sequence SEQ ID NO:41 or 46. These preferred molecules of the
invention comprising either SEQ ID NO:41 or SEQ ID NO:46 further
comprise from 18 to 60, more preferred from 18 to 55, more
preferred from 20 to 53, more preferred from 24 to 50, more
preferred from 25 to 45, more preferred from 26 to 43, more
preferred from 27 to 41, more preferred from 28 to 40, more
preferred from 29 to 40, or preferably comprises or consists of 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
53, 54, 55, 56, 57, 58, 59, or 60 nucleotides.
[0056] In a further embodiment, a molecule of the invention that is
antisense to SEQ ID NO:2: 5'-GGGAACAUGCUAAAUAC preferably comprises
or consists of the antisense nucleotide sequence of SEQ ID NO:35 or
SEQ ID NO:36. These preferred molecules of the invention comprising
either SEQ ID NO:35 or SEQ ID NO:36, further comprise from 17 to 60
nucleotides, more preferred from 18 to 30 nucleotides, more
preferred from 21 to 60, more preferred from 22 to 55, more
preferred from 23 to 53, more preferred from 24 to 50, more
preferred from 25 to 45, more preferred from 26 to 43, more
preferred from 27 to 41, more preferred from 28 to 40, more
preferred from 29 to 40, more preferred from 18 to 24 nucleotides,
or preferably comprises or consists of 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
58, 59, or 60 nucleotides.
[0057] In yet a further embodiment, a molecule of the invention
that is antisense to SEQ ID NO:3: 5'-AGACACAAAUUCCUGAGA preferably
comprises or consists of the antisense nucleotide sequence of SEQ
ID NO:39 or SEQ ID NO:40. These preferred molecules of the
invention comprising either SEQ ID NO:39 or SEQ ID NO:40 further
comprise from 17 to 60 nucleotides, more preferred from 18 to 30
nucleotides, more preferred from 17 to 60, more preferred from 22
to 55, more preferred from 23 to 53, more preferred from 24 to 50,
more preferred from 25 to 45, more preferred from 26 to 43, more
preferred from 27 to 41, more preferred from 28 to 40, more
preferred from 29 to 40, more preferred from 18 to 24 nucleotides,
or preferably comprises or consists of 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
58, 59, or 60 nucleotides.
[0058] In still a further embodiment, a molecule of the invention
that is antisense to SEQ ID NO:4: 5'-CUGUUGAGAAA preferably
comprises or consists of the antisense nucleotide sequence of SEQ
ID NO:37 or SEQ ID NO:38. These preferred molecules of the
invention comprising either SEQ ID NO:37 or SEQ ID NO:38 further
comprise from 11 to 60 nucleotides, more preferred from 11 to 30
nucleotides, more preferred from 11 to 60, or preferably comprises
or consists of 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,
42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,
59, or 60 nucleotides.
[0059] A nucleotide sequence of a molecule of the invention may
contain RNA residues, or one or more DNA residues, and/or one or
more nucleotide analogues or equivalents, as will be further
detailed herein below.
[0060] It is preferred that a molecule of the invention comprises
one or more residues that are modified to increase nuclease
resistance, and/or to increase the affinity of the antisense
nucleotide for the target sequence. Therefore, in a preferred
embodiment, the antisense nucleotide sequence comprises at least
one nucleotide analogue or equivalent, wherein a nucleotide
analogue or equivalent is defined as a residue having a modified
base, and/or a modified backbone, and/or a non-natural
internucleoside linkage, or a combination of these
modifications.
[0061] In a preferred embodiment, the nucleotide analogue or
equivalent comprises a modified backbone. Examples of such
backbones are provided by morpholino backbones, carbamate
backbones, siloxane backbones, sulfide, sulfoxide and sulfone
backbones, formacetyl and thioformacetyl backbones,
methyleneformacetyl backbones, riboacetyl backbones, alkene
containing backbones, sulfamate, sulfonate and sulfonamide
backbones, methyleneimino and methylenehydrazino backbones, and
amide backbones.
[0062] Phosphorodiamidate morpholino oligomers are modified
backbone oligonucleotides that have previously been investigated as
antisense agents. Morpholino oligonucleotides have an uncharged
backbone in which the deoxyribose sugar of DNA is replaced by a six
membered ring and the phosphodiester linkage is replaced by a
phosphorodiamidate linkage.
[0063] Morpholino oligonucleotides are resistant to enzymatic
degradation and appear to function as antisense agents by arresting
translation or interfering with pre-mRNA splicing rather than by
activating RNase H. Morpholino oligonucleotides have been
successfully delivered to tissue culture cells by methods that
physically disrupt the cell membrane, and one study comparing
several of these methods found that scrape loading was the most
efficient method of delivery; however, because the morpholino
backbone is uncharged, cationic lipids are not effective mediators
of morpholino oligonucleotide uptake in cells. A recent report
demonstrated triplex formation by a morpholino oligonucleotide and,
because of the non-ionic backbone, these studies showed that the
morpholino oligonucleotide was capable of triplex formation in the
absence of magnesium.
[0064] It is further preferred that the linkage between the
residues in a backbone do not include a phosphorus atom, such as a
linkage that is formed by short chain alkyl or cycloalkyl
internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl
internucleoside linkages, or one or more short chain heteroatomic
or heterocyclic internucleoside linkages.
[0065] A preferred nucleotide analogue or equivalent comprises a
Peptide Nucleic Acid (PNA), having a modified polyamide backbone
(Nielsen, et al. (1991) Science 254, 1497-1500). PNA-based
molecules are true mimics of DNA molecules in terms of base-pair
recognition. The backbone of the PNA is composed of
N-(2-aminoethyl)-glycine units linked by peptide bonds, wherein the
nucleobases are linked to the backbone by methylene carbonyl bonds.
An alternative backbone comprises a one-carbon extended pyrrolidine
PNA monomer (Govindaraju and Kumar (2005) Chem. Commun, 495-497).
Since the backbone of a PNA molecule contains no charged phosphate
groups, PNA-RNA hybrids are usually more stable than RNA-RNA or
RNA-DNA hybrids, respectively (Egholm et al (1993) Nature 365,
566-568).
[0066] A further preferred backbone comprises a morpholino
nucleotide analog or equivalent, in which the ribose or deoxyribose
sugar is replaced by a 6-membered morpholino ring. A most preferred
nucleotide analog or equivalent comprises a phosphorodiamidate
morpholino oligomer (PMO), in which the ribose or deoxyribose sugar
is replaced by a 6-membered morpholino ring, and the anionic
phosphodiester linkage between adjacent morpholino rings is
replaced by a non-ionic phosphorodiamidate linkage.
[0067] In yet a further embodiment, a nucleotide analogue or
equivalent of the invention comprises a substitution of one of the
non-bridging oxygens in the phosphodiester linkage. This
modification slightly destabilizes base-pairing but adds
significant resistance to nuclease degradation. A preferred
nucleotide analogue or equivalent comprises phosphorothioate,
chiral phosphorothioate, phosphorodithioate, phosphotriester,
aminoalkylphosphotriester, H-phosphonate, methyl and other alkyl
phosphonate including 3'-alkylene phosphonate, 5'-alkylene
phosphonate and chiral phosphonate, phosphinate, phosphoramidate
including 3'-amino phosphoramidate and aminoalkylphosphoramidate,
thionophosphoramidate, thionoalkylphosphonate,
thionoalkylphosphotriester, selenophosphate or boranophosphate.
[0068] A further preferred nucleotide analogue or equivalent of the
invention comprises one or more sugar moieties that are mono- or
disubstituted at the 2', 3' and/or 5' position such as a --OH; --F;
substituted or unsubstituted, linear or branched lower (C1-C10)
alkyl, alkenyl, alkynyl, alkaryl, allyl, or aralkyl, that may be
interrupted by one or more heteroatoms; O-, S-, or N-alkyl; O-, S-,
or N-alkenyl; O-, S- or N-alkynyl; O-, S-, or N-allyl;
O-alkyl-O-alkyl, -methoxy, -aminopropoxy; methoxyethoxy;
-dimethylaminooxyethoxy; and -dimethylaminoethoxyethoxy. The sugar
moiety can be a pyranose or derivative thereof, or a deoxypyranose
or derivative thereof, preferably ribose or derivative thereof, or
deoxyribose or derivative of. A preferred derivatized sugar moiety
comprises a Locked Nucleic Acid (LNA), in which the 2'-carbon atom
is linked to the 3' or 4' carbon atom of the sugar ring thereby
forming a bicyclic sugar moiety. A preferred LNA comprises
2'-0,4'-C-ethylene-bridged nucleic acid (Morita et al. 2001.
Nucleic Acid Res Supplement No. 1: 241-242). These substitutions
render the nucleotide analogue or equivalent RNase H and nuclease
resistant and increase the affinity for the target RNA.
[0069] In another embodiment, a nucleotide analogue or equivalent
of the invention comprises one or more base modifications or
substitutions. Modified bases comprise synthetic and natural bases
such as inosine, xanthine, hypoxanthine and other -aza, deaza,
-hydroxy, -halo, -thio, thiol, -alkyl, -alkenyl, -alkynyl,
thioalkyl derivatives of pyrimidine and purine bases that are or
will be known in the art.
[0070] It is understood by a skilled person that it is not
necessary for all positions in an antisense oligonucleotide to be
modified uniformly. In addition, more than one of the
aforementioned analogues or equivalents may be incorporated in a
single antisense oligonucleotide or even at a single position
within an antisense oligonucleotide. In certain embodiments, an
antisense oligonucleotide of the invention has at least two
different types of analogues or equivalents.
[0071] A preferred antisense oligonucleotide according to the
invention comprises a 2'-O alkyl phosphorothioate antisense
oligonucleotide, such as 2'-O-methyl modified ribose (RNA),
2'-O-ethyl modified ribose, 2'-O-propyl modified ribose, and/or
substituted derivatives of these modifications such as halogenated
derivatives.
[0072] A most preferred antisense oligonucleotide according to the
invention comprises a 2'-O-methyl phosphorothioate ribose.
[0073] It will also be understood by a skilled person that
different antisense oligonucleotides can be combined for
efficiently skipping of exon 44. In a preferred embodiment, a
combination of at least two antisense oligonucleotides are used in
a method of the invention, such as two different antisense
oligonucleotides, three different antisense oligonucleotides, four
different antisense oligonucleotides, or five different antisense
oligonucleotides.
[0074] An antisense oligonucleotide can be linked to a moiety that
enhances uptake of the antisense oligonucleotide in cells,
preferably myogenic cells or muscle cells. Examples of such
moieties are cholesterols, carbohydrates, vitamins, biotin, lipids,
phospholipids, cell-penetrating peptides including but not limited
to antennapedia, TAT, transportan and positively charged amino
acids such as oligoarginine, poly-arginine, oligolysine or
polylysine, antigen-binding domains such as provided by an
antibody, a Fab fragment of an antibody, or a single chain antigen
binding domain such as a cameloid single domain antigen-binding
domain. A preferred antisense oligonucleotide comprises a
peptide-linked PMO.
[0075] An oligonucleotide of the invention may be indirectly
administrated using suitable means known in the art. An
oligonucleotide may for example be provided to an individual or a
cell, tissue or organ of said individual in the form of an
expression vector wherein the expression vector encodes a
transcript comprising said oligonucleotide. The expression vector
is preferably introduced into a cell, tissue, organ or individual
via a gene delivery vehicle. In a preferred embodiment, there is
provided a viral-based expression vector comprising an expression
cassette or a transcription cassette that drives expression or
transcription of a molecule as identified herein. A cell can be
provided with a molecule capable of interfering with essential
sequences that result in highly efficient skipping of exon 44 by
plasmid-derived antisense oligonucleotide expression or viral
expression provided by adenovirus- or adeno-associated virus-based
vectors. Expression is preferably driven by a polymerase III
promoter, such as a U1, a U6, or a U7 RNA promoter. A preferred
delivery vehicle is a viral vector such as an adeno-associated
virus vector (AAV), or a retroviral vector such as a lentivirus
vector (Goyenvalle A, et al. Rescue of dystrophic muscle through U7
snRNA-mediated exon skipping. Science 2004; 306(5702):1796-9, De
Angelis F G, et al. Chimeric snRNA molecules carrying antisense
sequences against the splice junctions of exon 51 of the dystrophin
pre-mRNA induce exon skipping and restoration of a dystrophin
synthesis in Delta 48-50 DMD cells. Proc Natl Acad Sci USA 2002;
99(14):9456-61 or Denti M A, et al. Chimeric adeno-associated
virus/antisense U1 small nuclear RNA effectively rescues dystrophin
synthesis and muscle function by local treatment of mdx mice. Hum
Gene Ther 2006; 17(5):565-74) and the like. Also, plasmids,
artificial chromosomes, plasmids usable for targeted homologous
recombination and integration in the human genome of cells may be
suitably applied for delivery of an oligonucleotide as defined
herein. Preferred for the current invention are those vectors
wherein transcription is driven from PolIII promoters, and/or
wherein transcripts are in the form fusions with U1 or U7
transcripts, which yield good results for delivering small
transcripts. It is within the skill of the artisan to design
suitable transcripts. Preferred are PolIII driven transcripts.
Preferably, in the form of a fusion transcript with an U1 or U7
transcript (see the same Goyenvalle A et al, De Angelis F G et al
or Denti M A et al). Such fusions may be generated as described
(Gorman L, et al, Stable alteration of pre-mRNA splicing patterns
by modified U7 small nuclear RNAs. Proc Natl Acad Sci USA 1998;
95(9):4929-34 or Suter D, et al, Double-target antisense U7 snRNAs
promote efficient skipping of an aberrant exon in three human
beta-thalassemic mutations. Hum Mol Genet 1999; 8(13):2415-23).
[0076] The oligonucleotide may be delivered as is. However, the
oligonucleotide may also be encoded by the viral vector. Typically,
this is in the form of an RNA transcript that comprises the
sequence of the oligonucleotide in a part of the transcript.
[0077] One preferred antisense oligonucleotide expression system is
an adenovirus associated virus (AAV)-based vector. Single chain and
double chain AAV-based vectors have been developed that can be used
for prolonged expression of small antisense nucleotide sequences
for highly efficient skipping of exon 44 of DMD.
[0078] A preferred AAV-based vector comprises an expression
cassette that is driven by a polymerase III-promoter (Pol III). A
preferred Pol III promoter is, for example, a U1, a U6, or a U7 RNA
promoter.
[0079] The invention therefore also provides a viral-based vector,
comprising a Pol III-promoter driven expression cassette for
expression of an antisense oligonucleotide of the invention for
inducing skipping of exon 44 of the DMD gene.
[0080] Improvements in means for providing an individual or a cell,
tissue, organ of said individual with an oligonucleotide and/or an
equivalent thereof, are anticipated considering the progress that
has already thus far been achieved. Such future improvements may of
course be incorporated to achieve the mentioned effect on
restructuring of mRNA using a method of the invention. An
oligonucleotide and/or an equivalent thereof can be delivered as is
to an individual, a cell, tissue or organ of said individual. When
administering an oligonucleotide and/or an equivalent thereof, it
is preferred that an oligonucleotide and/or an equivalent thereof
is dissolved in a solution that is compatible with the delivery
method. Muscle or myogenic cells can be provided with a plasmid for
antisense oligonucleotide expression by providing the plasmid in an
aqueous solution. Alternatively, a plasmid can be provided by
transfection using known transfection agentia. For intravenous,
subcutaneous, intramuscular, intrathecal and/or intraventricular
administration it is preferred that the solution is a physiological
salt solution. Particularly preferred in the invention is the use
of an excipient or transfection agentia that will aid in delivery
of each of the constituents as defined herein to a cell and/or into
a cell, preferably a muscle cell. Preferred are excipients or
transfection agentia capable of forming complexes, nanoparticles,
micelles, vesicles and/or liposomes that deliver each constituent
as defined herein, complexed or trapped in a vesicle or liposome
through a cell membrane. Many of these excipients are known in the
art. Suitable excipients or transfection agentia comprise
polyethylenimine (PEI; ExGen500 (MBI Fermentas)), LipofectAMINE.TM.
2000 (Invitrogen) or derivatives thereof, or similar cationic
polymers, including polypropyleneimine or polyethylenimine
copolymers (PECs) and derivatives, synthetic amphiphils (SAINT-18),
Lipofectin.TM., DOTAP and/or viral capsid proteins that are capable
of self assembly into particles that can deliver each constitutent
as defined herein to a cell, preferably a muscle cell. Such
excipients have been shown to efficiently deliver an
oligonucleotide such as antisense nucleic acids to a wide variety
of cultured cells, including muscle cells. Their high transfection
potential is combined with an excepted low to moderate toxicity in
terms of overall cell survival. The ease of structural modification
can be used to allow further modifications and the analysis of
their further (in vivo) nucleic acid transfer characteristics and
toxicity.
[0081] Lipofectin represents an example of a liposomal transfection
agent. It consists of two lipid components, a cationic lipid
N-[1-(2,3 dioleoyloxy)propyl]-N,N,N-trimethylammonium chloride
(DOTMA) (cp. DOTAP which is the methylsulfate salt) and a neutral
lipid dioleoylphosphatidylethanolamine (DOPE). The neutral
component mediates the intracellular release. Another group of
delivery systems are polymeric nanoparticles.
[0082] Polycations such like diethylaminoethylaminoethyl
(DEAE)-dextran, which are well known as DNA transfection reagent
can be combined with butylcyanoacrylate (PBCA) and
hexylcyanoacrylate (PHCA) to formulate cationic nanoparticles that
can deliver each constituent as defined herein, preferably an
oligonucleotide across cell membranes into cells.
[0083] In addition to these common nanoparticle materials, the
cationic peptide protamine offers an alternative approach to
formulate an oligonucleotide with colloids. This colloidal
nanoparticle system can form so called proticles, which can be
prepared by a simple self-assembly process to package and mediate
intracellular release of an oligonucleotide. The skilled person may
select and adapt any of the above or other commercially available
alternative excipients and delivery systems to package and deliver
an oligonucleotide for use in the current invention to deliver it
for the treatment of Duchenne Muscular Dystrophy or Becker Muscular
Dystrophy in humans.
[0084] In addition, an oligonucleotide could be covalently or
non-covalently linked to a targeting ligand specifically designed
to facilitate the uptake into the cell, cytoplasm and/or its
nucleus. Such ligand could comprise (i) a compound (including but
not limited to peptide(-like) structures) recognising cell, tissue
or organ specific elements facilitating cellular uptake and/or (ii)
a chemical compound able to facilitate the uptake into cells and/or
the intracellular release of an oligonucleotide from vesicles,
e.g., endosomes or lysosomes.
[0085] Therefore, in a preferred embodiment, an oligonucleotide is
formulated in a composition or a medicament or a composition, which
is provided with at least an excipient and/or a targeting ligand
for delivery and/or a delivery device thereof to a cell and/or
enhancing its intracellular delivery. Accordingly, the invention
also encompasses a pharmaceutically acceptable composition
comprising an oligonucleotide and further comprising at least one
excipient and/or a targeting ligand for delivery and/or a delivery
device of said oligonucleotide to a cell and/or enhancing its
intracellular delivery.
[0086] It is to be understood that if a composition comprises an
additional constituent such as an adjunct compound as later defined
herein, each constituent of the composition may not be formulated
in one single combination or composition or preparation. Depending
on their identity, the skilled person will know which type of
formulation is the most appropriate for each constituent as defined
herein. In a preferred embodiment, the invention provides a
composition or a preparation which is in the form of a kit of parts
comprising an oligonucleotide and a further adjunct compound as
later defined herein.
[0087] A preferred oligonucleotide is for preventing or treating
Duchenne Muscular Dystrophy (DMD) or Becker Muscular Dystrophy
(BMD) in an individual. An individual, which may be treated using
an oligonucleotide of the invention may already have been diagnosed
as having a DMD or a BMD. Alternatively, an individual which may be
treated using an oligonucleotide of the invention may not have yet
been diagnosed as having a DMD or a BMD but may be an individual
having an increased risk of developing a DMD or a BMD in the future
given his or her genetic background. A preferred individual is a
human being.
[0088] If required, a molecule or a vector expressing an antisense
oligonucleotide of the invention can be incorporated into a
pharmaceutically active mixture by adding a pharmaceutically
acceptable carrier. Therefore, the invention also provides a
pharmaceutical composition comprising a molecule comprising an
antisense oligonucleotide according to the invention, or a
viral-based vector expressing the antisense oligonucleotide
according to the invention.
[0089] In a further aspect, there is provided a composition
comprising an oligonucleotide as defined herein. Preferably, said
composition comprises at least two distinct oligonucleotides as
defined herein. More preferably, these two distinct
oligonucleotides are designed to skip one or two or more exons.
Multi-skipping is encompassed by the present invention, wherein an
oligonucleotide of the invention inducing the skipping of exon 44
is used in combination with another oligonucleotide inducing the
skipping of another exon. In this context, another exon may be exon
43, 45 or 52. Multi exon skipping has been already disclosed in EP
1 619 249. The DMD gene is a large gene, with many different exons.
Considering that the gene is located on the X-chromosome, it is
mostly boys that are affected, although girls can also be affected
by the disease, as they may receive a bad copy of the gene from
both parents, or are suffering from a particularly biased
inactivation of the functional allele due to a particularly biased
X chromosome inactivation in their muscle cells. The protein is
encoded by a plurality of exons (79) over a range of at least 2.4
Mb. Defects may occur in any part of the DMD gene. Skipping of a
particular exon or particular exons can, very often, result in a
restructured mRNA that encodes a shorter than normal but at least
partially functional dystrophin protein. A practical problem in the
development of a medicament based on exon-skipping technology is
the plurality of mutations that may result in a deficiency in
functional dystrophin protein in the cell. Despite the fact that
already multiple different mutations can be corrected for by the
skipping of a single exon, this plurality of mutations, requires
the generation of a series of different pharmaceuticals as for
different mutations different exons need to be skipped. An
advantage of an oligonucleotide or of a composition comprising at
least two distinct oligonucleotide as later defined herein capable
of inducing skipping of two or more exons, is that more than one
exon can be skipped with a single pharmaceutical. This property is
not only practically very useful in that only a limited number of
pharmaceuticals need to be generated for treating many different
DMD or particular, severe BMD mutations. Another option now open to
the person skilled in the art is to select particularly functional
restructured dystrophin proteins and produce compounds capable of
generating these preferred dystrophin proteins. Such preferred end
results are further referred to as mild phenotype dystrophins.
[0090] In a preferred embodiment, said composition being preferably
a pharmaceutical composition said pharmaceutical composition
comprising a pharmaceutically acceptable carrier, adjuvant, diluent
and/or excipient. Such a pharmaceutical composition may comprise
any pharmaceutically acceptable carrier, filler, preservative,
adjuvant, solubilizer, diluent and/or excipient is also provided.
Such pharmaceutically acceptable carrier, filler, preservative,
adjuvant, solubilizer, diluent and/or excipient may for instance be
found in Remington: The Science and Practice of Pharmacy, 20th
Edition. Baltimore, Md.: Lippincott Williams & Wilkins, 2000.
Each feature of said composition has earlier been defined
herein.
[0091] If several oligonucleotides are used, concentration or dose
already defined herein may refer to the total concentration or dose
of all oligonucleotides used or the concentration or dose of each
oligonucleotide used or added. Therefore, in one embodiment, there
is provided a composition wherein each or the total amount of
oligonucleotide used is dosed in an amount ranged between 0.5 mg/kg
and 10 mg/kg.
[0092] The invention further provides the use of an antisense
oligonucleotide according to the invention, or a viral-based vector
that expresses an antisense oligonucleotide according to the
invention, for modulating splicing of the DMD mRNA. The splicing is
preferably modulated in human myogenic cells or muscle cells in
vitro. More preferred is that splicing is modulated in human
myogenic cells or muscle cells in vivo.
[0093] A preferred antisense oligonucleotide comprising one or more
nucleotide analogs or equivalents of the invention modulates
splicing in one or more muscle cells, including heart muscle cells,
upon systemic delivery. In this respect, systemic delivery of an
antisense oligonucleotide comprising a specific nucleotide analog
or equivalent might result in targeting a subset of muscle cells,
while an antisense oligonucleotide comprising a distinct nucleotide
analog or equivalent might result in targeting of a different
subset of muscle cells. Therefore, in one embodiment it is
preferred to use a combination of antisense oligonucleotides
comprising different nucleotide analogs or equivalents for
modulating skipping of exon 44 of the DMD mRNA.
[0094] The invention furthermore provides the use of an antisense
oligonucleotide according to the invention, or of a viral-based
vector expressing the antisense oligonucleotide according to the
invention, for the preparation of a medicament for the treatment of
a DMD or BMD patient. Therefore, in a further aspect, there is
provided the use of an oligonucleotide or of a composition as
defined herein for the manufacture of a medicament for preventing
or treating Duchenne Muscular Dystrophy or Becker Muscular
Dystrophy in an individual. Each feature of said use has earlier
been defined herein.
[0095] A treatment in a use or in a method according to the
invention is at least one week, at least one month, at least
several months, at least one year, at least 2, 3, 4, 5, 6 years or
more. Each molecule or oligonucleotide or equivalent thereof as
defined herein for use according to the invention may be suitable
for direct administration to a cell, tissue and/or an organ in vivo
of individuals affected by or at risk of developing DMD or BMD, and
may be administered directly in vivo, ex vivo or in vitro. The
frequency of administration of an oligonucleotide, composition,
compound or adjunct compound of the invention may depend on several
parameters such as the age of the patient, the mutation of the
patient, the number of molecules (i.e., dose), the formulation of
said molecule. The frequency may be ranged between at least once in
two weeks, or three weeks or four weeks or five weeks or a longer
time period.
[0096] Dose ranges of oligonucleotide according to the invention
are preferably designed on the basis of rising dose studies in
clinical trials (in vivo use) for which rigorous protocol
requirements exist. A molecule or an oligonucleotide as defined
herein may be used at a dose which is ranged between 0.1 and 20
mg/kg, preferably 0.5 and 10 mg/kg.
[0097] In a preferred embodiment, a concentration of an
oligonucleotide as defined herein, which is ranged between 0.1 nM
and 1 .mu.M is used. Preferably, this range is for in vitro use in
a cellular model such as muscular cells or muscular tissue. More
preferably, the concentration used is ranged between 0.3 to 400 nM,
even more preferably between 1 to 200 nM. If several
oligonucleotides are used, this concentration or dose may refer to
the total concentration or dose of oligonucleotides or the
concentration or dose of each oligonucleotide added.
[0098] The ranges of concentration or dose of oligonucleotide(s) as
given above are preferred concentrations or doses for in vitro or
ex vivo uses. The skilled person will understand that depending on
the oligonucleotide(s) used, the target cell to be treated, the
gene target and its expression levels, the medium used and the
transfection and incubation conditions, the concentration or dose
of oligonucleotide(s) used may further vary and may need to be
optimised any further.
[0099] An oligonucleotide as defined herein for use according to
the invention may be suitable for administration to a cell, tissue
and/or an organ in vivo of individuals affected by or at risk of
developing DMD or BMD, and may be administered in vivo, ex vivo or
in vitro. Said oligonucleotide may be directly or indirectly
administrated to a cell, tissue and/or an organ in vivo of an
individual affected by or at risk of developing DMD or BMD, and may
be administered directly or indirectly in vivo, ex vivo or in
vitro. As Duchenne and Becker muscular dystrophy have a pronounced
phenotype in muscle cells, it is preferred that said cells are
muscle cells, it is further preferred that said tissue is a
muscular tissue and/or it is further preferred that said organ
comprises or consists of a muscular tissue. A preferred organ is
the heart. Preferably, said cells comprise a gene encoding a mutant
dystrophin protein. Preferably, said cells are cells of an
individual suffering from DMD or BMD.
[0100] Unless otherwise indicated each embodiment as described
herein may be combined with another embodiment as described herein.
In this document and in its claims, the verb "to comprise" and its
conjugations is used in its non-limiting sense to mean that items
following the word are included, but items not specifically
mentioned are not excluded. In addition, the verb "to consist" may
be replaced by "to consist essentially of" meaning that a compound
or adjunct compound as defined herein may comprise additional
component(s) than the ones specifically identified, said additional
component(s) not altering the unique characteristic of the
invention.
[0101] In addition, reference to an element by the indefinite
article "a" or "an" does not exclude the possibility that more than
one of the elements is present, unless the context clearly requires
that there be one and only one of the elements. The indefinite
article "a" or "an" thus usually means "at least one". The word
"approximately" or "about" when used in association with a
numerical value (approximately 10, about 10) preferably means that
the value may be the given value of 10 more or less 1% of the
value.
[0102] The expression "in vivo" as used herein may mean in a
cellular system which may be isolated from the organism the cells
derive from. Preferred cells are muscle cells. In vivo may also
mean in a tissue or in a multicellular organism which is preferably
a patient as defined herein. Throughout the invention, in vivo is
opposed to in vitro which is generally associated with a cell free
system.
[0103] All patent and literature references cited in the present
specification are hereby incorporated by reference in their
entirety. Each embodiment as identified herein may be combined
together unless otherwise indicated.
[0104] The invention is further explained in the following
examples. These examples do not limit the scope of the invention,
but merely serve to clarify the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0105] FIGS. 1A-1C. Evaluation of AONs designed to induce the
skipping of exon 44 from the DMD gene in transfected muscle cells
from healthy control or a DMD patient with an exon 45 deletion.
[0106] (FIG. 1A) In differentiated muscle cells (myotubes) from a
patient with an exon 45 deletion, all tested (transfected) AONs
induced exon 44 skipping at a concentration of 150 nM, with PS188
(SEQ ID NO:5), PS190 (previously published as h44AON2; Aartsma-Rus
et al. Neuromuscul Disord 2002; 12 Suppl: S71), PS191 (SEQ ID NO:
39), PS193 (SEQ ID NO: 40), PS194 (SEQ ID NO: 38), and PS196 (SEQ
ID NO: 43) demonstrating highest efficiencies (between 84% and
94%).
[0107] (FIG. 1B) The majority of AONs was also tested by
transfection into healthy human control cells at 150 and 400 nM
concentrations. The results are summarized in this column chart.
PS188 (SEQ ID NO:5), PS190, PS191 (SEQ ID NO: 39), PS193 (SEQ ID
NO: 40), PS194 (SEQ ID NO: 38), and PS196 (SEQ ID NO: 43) were
confirmed to be most efficient in inducing exon 44 skipping. Note
that the exon 44 skipping levels in patient cells are typically
higher than in control cells as a result of the fact that, in
contrast to healthy cells, in patient cells exon 44 skipping is
frame-restoring and giving rise to a more functional and stable. No
exon 44 skipping was observed in non-transfected muscle cells in
all experiments (data not shown).
[0108] (FIG. 1C) Examples of PS197 (SEQ ID NO 44) and three
additional AONs, PS199 (SEQ ID NO 36), PS200 (SEQ ID NO 41), and
PS201 (SEQ ID NO 42), similarly tested in control muscle cells, at
transfection concentrations 150 nM and 400 nM. The exon 44 skipping
percentages varied between 1% (PS199) and 44% (PS200). M: DNA size
marker (100 bp ladder).
[0109] FIGS. 2A-2B. Further evaluation of PS188 (SEQ ID NO:5) by
transfection of human control muscle cells or peripheral blood
mononuclear cells (PB-MNCs).
[0110] (FIG. 2A) Dose-response experiment. In human control muscle
cells, PS188 showed increasing levels of exon 44 skipping at
transfection doses increasing from 50 nM to 400 nM (in triplo), up
to 45% at 400 nM.
[0111] (FIG. 2B) PB-MNCs of a healthy individual were transfected
with 200 nM PS188. Despite the fact that dystrophin is only
expressed at low levels in this type of cells, exon 44 skipping was
clearly observed. These results confirm the efficiency of PS188 in
inducing exon 44 skipping from the DMD gene. M: DNA size
marker.
[0112] FIGS. 3A-B. Further evaluation of PS188 (SEQ ID NO:5) by
administration to transgenic hDMD mice expressing the full length
human DMD gene, and to cynomolgus monkeys included in extensive
toxicity studies.
[0113] (FIG. 3A) Following intramuscular injection of 2.times.40
.mu.g PS188 into both gastrocnemius muscles (G1 and G2) of an hDMD
mouse, exon 44 skipping was observed, albeit at low levels. This
confirms the capacity of PS188 to induce human exon 44 skipping in
muscle tissue in vivo. The low levels were expected given the fact
that this mouse model has healthy muscle fibers typically showing
lower levels of AON uptake when compared to dystrophic muscle
fibers. NT: in non-treated hDMD muscle no exon 44 skipping was
observed. M: DNA size marker
[0114] (FIG. 3B) In monkeys included in toxicity studies on PS188,
exon 44 skipping was observed in peripheral blood mononuclear cells
(PB-MNCs) after 1-hour intravenous infusions every fourth day for
29 days at a dose-level of 6 mg/kg PS188. No exon 44 skipping was
observed in non-treated monkeys (NT). M: DNA size marker.
EXAMPLES
Example 1
[0115] Material and Methods
[0116] AON design was based on (partly) overlapping open secondary
structures of the target exon RNA as predicted by the m-fold
program (Mathews et al., J Mol Biol 1999; 288(5): 911-40), on
(partly) overlapping putative SR-protein binding sites as predicted
by the ESE-finder software (rulai.cshl.edu/tools/ESE/) (Cartegni et
al., Nucleic Acids Res 2003; 31(13): 3568-71), and on avoiding
G-stretches of 3 or more nucleotides or CpG pairs. AONs (see Table
1) were synthesized by Eurogentec (Belgium) and Prosensa
Therapeutics BV (Leiden, Netherlands), and contain 2'-O-methyl RNA
and full-length phosphorothioate backbones.
Tissue Culturing, Transfection and RT-PCR Analysis
[0117] Myotube cultures derived from a healthy individual ("human
control") or a DMD patient with an exon 45 deletion were processed
as described previously (Aartsma-Rus et al. Hum Mol Genet 2003;
12(8): 907-14; Havenga et al. J Virol 2002; 76(9): 4612-20). For
the screening of AONs, myotube cultures were transfected with 150
and/or 400 nM of each AON. Transfection reagent polyethylenimine
(PEI, ExGen500 MBI Fermentas) or a derivative (UNIFectylin,
Prosensa Therapeutics BV, Netherlands) was used, with 2 .mu.l
ExGen500 or UNIFectylin per .mu.g AON. A control AON with a
fluorescein label was used to confirm optimal transfection
efficiencies (typically over 90% fluorescent nuclei were obtained).
RNA was isolated 24 to 48 hours after transfection as described
(Aartsma-Rus et al. Neuromuscul Disord 2002; 12 Suppl: S71). Exon
skipping efficiencies were determined by nested RT-PCR analysis
using primers in the exons flanking exon 44 (Aartsma-Rus et al.
Neuromuscul Disord 2002; 12 Suppl: S71). PCR fragments were
isolated from agarose gels (using the QIAquick Gel Extraction Kit
(QIAGEN) for sequence verification (by the Leiden Genome Technology
Center (LGTC) using the BigDye Terminator Cycle Sequencing Ready
Reaction kit (PE Applied Biosystems), and ABI 3700 Sequencer (PE
Applied Biosystems). For quantification, the PCR products were
analyzed using the DNA 1000 LabChips Kit on the Agilent 2100
bioanalyzer (Agilent Technologies, USA).
Results
[0118] A series of AONs targeting sequences within exon 44 were
designed and tested both in healthy control and patient-derived
myotube cultures, by transfection and subsequent RT-PCR and
sequence analysis of isolated RNA. In myotubes derived from a DMD
patient with a deletion of exon 45, specific exon 44 skipping was
induced at 150 nM for every AON (PS187 to PS201) tested, with PS188
(SEQ ID NO:5), PS190 (previously published as h44AON2, Aartsma-Rus
et al. Neuromuscul Disord 2002; 12 Suppl: S71), PS191 (SEQ ID NO:
39), PS193 (SEQ ID NO: 40), PS194 (SEQ ID NO: 38), and PS196 (SEQ
ID NO: 43) demonstrating highest levels of skipping (between 84%
and 94% at 150 nM) (FIG. 1A).
[0119] Similar transfection experiments were done in control cells
from a healthy individual. Percentages of exon 44 skipping were
assessed and compared to those in the patient cell cultures (FIG.
1B). Inherent to nonsense-mediated RNA decay of the control
transcript after exon 44 skipping, the control percentages were
typically lower than those in the patient cells (see for instance
results with PS197 in FIG. 1A (patient cells) vs FIG. 1C (control
cells)).
[0120] Three additional AONs (PS199 (SEQ ID NO 36), PS200 (SEQ ID
NO 41), and PS201 (SEQ ID NO 42) were tested in control muscle
cells, at concentrations of 150 nM and 400 nM. The exon 44 skipping
percentages varied between 1% (PS199) and 44% (PS200) (FIG. 1C).
Based on all transfection experiments, the AONs PS187, PS188,
PS190, PS191, PS192, PS193, PS194, PS196 and PS200 were considered
most efficient, and AONs PS189, PS197, PS198, PS199, and PS201
least efficient.
[0121] PS188 (SEQ ID NO 5) was further tested in dose-response
experiments in healthy human control muscle cells, applying
increasing doses from 50 to 400 nM in triplo. Increasing levels of
exon 44 skipping were accordingly observed, up to 45% at 400
nMPS188 (FIG. 2A).
Example 2
Materials and Methods
[0122] A fresh healthy human control blood sample, collected in an
EDTA tube, was layered on top of a HistoPaque gradient. Upon
centrifugation, the second layer (of the four layers, from top to
bottom) with the mononuclear cells was collected, washed, and
centrifuged again. The cell pellet was resuspended in proliferation
culturing medium and counted. In a 6-wells plate, 8.times.10.sup.6
cells per well were plated and incubated at 37.degree. C., 5%
CO.sub.2 for 3 hrs. The cells were then transfected with 0 or 200
nM PS188 (SEQ ID NO:5; 2'OMePS RNA; Prosensa Therapeutics BV), in
duplo, per dish. RNA was isolated 72 hrs after transfection, and
analysed by RT-PCR analysis using DMD-gene specific primers
flanking exon 44 (Aartsma-Rus et al. Neuromuscul Disord 2002; 12
Suppl: S71). Sequence analysis (by the Leiden Genome Technology
Center (LGTC) using the BigDye Terminator Cycle Sequencing Ready
Reaction kit (PE Applied Biosystems), and ABI 3700 Sequencer (PE
Applied Biosystems) was performed on isolated PCR products (using
the QIAquick Gel Extraction Kit (QIAGEN) to confirm the specific
exon 44 skipping on RNA level.
Results
[0123] In transfected peripheral blood mononuclear cells (PB-MNCs)
from a healthy control individual, PS188 induced the production of
a novel shorter transcript fragment when applied at 200 nM (FIG.
2B). This fragment was isolated and sequenced and confirmed due to
the specific skipping of exon 44. In non-transfected PB-MNCs no
exon 44 skipping was observed. These results indicate that PS188 is
an efficient compound inducing human exon 44 skipping in vitro.
Example 3
Materials and Methods
Antisense Oligoribonucleotides (AONs).
[0124] Normal and mdx mice (Sicinski et al. (1989). Science 244:
1578-1580) were injected with the mouse-specific m46AON4 (van
Deutekom et al. (2001) Hum Mol Genet 10: 1547-1554), whereas the
hDMD mice with the human-specific PS196 (SEQ ID NO 43) or PS188
(SEQ ID NO 5). Both AONs contained a full-length phosphorothioate
backbone and 2'-O-methyl modified ribose molecules (PS196:
Eurogentec, Belgium; PS188: Prosensa Therapeutics BV).
Normal, Mdx and Transgenic hDMD Mice
[0125] Normal mice (C57Bl/6NCrL) and mdx mice (C57Bl/10ScSn-mdx/J)
were obtained from Charles River Laboratories (The Netherlands).
Transgenic hDMD mice were engineered in our own LUMC laboratories.
Briefly, embryonic stem (ES) cells were genetically modified
through fusions with yeast spheroplasts carrying a YAC of 2.7 Mb
that contained the full-length (2.4 Mb) human DMD gene. This YAC
was previously reconstructed by homologous recombination of smaller
overlapping YACs in yeast (Den Dunnen et al. (1992). Hum Mol Genet
1: 19-28). ES-cells showing integration of one copy of the
full-size YAC, as assessed by PFGE mapping, exon-PCR analysis
across the entire gene, and metaphase FISH analysis, were then used
to generate homozygous hDMD mice ('t Hoen et al., J. Biol. Chem.
2008). Transgenic hDMD mice do not appear to be physically affected
by the genetic modification. Appropriate expression of the human
DMD gene could be demonstrated in muscle, both at RNA and protein
level. The engineering of these mice was authorised by the Dutch
Ministry of Agriculture (LNV); project nr. VVA/BD01.284 (E21).
Administration of AONs.
[0126] The experiments on intramuscular AON-injections in mice were
authorised by the animal experimental commission (UDEC) of the
Medical Faculty of the Leiden University (project no. 00095,
03027). AONs were injected, either pure, or complexed to the
cationic polymer polyethylenimine (PEI; ExGen 500 (20.times.), MBI
Fermentas) at ratios of 1 ml PEI per nmol AON in a 5% w/v glucose
solution, or to 15 nmol SAINT-18TM (Synvolux Therapeutics B.V., The
Netherlands), according to the manufacturers' instructions. The
SAINT-18TM delivery system is based on a cationic pyridinium head
group and allows non-toxic delivery of antisense oligonucleotides.
Mice were anaesthetised by intraperitoneal injection of a 1:1 (v/v)
Hypnorm/Dormicum solution (Janssen Pharmaceutica, Belgium/Roche,
The Netherlands). Pure AON (PS188) was administered in a final
injection volume of 40 .mu.l by intramuscular injection into both
gastrocnemius muscles of the mice using a Hamilton syringe with a
22-Gauge needle. The mice received two injections of 40 .mu.g at a
24 h interval. They were sacrificed at different time-points
post-injection; for PS188-injected hDMD mice ten days after the
last injection. Muscles were isolated and frozen in liquid
nitrogen-cooled 2-methylbutane.
RT-PCR Analysis.
[0127] Muscle samples were homogenized in RNA-Bee solution (Campro
Scientific, The Netherlands). Total RNA was isolated and purified
according to the manufacturer's instructions. For cDNA synthesis
with the reverse transcriptase C. therm polymerase or Transcriptor
(Roche Diagnostics, The Netherlands), 300 ng of RNA was used in a
20 .mu.l reaction at 60.degree. C. for 30 min, reverse primed with
either mouse- or human-specific primers. First PCRs were performed
with outer primer sets (flanking exons 43-45 for PS188-injected
mice), for 20 cycles of 94.degree. C. (40 sec), 60.degree. C. (40
sec), and 72.degree. C. (60 sec). One .mu.l of this reaction
(diluted 1:10) was then re-amplified using nested primer
combinations in the exons directly flanking the target exon (exon
44 for PS188-injected mice), with 30 cycles of 94.degree. C. (40
sec), 60.degree. C. (40 sec), and 72.degree. C. (60 sec). PCR
products were analysed on 2% agarose gels. Skipping efficiencies
were determined by quantification of PCR products using the DNA
1000 LabChip.RTM. Kit and the Agilent 2100 bioanalyzer (Agilent
Technologies, The Netherlands). Primer sets and sequences were
described previously (Aartsma-Rus et al. (2002) Neuromuscul Disord
12 Suppl: S71.8,17; van Deutekom et al. (2001) Hum Mol Genet 10:
1547-1554).
Sequence Analysis.
[0128] RT-PCR products were isolated from 2% agarose gels using the
QIAquick Gel Extraction Kit (QIAGEN). Direct DNA sequencing was
carried out by the Leiden Genome Technology Center (LGTC) using the
BigDye Terminator Cycle Sequencing Ready Reaction kit (PE Applied
Biosystems), and analyzed on an ABI 3700 Sequencer (PE Applied
Biosystems).
MALDI-TOF Mass-Spectrometry.
[0129] RNA-Bee muscle homogenates were purified using a nucleic
acid purification kit (Nucleic Acid Purification Kit for
Sequazyme.TM. Pinpoint SNP Kit, Applied Biosystems) with 96 well
spin plates (Applied Biosystems) following the manufacturer's
instructions. Matrix solution (50 mg/ml 3-hydroxy picolinic acid
and 25 mM dibasic ammonium citrate in 50% acetonitrile) was applied
in 1 ml aliquots to an AnchorChip.TM. sample target (Bruker
Daltonics, Germany) and air-dried. Samples were spotted in 0.5 ml
aliquots onto the matrix crystals and air-dried. Mass
determinations were performed on a Reflex III MALDI-TOF
mass-spectrometer (Bruker Daltonics, Germany). Spectra were
acquired in reflector mode and accumulated for approximately 900
laser shots. Samples of labelled and unlabelled m46AON4 were
analyzed for comparison.
Results
Exon Skipping in Wild-Type Muscle
[0130] We first set up targeted exon skipping in mouse muscle in
vivo and optimised different parameters of administration. Initial
experiments were performed in wild type mice, and, while
nonsense-mediated RNA decay will cause underestimation of the exon
skipping efficiencies, the effect of the AONs was monitored on mRNA
level only. We injected increasing dosages from 0.9 nmol to 5.4
nmol of each antisense oligonucleotide. RT-PCR analysis of total
muscle RNA demonstrated the occurrence of a novel shorter
transcript fragment in all samples injected. Sequence analysis
confirmed the precise skipping of exon 44 in this product (data not
shown).
[0131] Cross-sections of the contra-lateral injected muscles were
analysed for dispersion and persistence of a fluorescein-labelled
control AON. Following injection of pure AON, we observed
fluorescent signals within some fibres for up to one week. At later
time points only weak signals were observed, and mainly within the
interstitial spaces. The use of PEI clearly enhanced both
dispersion and persistence of the fluorescent signal, even after 3
weeks. However, it also induced fibre degeneration and monocyte
infiltration absorbing most fluorescence. Using SAINT, most of the
signal was detected in the interstitial spaces for up to one week,
indicating that this reagent did not efficiently deliver the AON
into the muscle fibres. Since the fluorescent signal may not
correspond to the presence of intact and functional AONs, we
performed MALDI-TOF mass-spectrometry of injected muscle samples.
The analyses indicated that the fluorescent label was removed from
the AON within 24 hours. The labelled AON was only detectable for
up to two weeks when using PEI. The interstitial AONs were probably
more vulnerable to degradation than the intracellular AONs. The
unlabelled AON was observed for three to four weeks post-injection
in all three series, but it may only be functional when present
intracellularly, i.e., in the PEI series.
Human-Specific Exon Skipping in hDMD Muscle
[0132] Since the exon skipping strategy is a sequence-specific
therapeutic approach, the ideal pre-clinical validation would be a
target human DMD gene, in a mouse experimental background. We have
engineered such transgenic, "humanised" DMD (hDMD) mice carrying an
integrated and functional copy of the full-length human DMD gene.
Expression of human dystrophin in hDMD mouse muscle was
specifically detected by immunohistochemical analysis of
cross-sections, using a human-specific antibody (MANDYS106). On
muscle RNA level, RT-PCR analyses using either mouse- or
human-specific primers demonstrated correct transcription of the
human DMD gene. Furthermore, upon crossing with mdx mice, the hDMD
construct showed to complement the dystrophic defect, as was
assessed by histological and cDNA microarray analysis ('t Hoen et
al., J. Biol. Chem. 2008). hDMD mice have healthy muscle fibers
typically exhibiting a limited uptake of naked AONs. We injected
the human-specific AON PS196 (SEQ ID NO 43) complexed to PEI, or
PS188 (SEQ ID NO 5) without PEI, into the gastrocnemius muscles of
the hDMD mice (2.times.40 .mu.g injections within 24 hrs). At 7 to
10 days post-injection we clearly observed the skipping of the
targeted exon 44 from the human DMD transcript (FIG. 3A). Although
the human-specific AONs are highly homologous to the corresponding
mouse sequences, with only 2 or 3 mismatches in the respective
20-mers, the mouse endogenous transcripts were not affected to any
detectable level. PS188 induced exon 44 skipping, as confirmed by
sequence analysis. No exon 44 skipping was observed in non-treated
hDMD muscle. These results indicate that PS188 is an efficient
compound inducing human exon 44 skipping in muscle tissue.
Example 4
Material and Methods
[0133] As part of an extensive toxicity program for PS188,
non-fasted cynomolgus monkeys were treated by 1-hour intravenous
infusion (5 mL/kg/h) every fourth day for 29 days at the dose-level
of 6 mg/kg PS188 (SEQ ID NO 5; 2'OMePS RNA; Agilent Life Sciences,
USA). The PS188 formulations were freshly prepared on each
treatment day (on test days 1, 5, 9, 13, 17, 21, 25 and 29) shortly
before initiation of the administration (as soon as possible
before, at the most within one hour before start of
administration). Formulations were prepared by dissolving PS188 in
phosphate buffer; the purity and water content were taken into
account as provided in the Certificate of Analysis of the drug
substance. The amount of PS188 was adjusted to each animal's
current body weight. The animals were sacrificed 96 hours after the
last administration (day 33). Whole blood samples (10 ml) were
collected in EDTA tubes, and (after overnight shipment at room
temperature) layered on top of a HistoPaque gradient. Upon
centrifugation, the second layer (of the four layers, from top to
bottom) with the mononuclear cells was collected, washed, and
centrifuged again. RNA was isolated from the resulting cell pellet
and analysed by RT-PCR analysis using DMD-gene specific primers
flanking exon 44 (Aartsma-Rus et al. Neuromuscul Disord 2002; 12
Suppl: S71). Sequence analysis (by the Leiden Genome Technology
Center (LGTC) using the BigDye Terminator Cycle Sequencing Ready
Reaction kit (PE Applied Biosystems), and ABI 3700 Sequencer (PE
Applied Biosystems) was performed on isolated PCR products (using
the QIAquick Gel Extraction Kit (QIAGEN) to confirm the specific
exon 44 skipping on RNA level.
Results
[0134] In monkeys treated by 1-hour intravenous infusions every
fourth day for 29 days at the dose-level of 6 mg/kg PS188, exon 44
skipping was observed in peripheral blood mononuclear cells (FIG.
3B), despite the fact that these cells express only low levels of
dystrophin. The human and monkey DMD sequence targeted by PS188 is
in fact 100% identical. No exon 44 skipping was observed in
non-treated monkeys. These results indicate that PS188 is an
efficient compound inducing exon 44 skipping in vivo.
TABLE-US-00001 TABLE 1 Antisense oligonucleotide sequences. Table
1A 1 (PS 188) UCAGCUUCUGUUAGCCACUG SEQ ID NO 5 2
UUCAGCUUCUGUUAGCCACU SEQ ID NO 6 3 UUCAGCUUCUGUUAGCCACUG SEQ ID NO
7 4 UCAGCUUCUGUUAGCCACUGA SEQ ID NO 8 5 UUCAGCUUCUGUUAGCCACUGA SEQ
ID NO 9 6 UCAGCUUCUGUUAGCCACUGAU SEQ ID NO 10 7
UUCAGCUUCUGUUAGCCACUGAU SEQ ID NO 11 8 UCAGCUUCUGUUAGCCACUGAUU SEQ
ID NO 12 9 UUCAGCUUCUGUUAGCCACUGAUU SEQ ID NO 13 10
UCAGCUUCUGUUAGCCACUGAUUA SEQ ID NO 14 11 UUCAGCUUCUGUUAGCCACUGAUA
SEQ ID NO 15 12 UCAGCUUCUGUUAGCCACUGAUUA SEQ ID NO 16 A 13
UUCAGCUUCUGUUAGCCACUGAUU SEQ ID NO 17 AA 14
UCAGCUUCUGUUAGCCACUGAUUA SEQ ID NO 18 AA 15
UUCAGCUUCUGUUAGCCACUGAUU SEQ ID NO 19 AAA 16 CAGCUUCUGUUAGCCACUG
SEQ ID NO 20 17 CAGCUUCUGUUAGCCACUGAU SEQ ID NO 21 18
AGCUUCUGUUAGCCACUGAUU SEQ ID NO 22 19 CAGCUUCUGUUAGCCACUGAUU SEQ ID
NO 23 20 AGCUUCUGUUAGCCACUGAUUA SEQ ID NO 24 21
CAGCUUCUGUUAGCCACUGAUUA SEQ ID NO 25 22 AGCUUCUGUUAGCCACUGAUUAA SEQ
ID NO 26 23 CAGCUUCUGUUAGCCACUGAUUA SEQ ID NO 27 A 24
AGCUUCUGUUAGCCACUGAUUAA SEQ ID NO 28 A 25 CAGCUUCUGUUAGCCACUGAUUA
SEQ ID NO 29 AA 26 AGCUUCUGUUAGCCACUGAU SEQ ID NO 30 27
GCUUCUGUUAGCCACUGAUU SEQ ID NO 31 28 GCUUCUGUUAGCCACUGAUUA SEQ ID
NO 32 29 GCUUCUGUUAGCCACUGAUUAA SEQ ID NO 33 30
GCUUCUGUUAGCCACUGAUUAAA SEQ ID NO 34 31 (PS 192)
CCAUUUGUAUUUAGCAUGUUCCC SEQ ID NO 35 32 (PS 199)
AGAUACCAUUUGUAUUUAGC SEQ ID NO 36 33 (PS 187) GCCAUUUCUCAACAGAUCU
SEQ ID NO 37 34 (PS 194) GCCAUUUCUCAACAGAUCUGUCA SEQ ID NO 38 35
(PS 191) AUUCUCAGGAAUUUGUGUCUUUC SEQ ID NO 39 36 (PS 193)
UCUCAGGAAUUUGUGUCUUUC SEQ ID NO 40 37 (PS 200) GUUCAGCUUCUGUUAGCC
SEQ ID NO 41 38 (PS 201) CUGAUUAAAUAUCUUUAUAUC SEQ ID NO 42 Table
1B 39 (PS 196) GCCGCCAUUUCUCAACAG SEQ ID NO 43 40 (PS 197)
GUAUUUAGCAUGUUCCCA SEQ ID NO 44 41 (PS 198) CAGGAAUUUGUGUCUUUC SEQ
ID NO 45 42 (PS 189) UCUGUUAGCCACUGAUUAAAU SEQ ID NO 46
TABLE-US-00002 homo sapiens DMD amino acid sequence SEQ ID NO: 47
MLWWEEVEDCYEREDVQKKTFTKWVNAQFSKFGKQHIENLFSDLQDGRRLL
DLLEGLTGQKLPKEKGSTRVHALNNVNKALRVLQNNNVDLVNIGSTDIVDG
NHKLTLGLIWNIILHWQVKNVMKNIMAGLQQTNSEKILLSWVRQSTRNYPQ
VNVINFTTSWSDGLALNALIHSHRPDLFDWNSVVCQQSATQRLEHAFNIAR
YQLGIEKLLDPEDVDTTYPDKKSILMYITSLFQVLPQQVSIEAIQEVEMLP
RPPKVTKEEHFQLHHQMHYSQQITVSLAQGYERTSSPKPRFKSYAYTQAAY
VTTSDPTRSPFPSQHLEAPEDKSFGSSLMESEVNLDRYQTALEEVLSWLLS
AEDTLQAQGEISNDVEVVKDQFHTHEGYMMDLTAHQGRVGNILQLGSKLIG
TGKLSEDEETEVQEQMNLLNSRWECLRVASMEKQSNLHRVLMDLQNQKLKE
LNDWLTKTEERTRKMEEEPLGPDLEDLKRQVQQHKVLQEDLEQEQVRVNSL
THMVVVVDESSGDHATAALEEQLKVLGDRWANICRWTEDRWVLLQDILLKW
QRLTEEQCLFSAWLSEKEDAVNKIHTTGFKDQNEMLSSLQKLAVLKADLEK
KKQSMGKLYSLKQDLLSTLKNKSVTQKTEAWLDNFARCWDNLVQKLEKSTA
QISQAVTTTQPSLTQTTVMETVTTVTTREQILVKHAQEELPPPPPQKKRQI
TVDSEIRKRLDVDITELHSWITRSEAVLQSPEFAIERKEGNESDLKEKVNA
IEREKAEKFRKLQDASRSAQALVEQMVNEGVNADSIKQASEQLNSRWIEFC
QLLSERLNWLEYQNNIIAFYNQLQQLEQMTTTAENWLKIQPTTPSEPTAIK
SQLKICKDEVNRLSGLQPQIERLKIQSIALKEKGQGPMELDADEVAFTNHF
KQVFSDVQAREKELQTIFDTLPPMRYQETMSAIRTWVQQSETKLSIPQLSV
TDYEIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQS
EFEEIEGRWKKLSSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEVDVFL
KEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAEPE
FASRLETELKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWM
TQAEEEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSV
IAQAPPVAQEALKKELETLTTNYQWLCTRLNGKCKTLEEVWACWHELLSYL
EKANKWLNEVEFKLKTTENIPGGAEEISEVLDSLENLMRHSEDNPNQIRIL
AQTLTDGGVMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEK
SLHLIQESLTFIDKQLAAYIADKVDAAQMPQEAQKIQSDLTSHEISLEEMK
KHNQGKEAAQRVLSQIDVAQKKLQDVSMKFRLFQKPANFEQRLQESKMILD
EVKMHLPALETKSVEQEVVQSQLNHCVNLYKSLSEVKSEVEMVIKTGRQIV
QKKQTENPKELDERVTALKLHYNELGAKVTERKQQLEKCLKLSRKMRKEMN
VLTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSIT
EVGEALKTVLGKKETLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMET
FDQNVDHITKWIIQADTLLDESEKKKPQQKEDVLKRLKAELNDIRPKVDST
RDQAANLMANRGDHCRKLVEPQISELNHRFAAISHRIKTGKASIPLKELEQ
FNSDIQKLLEPLEAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQ
RITDERKREEIKIKQQLLQTKHNALKDLRSQRRKKALEISHQWYQYKRQAD
DLLKCLDDIEKKLASLPEPRDERKIKEIDRELQKKKEELNAVRRQAEGLSE
DGAAMAVEPTQIQLSKRWREIESKFAQFRRLNFAQIHTVREETMMVMTEDM
PLEISYVPSTYLTEITHVSQALLEVEQLLNAPDLCAKDFEDLFKQEESLKN
IKDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKM
YKDRQGRFDRSVEKWRRFHYDIKIFNQWLTEAEQFLRKTQIPENWEHAKYK
WYLKELQDGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQ
EVCKQLSDRKKRLEEQKNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQ
QLKEKLEQVKLLVEELPLRQGILKQLNETGGPVLVSAPISPEEQDKLENKL
KQTNLQWIKVSRALPEKQGEIEAQIKDLGQLEKKLEDLEEQLNHLLLWLSP
IRNQLEIYNQPNQEGPFDVQETEIAVQAKQPDVEEILSKGQHLYKEKPATQ
PVKRKLEDLSSEWKAVNRLLQELRAKQPDLAPGLTTIGASPTQTVTLVTQP
VVTKETAISKLEMPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVM
VGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTII
TDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA
KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS
ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLA
WLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHN
LDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSD
QWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELK
TKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQ
AEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKG
SWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQL
SPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMK
LRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLE
QEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLED
KYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVR
SCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNI
CKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSG
EDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWP
VDSAPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDE
HLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRN
LQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG
RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRS
DSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG RNTPGKPMREDTM
Sequence CWU 1
1
47116DNAHomo sapiens 1guggcuaaca gaagcu 16217DNAHomo sapiens
2gggaacaugc uaaauac 17318DNAHomo sapiens 3agacacaaau uccugaga
18411DNAHomo sapiens 4cuguugagaa a 11520RNAArtificialsynthetic
oligonucleotide 5ucagcuucug uuagccacug 20620RNAArtificialsynthetic
oligonucleotide 6uucagcuucu guuagccacu 20721RNAArtificialsynthetic
oligonucleotide 7uucagcuucu guuagccacu g
21821RNAArtificialsynthetic oligonucleotide 8ucagcuucug uuagccacug
a 21922RNAArtificialsynthetic oligonucleotide 9uucagcuucu
guuagccacu ga 221022RNAArtificialsynthetic oligonucleotide
10ucagcuucug uuagccacug au 221123RNAArtificialsynthetic
oligonucleotide 11uucagcuucu guuagccacu gau
231223RNAArtificialsynthetic oligonucleotide 12ucagcuucug
uuagccacug auu 231324RNAArtificialsynthetic oligonucleotide
13uucagcuucu guuagccacu gauu 241424RNAArtificialsynthetic
oligonucleotide 14ucagcuucug uuagccacug auua
241524RNAArtificialsynthetic oligonucleotide 15uucagcuucu
guuagccacu gaua 241625RNAArtificialsynthetic oligonucleotide
16ucagcuucug uuagccacug auuaa 251726RNAArtificialsynthetic
oligonucleotide 17uucagcuucu guuagccacu gauuaa
261826RNAArtificialsynthetic oligonucleotide 18ucagcuucug
uuagccacug auuaaa 261927RNAArtificialsynthetic oligonucleotide
19uucagcuucu guuagccacu gauuaaa 272019RNAArtificialsynthetic
oligonucleotide 20cagcuucugu uagccacug 192121RNAArtificialsynthetic
oligonucleotide 21cagcuucugu uagccacuga u
212221RNAArtificialsynthetic oligonucleotide 22agcuucuguu
agccacugau u 212322RNAArtificialsynthetic oligonucleotide
23cagcuucugu uagccacuga uu 222422RNAArtificialsynthetic
oligonucleotide 24agcuucuguu agccacugau ua
222523RNAArtificialsynthetic oligonucleotide 25cagcuucugu
uagccacuga uua 232623RNAArtificialsynthetic oligonucleotide
26agcuucuguu agccacugau uaa 232724RNAArtificialsynthetic
oligonucleotide 27cagcuucugu uagccacuga uuaa
242824RNAArtificialsynthetic oligonucleotide 28agcuucuguu
agccacugau uaaa 242925RNAArtificialsynthetic oligonucleotide
29cagcuucugu uagccacuga uuaaa 253020RNAArtificialsynthetic
oligonucleotide 30agcuucuguu agccacugau
203120RNAArtificialsynthetic oligonucleotide 31gcuucuguua
gccacugauu 203221RNAArtificialsynthetic oligonucleotide
32gcuucuguua gccacugauu a 213322RNAArtificialsynthetic
oligonucleotide 33gcuucuguua gccacugauu aa
223423RNAArtificialsynthetic oligonucleotide 34gcuucuguua
gccacugauu aaa 233523RNAArtificialsynthetic oligonucleotide
35ccauuuguau uuagcauguu ccc 233620RNAArtificialsynthetic
oligonucleotide 36agauaccauu uguauuuagc
203719RNAArtificialsynthetic oligonucleotide 37gccauuucuc aacagaucu
193823RNAArtificialsynthetic oligonucleotide 38gccauuucuc
aacagaucug uca 233923RNAArtificialsynthetic oligonucleotide
39auucucagga auuugugucu uuc 234021RNAArtificialsynthetic
oligonucleotide 40ucucaggaau uugugucuuu c
214118RNAArtificialsynthetic oligonucleotide 41guucagcuuc uguuagcc
184221RNAArtificialsynthetic oligonucleotide 42cugauuaaau
aucuuuauau c 214318RNAArtificialsynthetic oligonucleotide
43gccgccauuu cucaacag 184418RNAArtificialsynthetic oligonucleotide
44guauuuagca uguuccca 184518RNAArtificialsynthetic oligonucleotide
45caggaauuug ugucuuuc 184621DNAArtificialsynthetic oligonucleotide
46ucuguuagcc acugauuaaa u 21473685PRTHomo sapiens 47Met Leu Trp Trp
Glu Glu Val Glu Asp Cys Tyr Glu Arg Glu Asp Val1 5 10 15Gln Lys Lys
Thr Phe Thr Lys Trp Val Asn Ala Gln Phe Ser Lys Phe 20 25 30Gly Lys
Gln His Ile Glu Asn Leu Phe Ser Asp Leu Gln Asp Gly Arg 35 40 45Arg
Leu Leu Asp Leu Leu Glu Gly Leu Thr Gly Gln Lys Leu Pro Lys 50 55
60Glu Lys Gly Ser Thr Arg Val His Ala Leu Asn Asn Val Asn Lys Ala65
70 75 80Leu Arg Val Leu Gln Asn Asn Asn Val Asp Leu Val Asn Ile Gly
Ser 85 90 95Thr Asp Ile Val Asp Gly Asn His Lys Leu Thr Leu Gly Leu
Ile Trp 100 105 110Asn Ile Ile Leu His Trp Gln Val Lys Asn Val Met
Lys Asn Ile Met 115 120 125Ala Gly Leu Gln Gln Thr Asn Ser Glu Lys
Ile Leu Leu Ser Trp Val 130 135 140Arg Gln Ser Thr Arg Asn Tyr Pro
Gln Val Asn Val Ile Asn Phe Thr145 150 155 160Thr Ser Trp Ser Asp
Gly Leu Ala Leu Asn Ala Leu Ile His Ser His 165 170 175Arg Pro Asp
Leu Phe Asp Trp Asn Ser Val Val Cys Gln Gln Ser Ala 180 185 190Thr
Gln Arg Leu Glu His Ala Phe Asn Ile Ala Arg Tyr Gln Leu Gly 195 200
205Ile Glu Lys Leu Leu Asp Pro Glu Asp Val Asp Thr Thr Tyr Pro Asp
210 215 220Lys Lys Ser Ile Leu Met Tyr Ile Thr Ser Leu Phe Gln Val
Leu Pro225 230 235 240Gln Gln Val Ser Ile Glu Ala Ile Gln Glu Val
Glu Met Leu Pro Arg 245 250 255Pro Pro Lys Val Thr Lys Glu Glu His
Phe Gln Leu His His Gln Met 260 265 270His Tyr Ser Gln Gln Ile Thr
Val Ser Leu Ala Gln Gly Tyr Glu Arg 275 280 285Thr Ser Ser Pro Lys
Pro Arg Phe Lys Ser Tyr Ala Tyr Thr Gln Ala 290 295 300Ala Tyr Val
Thr Thr Ser Asp Pro Thr Arg Ser Pro Phe Pro Ser Gln305 310 315
320His Leu Glu Ala Pro Glu Asp Lys Ser Phe Gly Ser Ser Leu Met Glu
325 330 335Ser Glu Val Asn Leu Asp Arg Tyr Gln Thr Ala Leu Glu Glu
Val Leu 340 345 350Ser Trp Leu Leu Ser Ala Glu Asp Thr Leu Gln Ala
Gln Gly Glu Ile 355 360 365Ser Asn Asp Val Glu Val Val Lys Asp Gln
Phe His Thr His Glu Gly 370 375 380Tyr Met Met Asp Leu Thr Ala His
Gln Gly Arg Val Gly Asn Ile Leu385 390 395 400Gln Leu Gly Ser Lys
Leu Ile Gly Thr Gly Lys Leu Ser Glu Asp Glu 405 410 415Glu Thr Glu
Val Gln Glu Gln Met Asn Leu Leu Asn Ser Arg Trp Glu 420 425 430Cys
Leu Arg Val Ala Ser Met Glu Lys Gln Ser Asn Leu His Arg Val 435 440
445Leu Met Asp Leu Gln Asn Gln Lys Leu Lys Glu Leu Asn Asp Trp Leu
450 455 460Thr Lys Thr Glu Glu Arg Thr Arg Lys Met Glu Glu Glu Pro
Leu Gly465 470 475 480Pro Asp Leu Glu Asp Leu Lys Arg Gln Val Gln
Gln His Lys Val Leu 485 490 495Gln Glu Asp Leu Glu Gln Glu Gln Val
Arg Val Asn Ser Leu Thr His 500 505 510Met Val Val Val Val Asp Glu
Ser Ser Gly Asp His Ala Thr Ala Ala 515 520 525Leu Glu Glu Gln Leu
Lys Val Leu Gly Asp Arg Trp Ala Asn Ile Cys 530 535 540Arg Trp Thr
Glu Asp Arg Trp Val Leu Leu Gln Asp Ile Leu Leu Lys545 550 555
560Trp Gln Arg Leu Thr Glu Glu Gln Cys Leu Phe Ser Ala Trp Leu Ser
565 570 575Glu Lys Glu Asp Ala Val Asn Lys Ile His Thr Thr Gly Phe
Lys Asp 580 585 590Gln Asn Glu Met Leu Ser Ser Leu Gln Lys Leu Ala
Val Leu Lys Ala 595 600 605Asp Leu Glu Lys Lys Lys Gln Ser Met Gly
Lys Leu Tyr Ser Leu Lys 610 615 620Gln Asp Leu Leu Ser Thr Leu Lys
Asn Lys Ser Val Thr Gln Lys Thr625 630 635 640Glu Ala Trp Leu Asp
Asn Phe Ala Arg Cys Trp Asp Asn Leu Val Gln 645 650 655Lys Leu Glu
Lys Ser Thr Ala Gln Ile Ser Gln Ala Val Thr Thr Thr 660 665 670Gln
Pro Ser Leu Thr Gln Thr Thr Val Met Glu Thr Val Thr Thr Val 675 680
685Thr Thr Arg Glu Gln Ile Leu Val Lys His Ala Gln Glu Glu Leu Pro
690 695 700Pro Pro Pro Pro Gln Lys Lys Arg Gln Ile Thr Val Asp Ser
Glu Ile705 710 715 720Arg Lys Arg Leu Asp Val Asp Ile Thr Glu Leu
His Ser Trp Ile Thr 725 730 735Arg Ser Glu Ala Val Leu Gln Ser Pro
Glu Phe Ala Ile Phe Arg Lys 740 745 750Glu Gly Asn Phe Ser Asp Leu
Lys Glu Lys Val Asn Ala Ile Glu Arg 755 760 765Glu Lys Ala Glu Lys
Phe Arg Lys Leu Gln Asp Ala Ser Arg Ser Ala 770 775 780Gln Ala Leu
Val Glu Gln Met Val Asn Glu Gly Val Asn Ala Asp Ser785 790 795
800Ile Lys Gln Ala Ser Glu Gln Leu Asn Ser Arg Trp Ile Glu Phe Cys
805 810 815Gln Leu Leu Ser Glu Arg Leu Asn Trp Leu Glu Tyr Gln Asn
Asn Ile 820 825 830Ile Ala Phe Tyr Asn Gln Leu Gln Gln Leu Glu Gln
Met Thr Thr Thr 835 840 845Ala Glu Asn Trp Leu Lys Ile Gln Pro Thr
Thr Pro Ser Glu Pro Thr 850 855 860Ala Ile Lys Ser Gln Leu Lys Ile
Cys Lys Asp Glu Val Asn Arg Leu865 870 875 880Ser Gly Leu Gln Pro
Gln Ile Glu Arg Leu Lys Ile Gln Ser Ile Ala 885 890 895Leu Lys Glu
Lys Gly Gln Gly Pro Met Phe Leu Asp Ala Asp Phe Val 900 905 910Ala
Phe Thr Asn His Phe Lys Gln Val Phe Ser Asp Val Gln Ala Arg 915 920
925Glu Lys Glu Leu Gln Thr Ile Phe Asp Thr Leu Pro Pro Met Arg Tyr
930 935 940Gln Glu Thr Met Ser Ala Ile Arg Thr Trp Val Gln Gln Ser
Glu Thr945 950 955 960Lys Leu Ser Ile Pro Gln Leu Ser Val Thr Asp
Tyr Glu Ile Met Glu 965 970 975Gln Arg Leu Gly Glu Leu Gln Ala Leu
Gln Ser Ser Leu Gln Glu Gln 980 985 990Gln Ser Gly Leu Tyr Tyr Leu
Ser Thr Thr Val Lys Glu Met Ser Lys 995 1000 1005Lys Ala Pro Ser
Glu Ile Ser Arg Lys Tyr Gln Ser Glu Phe Glu 1010 1015 1020Glu Ile
Glu Gly Arg Trp Lys Lys Leu Ser Ser Gln Leu Val Glu 1025 1030
1035His Cys Gln Lys Leu Glu Glu Gln Met Asn Lys Leu Arg Lys Ile
1040 1045 1050Gln Asn His Ile Gln Thr Leu Lys Lys Trp Met Ala Glu
Val Asp 1055 1060 1065Val Phe Leu Lys Glu Glu Trp Pro Ala Leu Gly
Asp Ser Glu Ile 1070 1075 1080Leu Lys Lys Gln Leu Lys Gln Cys Arg
Leu Leu Val Ser Asp Ile 1085 1090 1095Gln Thr Ile Gln Pro Ser Leu
Asn Ser Val Asn Glu Gly Gly Gln 1100 1105 1110Lys Ile Lys Asn Glu
Ala Glu Pro Glu Phe Ala Ser Arg Leu Glu 1115 1120 1125Thr Glu Leu
Lys Glu Leu Asn Thr Gln Trp Asp His Met Cys Gln 1130 1135 1140Gln
Val Tyr Ala Arg Lys Glu Ala Leu Lys Gly Gly Leu Glu Lys 1145 1150
1155Thr Val Ser Leu Gln Lys Asp Leu Ser Glu Met His Glu Trp Met
1160 1165 1170Thr Gln Ala Glu Glu Glu Tyr Leu Glu Arg Asp Phe Glu
Tyr Lys 1175 1180 1185Thr Pro Asp Glu Leu Gln Lys Ala Val Glu Glu
Met Lys Arg Ala 1190 1195 1200Lys Glu Glu Ala Gln Gln Lys Glu Ala
Lys Val Lys Leu Leu Thr 1205 1210 1215Glu Ser Val Asn Ser Val Ile
Ala Gln Ala Pro Pro Val Ala Gln 1220 1225 1230Glu Ala Leu Lys Lys
Glu Leu Glu Thr Leu Thr Thr Asn Tyr Gln 1235 1240 1245Trp Leu Cys
Thr Arg Leu Asn Gly Lys Cys Lys Thr Leu Glu Glu 1250 1255 1260Val
Trp Ala Cys Trp His Glu Leu Leu Ser Tyr Leu Glu Lys Ala 1265 1270
1275Asn Lys Trp Leu Asn Glu Val Glu Phe Lys Leu Lys Thr Thr Glu
1280 1285 1290Asn Ile Pro Gly Gly Ala Glu Glu Ile Ser Glu Val Leu
Asp Ser 1295 1300 1305Leu Glu Asn Leu Met Arg His Ser Glu Asp Asn
Pro Asn Gln Ile 1310 1315 1320Arg Ile Leu Ala Gln Thr Leu Thr Asp
Gly Gly Val Met Asp Glu 1325 1330 1335Leu Ile Asn Glu Glu Leu Glu
Thr Phe Asn Ser Arg Trp Arg Glu 1340 1345 1350Leu His Glu Glu Ala
Val Arg Arg Gln Lys Leu Leu Glu Gln Ser 1355 1360 1365Ile Gln Ser
Ala Gln Glu Thr Glu Lys Ser Leu His Leu Ile Gln 1370 1375 1380Glu
Ser Leu Thr Phe Ile Asp Lys Gln Leu Ala Ala Tyr Ile Ala 1385 1390
1395Asp Lys Val Asp Ala Ala Gln Met Pro Gln Glu Ala Gln Lys Ile
1400 1405 1410Gln Ser Asp Leu Thr Ser His Glu Ile Ser Leu Glu Glu
Met Lys 1415 1420 1425Lys His Asn Gln Gly Lys Glu Ala Ala Gln Arg
Val Leu Ser Gln 1430 1435 1440Ile Asp Val Ala Gln Lys Lys Leu Gln
Asp Val Ser Met Lys Phe 1445 1450 1455Arg Leu Phe Gln Lys Pro Ala
Asn Phe Glu Gln Arg Leu Gln Glu 1460 1465 1470Ser Lys Met Ile Leu
Asp Glu Val Lys Met His Leu Pro Ala Leu 1475 1480 1485Glu Thr Lys
Ser Val Glu Gln Glu Val Val Gln Ser Gln Leu Asn 1490 1495 1500His
Cys Val Asn Leu Tyr Lys Ser Leu Ser Glu Val Lys Ser Glu 1505 1510
1515Val Glu Met Val Ile Lys Thr Gly Arg Gln Ile Val Gln Lys Lys
1520 1525 1530Gln Thr Glu Asn Pro Lys Glu Leu Asp Glu Arg Val Thr
Ala Leu 1535 1540 1545Lys Leu His Tyr Asn Glu Leu Gly Ala Lys Val
Thr Glu Arg Lys 1550 1555 1560Gln Gln Leu Glu Lys Cys Leu Lys Leu
Ser Arg Lys Met Arg Lys 1565 1570 1575Glu Met Asn Val Leu Thr Glu
Trp Leu Ala Ala Thr Asp Met Glu 1580 1585 1590Leu Thr Lys Arg Ser
Ala Val Glu Gly Met Pro Ser Asn Leu Asp 1595 1600 1605Ser Glu Val
Ala Trp Gly Lys Ala Thr Gln Lys Glu Ile Glu Lys 1610 1615 1620Gln
Lys Val His Leu Lys Ser Ile Thr Glu Val Gly Glu Ala Leu 1625 1630
1635Lys Thr Val Leu Gly Lys Lys Glu Thr Leu Val Glu Asp Lys Leu
1640 1645 1650Ser Leu Leu Asn Ser Asn Trp Ile Ala Val Thr Ser Arg
Ala Glu 1655 1660 1665Glu Trp Leu Asn Leu Leu Leu Glu Tyr Gln Lys
His Met Glu Thr 1670 1675 1680Phe Asp Gln Asn Val Asp His Ile Thr
Lys Trp Ile Ile Gln Ala 1685 1690 1695Asp Thr Leu Leu Asp Glu Ser
Glu Lys Lys Lys Pro Gln Gln Lys 1700
1705 1710Glu Asp Val Leu Lys Arg Leu Lys Ala Glu Leu Asn Asp Ile
Arg 1715 1720 1725Pro Lys Val Asp Ser Thr Arg Asp Gln Ala Ala Asn
Leu Met Ala 1730 1735 1740Asn Arg Gly Asp His Cys Arg Lys Leu Val
Glu Pro Gln Ile Ser 1745 1750 1755Glu Leu Asn His Arg Phe Ala Ala
Ile Ser His Arg Ile Lys Thr 1760 1765 1770Gly Lys Ala Ser Ile Pro
Leu Lys Glu Leu Glu Gln Phe Asn Ser 1775 1780 1785Asp Ile Gln Lys
Leu Leu Glu Pro Leu Glu Ala Glu Ile Gln Gln 1790 1795 1800Gly Val
Asn Leu Lys Glu Glu Asp Phe Asn Lys Asp Met Asn Glu 1805 1810
1815Asp Asn Glu Gly Thr Val Lys Glu Leu Leu Gln Arg Gly Asp Asn
1820 1825 1830Leu Gln Gln Arg Ile Thr Asp Glu Arg Lys Arg Glu Glu
Ile Lys 1835 1840 1845Ile Lys Gln Gln Leu Leu Gln Thr Lys His Asn
Ala Leu Lys Asp 1850 1855 1860Leu Arg Ser Gln Arg Arg Lys Lys Ala
Leu Glu Ile Ser His Gln 1865 1870 1875Trp Tyr Gln Tyr Lys Arg Gln
Ala Asp Asp Leu Leu Lys Cys Leu 1880 1885 1890Asp Asp Ile Glu Lys
Lys Leu Ala Ser Leu Pro Glu Pro Arg Asp 1895 1900 1905Glu Arg Lys
Ile Lys Glu Ile Asp Arg Glu Leu Gln Lys Lys Lys 1910 1915 1920Glu
Glu Leu Asn Ala Val Arg Arg Gln Ala Glu Gly Leu Ser Glu 1925 1930
1935Asp Gly Ala Ala Met Ala Val Glu Pro Thr Gln Ile Gln Leu Ser
1940 1945 1950Lys Arg Trp Arg Glu Ile Glu Ser Lys Phe Ala Gln Phe
Arg Arg 1955 1960 1965Leu Asn Phe Ala Gln Ile His Thr Val Arg Glu
Glu Thr Met Met 1970 1975 1980Val Met Thr Glu Asp Met Pro Leu Glu
Ile Ser Tyr Val Pro Ser 1985 1990 1995Thr Tyr Leu Thr Glu Ile Thr
His Val Ser Gln Ala Leu Leu Glu 2000 2005 2010Val Glu Gln Leu Leu
Asn Ala Pro Asp Leu Cys Ala Lys Asp Phe 2015 2020 2025Glu Asp Leu
Phe Lys Gln Glu Glu Ser Leu Lys Asn Ile Lys Asp 2030 2035 2040Ser
Leu Gln Gln Ser Ser Gly Arg Ile Asp Ile Ile His Ser Lys 2045 2050
2055Lys Thr Ala Ala Leu Gln Ser Ala Thr Pro Val Glu Arg Val Lys
2060 2065 2070Leu Gln Glu Ala Leu Ser Gln Leu Asp Phe Gln Trp Glu
Lys Val 2075 2080 2085Asn Lys Met Tyr Lys Asp Arg Gln Gly Arg Phe
Asp Arg Ser Val 2090 2095 2100Glu Lys Trp Arg Arg Phe His Tyr Asp
Ile Lys Ile Phe Asn Gln 2105 2110 2115Trp Leu Thr Glu Ala Glu Gln
Phe Leu Arg Lys Thr Gln Ile Pro 2120 2125 2130Glu Asn Trp Glu His
Ala Lys Tyr Lys Trp Tyr Leu Lys Glu Leu 2135 2140 2145Gln Asp Gly
Ile Gly Gln Arg Gln Thr Val Val Arg Thr Leu Asn 2150 2155 2160Ala
Thr Gly Glu Glu Ile Ile Gln Gln Ser Ser Lys Thr Asp Ala 2165 2170
2175Ser Ile Leu Gln Glu Lys Leu Gly Ser Leu Asn Leu Arg Trp Gln
2180 2185 2190Glu Val Cys Lys Gln Leu Ser Asp Arg Lys Lys Arg Leu
Glu Glu 2195 2200 2205Gln Lys Asn Ile Leu Ser Glu Phe Gln Arg Asp
Leu Asn Glu Phe 2210 2215 2220Val Leu Trp Leu Glu Glu Ala Asp Asn
Ile Ala Ser Ile Pro Leu 2225 2230 2235Glu Pro Gly Lys Glu Gln Gln
Leu Lys Glu Lys Leu Glu Gln Val 2240 2245 2250Lys Leu Leu Val Glu
Glu Leu Pro Leu Arg Gln Gly Ile Leu Lys 2255 2260 2265Gln Leu Asn
Glu Thr Gly Gly Pro Val Leu Val Ser Ala Pro Ile 2270 2275 2280Ser
Pro Glu Glu Gln Asp Lys Leu Glu Asn Lys Leu Lys Gln Thr 2285 2290
2295Asn Leu Gln Trp Ile Lys Val Ser Arg Ala Leu Pro Glu Lys Gln
2300 2305 2310Gly Glu Ile Glu Ala Gln Ile Lys Asp Leu Gly Gln Leu
Glu Lys 2315 2320 2325Lys Leu Glu Asp Leu Glu Glu Gln Leu Asn His
Leu Leu Leu Trp 2330 2335 2340Leu Ser Pro Ile Arg Asn Gln Leu Glu
Ile Tyr Asn Gln Pro Asn 2345 2350 2355Gln Glu Gly Pro Phe Asp Val
Gln Glu Thr Glu Ile Ala Val Gln 2360 2365 2370Ala Lys Gln Pro Asp
Val Glu Glu Ile Leu Ser Lys Gly Gln His 2375 2380 2385Leu Tyr Lys
Glu Lys Pro Ala Thr Gln Pro Val Lys Arg Lys Leu 2390 2395 2400Glu
Asp Leu Ser Ser Glu Trp Lys Ala Val Asn Arg Leu Leu Gln 2405 2410
2415Glu Leu Arg Ala Lys Gln Pro Asp Leu Ala Pro Gly Leu Thr Thr
2420 2425 2430Ile Gly Ala Ser Pro Thr Gln Thr Val Thr Leu Val Thr
Gln Pro 2435 2440 2445Val Val Thr Lys Glu Thr Ala Ile Ser Lys Leu
Glu Met Pro Ser 2450 2455 2460Ser Leu Met Leu Glu Val Pro Ala Leu
Ala Asp Phe Asn Arg Ala 2465 2470 2475Trp Thr Glu Leu Thr Asp Trp
Leu Ser Leu Leu Asp Gln Val Ile 2480 2485 2490Lys Ser Gln Arg Val
Met Val Gly Asp Leu Glu Asp Ile Asn Glu 2495 2500 2505Met Ile Ile
Lys Gln Lys Ala Thr Met Gln Asp Leu Glu Gln Arg 2510 2515 2520Arg
Pro Gln Leu Glu Glu Leu Ile Thr Ala Ala Gln Asn Leu Lys 2525 2530
2535Asn Lys Thr Ser Asn Gln Glu Ala Arg Thr Ile Ile Thr Asp Arg
2540 2545 2550Ile Glu Arg Ile Gln Asn Gln Trp Asp Glu Val Gln Glu
His Leu 2555 2560 2565Gln Asn Arg Arg Gln Gln Leu Asn Glu Met Leu
Lys Asp Ser Thr 2570 2575 2580Gln Trp Leu Glu Ala Lys Glu Glu Ala
Glu Gln Val Leu Gly Gln 2585 2590 2595Ala Arg Ala Lys Leu Glu Ser
Trp Lys Glu Gly Pro Tyr Thr Val 2600 2605 2610Asp Ala Ile Gln Lys
Lys Ile Thr Glu Thr Lys Gln Leu Ala Lys 2615 2620 2625Asp Leu Arg
Gln Trp Gln Thr Asn Val Asp Val Ala Asn Asp Leu 2630 2635 2640Ala
Leu Lys Leu Leu Arg Asp Tyr Ser Ala Asp Asp Thr Arg Lys 2645 2650
2655Val His Met Ile Thr Glu Asn Ile Asn Ala Ser Trp Arg Ser Ile
2660 2665 2670His Lys Arg Val Ser Glu Arg Glu Ala Ala Leu Glu Glu
Thr His 2675 2680 2685Arg Leu Leu Gln Gln Phe Pro Leu Asp Leu Glu
Lys Phe Leu Ala 2690 2695 2700Trp Leu Thr Glu Ala Glu Thr Thr Ala
Asn Val Leu Gln Asp Ala 2705 2710 2715Thr Arg Lys Glu Arg Leu Leu
Glu Asp Ser Lys Gly Val Lys Glu 2720 2725 2730Leu Met Lys Gln Trp
Gln Asp Leu Gln Gly Glu Ile Glu Ala His 2735 2740 2745Thr Asp Val
Tyr His Asn Leu Asp Glu Asn Ser Gln Lys Ile Leu 2750 2755 2760Arg
Ser Leu Glu Gly Ser Asp Asp Ala Val Leu Leu Gln Arg Arg 2765 2770
2775Leu Asp Asn Met Asn Phe Lys Trp Ser Glu Leu Arg Lys Lys Ser
2780 2785 2790Leu Asn Ile Arg Ser His Leu Glu Ala Ser Ser Asp Gln
Trp Lys 2795 2800 2805Arg Leu His Leu Ser Leu Gln Glu Leu Leu Val
Trp Leu Gln Leu 2810 2815 2820Lys Asp Asp Glu Leu Ser Arg Gln Ala
Pro Ile Gly Gly Asp Phe 2825 2830 2835Pro Ala Val Gln Lys Gln Asn
Asp Val His Arg Ala Phe Lys Arg 2840 2845 2850Glu Leu Lys Thr Lys
Glu Pro Val Ile Met Ser Thr Leu Glu Thr 2855 2860 2865Val Arg Ile
Phe Leu Thr Glu Gln Pro Leu Glu Gly Leu Glu Lys 2870 2875 2880Leu
Tyr Gln Glu Pro Arg Glu Leu Pro Pro Glu Glu Arg Ala Gln 2885 2890
2895Asn Val Thr Arg Leu Leu Arg Lys Gln Ala Glu Glu Val Asn Thr
2900 2905 2910Glu Trp Glu Lys Leu Asn Leu His Ser Ala Asp Trp Gln
Arg Lys 2915 2920 2925Ile Asp Glu Thr Leu Glu Arg Leu Gln Glu Leu
Gln Glu Ala Thr 2930 2935 2940Asp Glu Leu Asp Leu Lys Leu Arg Gln
Ala Glu Val Ile Lys Gly 2945 2950 2955Ser Trp Gln Pro Val Gly Asp
Leu Leu Ile Asp Ser Leu Gln Asp 2960 2965 2970His Leu Glu Lys Val
Lys Ala Leu Arg Gly Glu Ile Ala Pro Leu 2975 2980 2985Lys Glu Asn
Val Ser His Val Asn Asp Leu Ala Arg Gln Leu Thr 2990 2995 3000Thr
Leu Gly Ile Gln Leu Ser Pro Tyr Asn Leu Ser Thr Leu Glu 3005 3010
3015Asp Leu Asn Thr Arg Trp Lys Leu Leu Gln Val Ala Val Glu Asp
3020 3025 3030Arg Val Arg Gln Leu His Glu Ala His Arg Asp Phe Gly
Pro Ala 3035 3040 3045Ser Gln His Phe Leu Ser Thr Ser Val Gln Gly
Pro Trp Glu Arg 3050 3055 3060Ala Ile Ser Pro Asn Lys Val Pro Tyr
Tyr Ile Asn His Glu Thr 3065 3070 3075Gln Thr Thr Cys Trp Asp His
Pro Lys Met Thr Glu Leu Tyr Gln 3080 3085 3090Ser Leu Ala Asp Leu
Asn Asn Val Arg Phe Ser Ala Tyr Arg Thr 3095 3100 3105Ala Met Lys
Leu Arg Arg Leu Gln Lys Ala Leu Cys Leu Asp Leu 3110 3115 3120Leu
Ser Leu Ser Ala Ala Cys Asp Ala Leu Asp Gln His Asn Leu 3125 3130
3135Lys Gln Asn Asp Gln Pro Met Asp Ile Leu Gln Ile Ile Asn Cys
3140 3145 3150Leu Thr Thr Ile Tyr Asp Arg Leu Glu Gln Glu His Asn
Asn Leu 3155 3160 3165Val Asn Val Pro Leu Cys Val Asp Met Cys Leu
Asn Trp Leu Leu 3170 3175 3180Asn Val Tyr Asp Thr Gly Arg Thr Gly
Arg Ile Arg Val Leu Ser 3185 3190 3195Phe Lys Thr Gly Ile Ile Ser
Leu Cys Lys Ala His Leu Glu Asp 3200 3205 3210Lys Tyr Arg Tyr Leu
Phe Lys Gln Val Ala Ser Ser Thr Gly Phe 3215 3220 3225Cys Asp Gln
Arg Arg Leu Gly Leu Leu Leu His Asp Ser Ile Gln 3230 3235 3240Ile
Pro Arg Gln Leu Gly Glu Val Ala Ser Phe Gly Gly Ser Asn 3245 3250
3255Ile Glu Pro Ser Val Arg Ser Cys Phe Gln Phe Ala Asn Asn Lys
3260 3265 3270Pro Glu Ile Glu Ala Ala Leu Phe Leu Asp Trp Met Arg
Leu Glu 3275 3280 3285Pro Gln Ser Met Val Trp Leu Pro Val Leu His
Arg Val Ala Ala 3290 3295 3300Ala Glu Thr Ala Lys His Gln Ala Lys
Cys Asn Ile Cys Lys Glu 3305 3310 3315Cys Pro Ile Ile Gly Phe Arg
Tyr Arg Ser Leu Lys His Phe Asn 3320 3325 3330Tyr Asp Ile Cys Gln
Ser Cys Phe Phe Ser Gly Arg Val Ala Lys 3335 3340 3345Gly His Lys
Met His Tyr Pro Met Val Glu Tyr Cys Thr Pro Thr 3350 3355 3360Thr
Ser Gly Glu Asp Val Arg Asp Phe Ala Lys Val Leu Lys Asn 3365 3370
3375Lys Phe Arg Thr Lys Arg Tyr Phe Ala Lys His Pro Arg Met Gly
3380 3385 3390Tyr Leu Pro Val Gln Thr Val Leu Glu Gly Asp Asn Met
Glu Thr 3395 3400 3405Pro Val Thr Leu Ile Asn Phe Trp Pro Val Asp
Ser Ala Pro Ala 3410 3415 3420Ser Ser Pro Gln Leu Ser His Asp Asp
Thr His Ser Arg Ile Glu 3425 3430 3435His Tyr Ala Ser Arg Leu Ala
Glu Met Glu Asn Ser Asn Gly Ser 3440 3445 3450Tyr Leu Asn Asp Ser
Ile Ser Pro Asn Glu Ser Ile Asp Asp Glu 3455 3460 3465His Leu Leu
Ile Gln His Tyr Cys Gln Ser Leu Asn Gln Asp Ser 3470 3475 3480Pro
Leu Ser Gln Pro Arg Ser Pro Ala Gln Ile Leu Ile Ser Leu 3485 3490
3495Glu Ser Glu Glu Arg Gly Glu Leu Glu Arg Ile Leu Ala Asp Leu
3500 3505 3510Glu Glu Glu Asn Arg Asn Leu Gln Ala Glu Tyr Asp Arg
Leu Lys 3515 3520 3525Gln Gln His Glu His Lys Gly Leu Ser Pro Leu
Pro Ser Pro Pro 3530 3535 3540Glu Met Met Pro Thr Ser Pro Gln Ser
Pro Arg Asp Ala Glu Leu 3545 3550 3555Ile Ala Glu Ala Lys Leu Leu
Arg Gln His Lys Gly Arg Leu Glu 3560 3565 3570Ala Arg Met Gln Ile
Leu Glu Asp His Asn Lys Gln Leu Glu Ser 3575 3580 3585Gln Leu His
Arg Leu Arg Gln Leu Leu Glu Gln Pro Gln Ala Glu 3590 3595 3600Ala
Lys Val Asn Gly Thr Thr Val Ser Ser Pro Ser Thr Ser Leu 3605 3610
3615Gln Arg Ser Asp Ser Ser Gln Pro Met Leu Leu Arg Val Val Gly
3620 3625 3630Ser Gln Thr Ser Asp Ser Met Gly Glu Glu Asp Leu Leu
Ser Pro 3635 3640 3645Pro Gln Asp Thr Ser Thr Gly Leu Glu Glu Val
Met Glu Gln Leu 3650 3655 3660Asn Asn Ser Phe Pro Ser Ser Arg Gly
Arg Asn Thr Pro Gly Lys 3665 3670 3675Pro Met Arg Glu Asp Thr Met
3680 3685
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