# Patent

## Title
Antisense oligonucleotides for inducing exon skipping and methods of use thereof

## Abstract

An antisense molecule capable of binding to a selected target site to induce exon skipping in the dystrophin gene, as set forth in SEQ ID NO: 1 to 202.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. patent application Ser. No. 11/570,691, filed Jan. 15, 2008, which is a 35 U.S.C. §371 National Phase Application of PCT/AU2005/000943, filed Jun. 28, 2005, which claims priority to Australian Patent Application No. 2004903474, filed Jun. 28, 2004; these applications are incorporated herein by reference in their entireties.


STATEMENT REGARDING SEQUENCE LISTING
The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 42397123.txt. The text file is 61,878 bytes in size, was created on Mar. 2, 2012, and is being submitted electronically via EFS-Web.
FIELD OF THE INVENTION
The present invention relates to novel antisense compounds and compositions suitable for facilitating exon skipping. It also provides methods for inducing exon skipping using the novel antisense compounds as well as therapeutic compositions adapted for use in the methods of the invention.
BACKGROUND ART
Significant effort is currently being expended researching methods for suppressing or compensating for disease-causing mutations in genes. Antisense technologies are being developed using a range of chemistries to affect gene expression at a variety of different levels (transcription, splicing, stability, translation). Much of that research has focused on the use of antisense compounds to correct or compensate for abnormal or disease-associated genes in a myriad of different conditions.
Antisense molecules are able to inhibit gene expression with exquisite specificity and because of this many research efforts concerning oligonucleotides as modulators of gene expression have focused on inhibiting the expression of targeted genes such as oncogenes or viral genes. The antisense oligonucleotides are directed either against RNA (sense strand) or against DNA where they form triplex structures inhibiting transcription by RNA polymerase II. To achieve a desired effect in specific gene down-regulation, the oligonucleotides must either promote the decay of the targeted mRNA or block translation of that mRNA, thereby effectively preventing de novo synthesis of the undesirable target protein.
Such techniques are not useful where the object is to up-regulate production of the native protein or compensate for mutations which induce premature termination of translation such as nonsense or frame-shifting mutations. Furthermore, in cases where a normally functional protein is prematurely terminated because of mutations therein, a means for restoring some functional protein production through antisense technology has been shown to be possible through intervention during the splicing processes (Sierakowska H, et al., (1996) Proc Natl Acad Sci USA 93, 12840-12844; Wilton S D, et al., (1999) Neuromusc Disorders 9, 330-338; van Deutekom J C et al., (2001) Human Mol Genet 10, 1547-1554). In these cases, the defective gene transcript should not be subjected to targeted degradation so the antisense oligonucleotide chemistry should not promote target mRNA decay.
In a variety of genetic diseases, the effects of mutations on the eventual expression of a gene can be modulated through a process of targeted exon skipping during the splicing process. The splicing process is directed by complex multi-particle machinery that brings adjacent exon-intron junctions in pre-mRNA into close proximity and performs cleavage of phosphodiester bonds at the ends of the introns with their subsequent reformation between exons that are to be spliced together. This complex and highly precise process is mediated by sequence motifs in the pre-mRNA that are relatively short semi-conserved RNA segments to which bind the various nuclear splicing factors that are then involved in the splicing reactions. By changing the way the splicing machinery reads or recognises the motifs involved in pre-mRNA processing, it is possible to create differentially spliced mRNA molecules. It has now been recognised that the majority of human genes are alternatively spliced during normal gene expression, although the mechanisms invoked have not been identified. Using antisense oligonucleotides, it has been shown that errors and deficiencies in a coded mRNA could be bypassed or removed from the mature gene transcripts.
In nature, the extent of genetic deletion or exon skipping in the splicing process is not fully understood, although many instances have been documented to occur, generally at very low levels (Sherrat T G, et al., (1993) Am J Hum Genet 53, 1007-1015). However, it is recognised that if exons associated with disease-causing mutations can be specifically deleted from some genes, a shortened protein product can sometimes be produced that has similar biological properties of the native protein or has sufficient biological activity to ameliorate the disease caused by mutations associated with the target exon (Lu Q L, et al., (2003) Nature Medicine 9, 1009-1014; Aartsma-Rus A et al., (2004) Am J Hum Genet 74: 83-92).
This process of targeted exon skipping is likely to be particularly useful in long genes where there are many exons and introns, where there is redundancy in the genetic constitution of the exons or where a protein is able to function without one or more particular exons (e.g. with the dystrophin gene, which consists of 79 exons; or possibly some collagen genes which encode for repeated blocks of sequence or the huge nebulin or titin genes which are comprised of  ̃80 and over 370 exons, respectively).
Efforts to redirect gene processing for the treatment of genetic diseases associated with truncations caused by mutations in various genes have focused on the use of antisense oligonucleotides that either: (1) fully or partially overlap with the elements involved in the splicing process; or (2) bind to the pre-mRNA at a position sufficiently close to the element to disrupt the binding and function of the splicing factors that would normally mediate a particular splicing reaction which occurs at that element (e.g., binds to the pre-mRNA at a position within 3, 6, or 9 nucleotides of the element to be blocked).
For example, modulation of mutant dystrophin pre-mRNA splicing with antisense oligoribonucleotides has been reported both in vitro and in vivo. In one type of dystrophin mutation reported in Japan, a 52-base pair deletion mutation causes exon 19 to be removed with the flanking introns during the splicing process (Matsuo et al., (1991) J Clin Invest. 87:2127-2131). An in vitro minigene splicing system has been used to show that a 31-mer 2′-O-methyl oligoribonucleotide complementary to the 5′ half of the deleted sequence in dystrophin Kobe exon 19 inhibited splicing of wild-type pre-mRNA (Takeshima et al. (1995), J. Clin. Invest., 95, 515-520). The same oligonucleotide was used to induce exon skipping from the native dystrophin gene transcript in human cultured lymphoblastoid cells.
Dunckley et al., (1997) Nucleosides & Nucleotides, 16, 1665-1668 described in vitro constructs for analysis of splicing around exon 23 of mutated dystrophin in the mdx mouse mutant, a model for muscular dystrophy. Plans to analyse these constructs in vitro using 2′ modified oligonucleotides targeted to splice sites within and adjacent to mouse dystrophin exon 23 were discussed, though no target sites or sequences were given.
2′-O-methyl oligoribonucleotides were subsequently reported to correct dystrophin deficiency in myoblasts from the mdx mouse from this group. An antisense oligonucleotide targeted to the 3′ splice site of murine dystrophin intron 22 was reported to cause skipping of the mutant exon as well as several flanking exons and created a novel in-frame dystrophin transcript with a novel internal deletion. This mutated dystrophin was expressed in 1-2% of antisense treated mdx myotubes. Use of other oligonucleotide modifications such as 2′-O-methoxyethyl phosphodiesters are described (Dunckley et al. (1998) Human Mol. Genetics, 5, 1083-90).
Thus, antisense molecules may provide a tool in the treatment of genetic disorders such as Duchenne Muscular Dystrophy (DMD). However, attempts to induce exon skipping using antisense molecules have had mixed success. Studies on dystrophin exon 19, where successful skipping of that exon from the dystrophin pre-mRNA was achieved using a variety of antisense molecules directed at the flanking splice sites or motifs within the exon involved in exon definition as described by Errington et al. (2003) J Gen Med 5, 518-527′′.
In contrast to the apparent ease of exon 19 skipping, the first report of exon 23 skipping in the mdx mouse by Dunckley et al., (1998) is now considered to be reporting only a naturally occurring revertant transcript or artefact rather than any true antisense activity. In addition to not consistently generating transcripts missing exon 23, Dunckley et al., (1998) did not show any time course of induced exon skipping, or even titration of antisense oligonucleotides, to demonstrate dose dependent effects where the levels of exon skipping corresponded with increasing or decreasing amounts of antisense oligonucleotide. Furthermore, this work could not be replicated by other researchers.
The first example of specific and reproducible exon skipping in the mdx mouse model was reported by Wilton et al., (1999) Neuromuscular Disorders 9, 330-338. By directing an antisense molecule to the donor splice site, consistent and efficient exon 23 skipping was induced in the dystrophin mRNA within 6 hours of treatment of the cultured cells. Wilton et al., (1999), also describe targeting the acceptor region of the mouse dystrophin pre-mRNA with longer antisense oligonucleotides and being unable to repeat the published results of Dunckley et al., (1998). No exon skipping, either 23 alone or multiple removal of several flanking exons, could be reproducibly detected using a selection of antisense oligonucleotides directed at the acceptor splice site of intron 22.
While the first antisense oligonucleotide directed at the intron 23 donor splice site induced consistent exon skipping in primary cultured myoblasts, this compound was found to be much less efficient in immortalized cell cultures expressing higher levels of dystrophin. However, with refined targeting and antisense oligonucleotide design, the efficiency of specific exon removal was increased by almost an order of magnitude (see Mann C J et al., (2002) J Gen Med 4, 644-654).
Thus, there remains a need to provide antisense oligonucleotides capable of binding to and modifying the splicing of a target nucleotide sequence. Simply directing the antisense oligonucleotides to motifs presumed to be crucial for splicing is no guarantee of the efficacy of that compound in a therapeutic setting.
SUMMARY OF THE INVENTION
The present invention provides antisense molecule compounds and compositions suitable for binding to RNA motifs involved in the splicing of pre-mRNA that are able to induce specific and efficient exon skipping and a method for their use thereof.
The choice of target selection plays a crucial role in the efficiency of exon skipping and hence its subsequent application of a potential therapy. Simply designing antisense molecules to target regions of pre-mRNA presumed to be involved in splicing is no guarantee of inducing efficient and specific exon skipping. The most obvious or readily defined targets for splicing intervention are the donor and acceptor splice sites although there are less defined or conserved motifs including exonic splicing enhancers, silencing elements and branch points.
The acceptor and donor splice sites have consensus sequences of about 16 and 8 bases respectively (see FIG. 1 for schematic representation of motifs and domains involved in exon recognition, intron removal and the splicing process).
According to a first aspect, the invention provides antisense molecules capable of binding to a selected target to induce exon skipping.
For example, to induce exon skipping in exons 3 to 8, 10 to 16, 19 to 40, 42 to 44, 46, 47, and 50 to 53 in the Dystrophin gene transcript the antisense molecules are preferably selected from the group listed in Table 1A.
In a further example, it is possible to combine two or more antisense oligonucleotides of the present invention together to induce multiple exon skipping in exons 19-20, and 53. This is a similar concept to targeting of a single exon. A combination or “cocktail” of antisense oligonucleotides are directed at adjacent exons to induce efficient exon skipping.
In another example, to induce exon skipping in exons 19-20, 31, 34 and 53 it is possible to improve exon skipping of a single exon by joining together two or more antisense oligonucleotide molecules. This concept is termed by the inventor as a “weasel”, an example of a cunningly designed antisense oligonucleotide. A similar concept has been described in Aartsma-Rus A et al., (2004) Am J Hum Genet 74: 83-92).
According to a second aspect, the present invention provides antisense molecules selected and or adapted to aid in the prophylactic or therapeutic treatment of a genetic disorder comprising at least an antisense molecule in a form suitable for delivery to a patient.
According to a third aspect, the invention provides a method for treating a patient suffering from a genetic disease wherein there is a mutation in a gene encoding a particular protein and the affect of the mutation can be abrogated by exon skipping, comprising the steps of: (a) selecting an antisense molecule in accordance with the methods described herein; and (b) administering the molecule to a patient in need of such treatment.
The invention also addresses the use of purified and isolated antisense oligonucleotides of the invention, for the manufacture of a medicament for treatment of a genetic disease.
The invention further provides a method of treating a condition characterised by Duchenne muscular dystrophy, which method comprises administering to a patient in need of treatment an effective amount of an appropriately designed antisense oligonucleotide of the invention, relevant to the particular genetic lesion in that patient. Further, the invention provides a method for prophylactically treating a patient to prevent or at least minimise Duchene muscular dystrophy, comprising the step of: administering to the patient an effective amount of an antisense oligonucleotide or a pharmaceutical composition comprising one or more of these biological molecules.
The invention also provides kits for treating a genetic disease, which kits comprise at least a antisense oligonucleotide of the present invention, packaged in a suitable container and instructions for its use.
Other aspects and advantages of the invention will become apparent to those skilled in the art from a review of the ensuing description, which proceeds with reference to the following figures.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 Schematic representation of motifs and domains involved in exon recognition, intron removal and the splicing process (SEQ ID NOS:213 and 214).
FIG. 2. Diagrammatic representation of the concept of antisense oligonucleotide induced exon skipping to by-pass disease-causing mutations (not drawn to scale). The hatched box represents an exon carrying a mutation that prevents the translation of the rest of the mRNA into a protein. The solid black bar represents an antisense oligonucleotide that prevents inclusion of that exon in the mature mRNA.
FIG. 3 Gel electrophoresis showing differing efficiencies of two antisense molecules directed at exon 8 acceptor splice site. The preferred compound [H8A(−06+18)] induces strong and consistent exon skipping at a transfection concentration of 20 nanomolar in cultured normal human muscle cells. The less preferred antisense oligonucleotide [H8A(−06+14)] also induces efficient exon skipping, but at much higher concentrations. Other antisense oligonucleotides directed at exon 8 either only induced lower levels of exon skipping or no detectable skipping at all (not shown).
FIG. 4 Gel electrophoresis showing differing efficiencies of two antisense molecules directed at internal domains within exon 7, presumably exon splicing enhancers. The preferred compound [H7A(+45+67)] induces strong and consistent exon skipping at a transfection concentration of 20 nanomolar in cultured human muscle cells. The less preferred antisense oligonucleotide [H7A(+2+26)] induces only low levels of exon skipping at the higher transfection concentrations. Other antisense oligonucleotides directed at exon 7 either only induced lower levels of exon skipping or no detectable skipping at all (not shown).
FIG. 5 Gel electrophoresis showing an example of low efficiency exon 6 skipping using two non-preferred antisense molecules directed at human exon 6 donor splice site. Levels of induced exon 6 skipping are either very low [H6D(+04−21)] or almost undetectable [H6D(+18−04)]. These are examples of non-preferred antisense oligonucleotides to demonstrate that antisense oligonucleotide design plays a crucial role in the efficacy of these compounds.
FIG. 6 Gel electrophoresis showing strong and efficient human exon 6 skipping using an antisense molecules [H6A(+69+91)] directed at an exon 6 internal domain, presumably an exon splicing enhancer. This preferred compound induces consistent exon skipping at a transfection concentration of 20 nanomolar in cultured human muscle cells.
FIG. 7 Gel electrophoresis showing strong human exon 4 skipping using an antisense molecule H4A(+13+32) directed at an exon 6 internal domain, presumably an exon splicing enhancer. This preferred compound induces strong and consistent exon skipping at a transfection concentration of 20 nanomolar in cultured human muscle cells.
FIG. 8 Gel electrophoresis showing (8B) strong human exon 11 skipping using antisense molecule H11A(+75+97) directed at an exon 11 internal domain; and (8B) strong human exon 12 skipping using antisense molecule H12A(+52+75) directed at exon 12 internal domain.
FIG. 9 Gel electrophoresis showing (9A) strong human exon 15 skipping using antisense molecules H15A(+48+71) and H15A(−12+19) directed at an exon 15 internal domain; and (9B) strong human exon 16 skipping using antisense molecules H16A(−12+19) and H16A(−06+25).
FIG. 10 Gel electrophoresis showing human exon 19/20 skipping using antisense molecules H20A(+44+71) and H20A(+149+170) directed at an exon 20 and a “cocktail” of antisense oligonucleotides H19A(+35+65, H20A(+44+71) and H20A(+149+170) directed at exons 19/20.
FIG. 11 Gel electrophoresis showing human exon 19/20 skipping using “weasels” directed at exons 19 and 20.
FIG. 12 Gel electrophoresis showing exon 22 skipping using antisense molecules H22A(+125+106), H22A(+47+69), H22A(+80+101) and H22D(+13−11) directed at exon 22.
FIG. 13 Gel electrophoresis showing exon 31 skipping using antisense molecules H31D(+01−25) and H31D(+03−22); and a “cocktail” of antisense molecules directed at exon 31.
FIG. 14 Gel electrophoresis showing exon 33 skipping using antisense molecules H33A(+30+56) and H33A(+64+88) directed at exon 33.
FIG. 15 Gel electrophoresis showing exon 35 skipping using antisense molecules H35A(+141+161), H35A(+116+135), and H35A(+24+43) and a “cocktail of two antisense molecules, directed at exon 35.
FIG. 16 Gel electrophoresis showing exon 36 skipping using antisense molecules H32A(+49+73) and H36A(+26+50) directed at exon 36.
FIG. 17 Gel electrophoresis showing exon 37 skipping using antisense molecules H37A(+82+105) and H37A(+134+157) directed at exon 37.
FIG. 18 Gel electrophoresis showing exon 38 skipping using antisense molecule H38A(+88+112) directed at exon 38.
FIG. 19 Gel electrophoresis showing exon 40 skipping using antisense molecule H40A(−05+17) directed at exon 40.
FIG. 20 Gel electrophoresis showing exon 42 skipping using antisense molecule H42A(−04+23) directed at exon 42.
FIG. 21 Gel electrophoresis showing exon 46 skipping using antisense molecule H46A(+86+115) directed at exon 46
FIG. 22 Gel electrophoresis showing exon 51, exon 52 and exon 53 skipping using various antisense molecules directed at exons 51, 52 and 53, respectively. A “cocktail” of antisense molecules is also shown directed at exon 53.







TABLE 1A







Brief Description of the Sequence listings











NUCLEOTIDE SEQUENCE


SEQ ID
SEQUENCE
(5′ - 3′)












1
H8A(−06+18)
GAU AGG UGG UAU CAA CAU




CUG UAA


 


2
H8A(−03+18)
GAU AGG UGG UAU CAA CAU




CUG


 


3
H8A(−07+18)
GAU AGG UGG UAU CAA CAU




CUG UAA G


 


4
H8A(−06+14)
GGU GGU AUC AAC AUC UGU




AA


 


5
H8A(−10+10)
GUA UCA ACA UCU GUA AGC




AC


 


6
H7A(+45+67)
UGC AUG UUC CAG UCG UUG




UGU GG


 


7
H7A(+02+26)
CAC UAU UCC AGU CAA AUA




GGU CUG G


 


8
H7D(+15−10)
AUU UAC CAA CCU UCA GGA




UCG AGU A


 


9
H7A(−18+03)
GGC CUA AAA CAC AUA CAC




AUA


 


10
C6A(−10+10)
CAU UUU UGA CCU ACA UGU




GG


 


11
C6A(−14+06)
UUU GAC CUA CAU GUG GAA




AG


 


12
C6A(−14+12)
UAC AUU UUU GAC CUA CAU




GUG GAA AG


 


13
C6A(−13+09)
AUU UUU GAC CUA CAU GGG




AAA G


 


14
CH6A(+69+91)
UAC GAG UUG AUU GUC GGA




CCC AG


 


15
C6D(+12−13)
GUG GUC UCC UUA CCU AUG




ACU GUG G


 


16
C6D(+06−11)
GGU CUC CUU ACC UAU GA


 


17
H6D(+04−21)
UGU CUC AGU AAU CUU CUU




ACC UAU


 


18
H6D(+18−04)
UCU UAC CUA UGA CUA UGG




AUG AGA


 


19
H4A(+13+32)
GCA UGA ACU CUU GUG GAU




CC


 


20
H4D(+04−16)
CCA GGG UAC UAC UUA CAU




UA


 


21
H4D(−24−44)
AUC GUG UGU CAC AGC AUC




CAG


 


22
H4A(+11+40)
UGU UCA GGG CAU GAA CUC




UUG UGG AUC CUU


 


23
H3A(+30+60)
UAG GAG GCG CCU CCC AUC




CUG UAG GUC ACU G


 


24
H3A(+35+65)
AGG UCU AGG AGG CGC CUC




CCA UCC UGU AGG U


 


25
H3A(+30+54)
GCG CCU CCC AUC CUG UAG




GUC ACU G


 


26
H3D(+46−21)
CUU CGA GGA GGU CUA GGA




GGC GCC UC


 


27
H3A(+30+50)
CUC CCA UCC UGU AGG UCA




CUG


 


28
H3D(+19−03)
UAC CAG UUU UUG CCC UGU




CAG G


 


29
H3A(−06+20)
UCA AUA UGC UGC UUC CCA




AAC UGA AA


 


30
H3A(+37+61)
CUA GGA GGC GCC UCC CAU




CCU GUA G


 


31
H5A(+20+50)
UUA UGA UUU CCA UCU ACG




AUG UCA GUA CUU C


 


32
H5D(+25−05)
CUU ACC UGC CAG UGG AGG




AUU AUA UUC CAA A


 


33
H5D(+10−15)
CAU CAG GAU UCU UAC CUG




CCA GUG G


 


34
H5A(+10+34)
CGA UGU CAG UAC UUC CAA




UAU UCA C


 


35
H5D(−04−21)
ACC AUU CAU CAG GAU UCU


 


36
H5D(+16−02)
ACC UGC CAG UGG AGG AUU


 


37
H5A(−07+20)
CCA AUA UUC ACU AAA UCA




ACC UGU UAA


 


38
H5D(+18−12)
CAG GAU UCU UAC CUG CCA




GUG GAG GAU UAU


 


39
H5A(+05+35)
ACG AUG UCA GUA CUU CCA




AUA UUC ACU AAA U


 


40
H5A(+15+45)
AUU UCC AUC UAC GAU GUC




AGU ACU UCC AAU A


 


41
H10A(−05+16)
CAG GAG CUU CCA AAU GCU




GCA


 


42
H10A(−05+24)
CUU GUC UUC AGG AGC UUC




CAA AUG CUG CA


 


43
H10A(+98+119)
UCC UCA GCA GAA AGA AGC




CAC G


 


44
H10A(+130+149)
UUA GAA AUC UCU CCU UGU




GC


 


45
H10A(−33−14)
UAA AUU GGG UGU UAC ACA




AU


 


46
H11D(+26+49)
CCC UGA GGC AUU CCC AUC




UUG AAU


 


47
H11D(+11−09)
AGG ACU UAC UUG CUU UGU




UU


 


48
H11A(+118+140)
CUU GAA UUU AGG AGA UUC




AUC UG


 


49
H11A(+75+97)
CAU CUU CUG AUA AUU UUC




CUG UU


 


50
H12A(+52+75)
UCU UCU GUU UUU GUU AGC




CAG UCA


 


51
H12A(−10+10)
UCU AUG UAA ACU GAA AAU




UU


 


52
H12A(+11+30)
UUC UGG AGA UCC AUU AAA




AC


 


53
H13A(+77+100)
CAG CAG UUG CGU GAU CUC




CAC UAG


 


54
H13A(+55+75)
UUC AUC AAC UAC CAC CAC




CAU


 


55
H13D(+06−19)
CUA AGC AAA AUA AUC UGA




CCU UAA G


 


56
H14A(+37+64)
CUU GUA AAA GAA CCC AGC




GGU CUU CUG U


 


57
H14A(+14+35)
CAU CUA CAG AUG UUU GCC




CAU C


 


58
H14A(+51+73)
GAA GGA UGU CUU GUA AAA




GAA CC


 


59
H14D(−02+18)
ACC UGU UCU UCA GUA AGA




CG


 


60
H14D(+14−10)
CAU GAC ACA CCU GUU CUU




CAG UAA


 


61
H14A(+61+80)
CAU UUG AGA AGG AUG UCU




UG


 


62
H14A(−12+12)
AUC UCC CAA UAC CUG GAG




AAG AGA


 


63
H15A(−12+19)
GCC AUG CAC UAA AAA GGC




ACU GCA AGA CAU U


 


64
H15A(+48+71)
UCU UUA AAG CCA GUU GUG




UGA AUC


 


65
H15A(+08+28)
UUU CUG AAA GCC AUG CAC




UAA


 


66
H15D(+17−08)
GUA CAU ACG GCC AGU UUU




UGA AGA C


 


67
H16A(−12+19)
CUA GAU CCG CUU UUA AAA




CCU GUU AAA ACA A


 


68
H16A(−06+25)
UCU UUU CUA GAU CCG CUU




UUA AAA CCU GUU A


 


69
H16A(−06+19)
CUA GAU CCG CUU UUA AAA




CCU GUU A


 


70
H16A(+87+109)
CCG UCU UCU GGG UCA CUG




ACU UA


 


71
H16A(−07+19)
CUA GAU CCG CUU UUA AAA




CCU GUU AA


 


72
H16A(−07+13)
CCG CUU UUA AAA CCU GUU




AA


 


73
H16A(+12+37)
UGG AUU GCU UUU UCU UUU




CUA GAU CC


 


74
H16A(+92+116)
CAU GCU UCC GUC UUC UGG




GUC ACU G


 


75
H16A(+45+67)
G AUC UUG UUU GAG UGA AUA




CAG U


 


76
H16A(+105+126)
GUU AUC CAG CCA UGC UUC




CGU C


 


77
H16D(+05−20)
UGA UAA UUG GUA UCA CUA




ACC UGU G


 


78
H16D(+12−11)
GUA UCA CUA ACC UGU GCU




GUA C


 


79
H19A(+35+53)
CUG CUG GCA UCU UGC AGU U


 


80
H19A(+35+65)
GCC UGA GCU GAU CUG CUG




GCA UCU UGC AGU U


 


81
H20A(+44+71)
CUG GCA GAA UUC GAU CCA




CCG GCU GUU C


 


82
H20A(+147+168)
CAG CAG UAG UUG UCA UCU




GCU C


 


83
H20A(+185+203)
UGA UGG GGU GGU GGG UUG G


 


84
H20A(−08+17)
AUC UGC AUU AAC ACC CUC




UAG AAA G


 


85
H20A(+30+53)
CCG GCU GUU CAG UUG UUC




UGA GGC


 


86
H20A(−11+17)
AUC UGC AUU AAC ACC CUC




UAG AAA GAA A


 


87
H20D(+08−20)
GAA GGA GAA GAG AUU CUU




ACC UUA CAA A


 


88
H20A(+44+63)
AUU CGA UCC ACC GGC UGU UC


 


89
H20A(+149+168
CAG CAG UAG UUG UCA UCU GC


 


90
H21A(−06+16)
GCC GGU UGA CUU CAU CCU




GUG C


 


91
H21A(+85+106)
CUG CAU CCA GGA ACA UGG




GUC C


 


92
H21A(+85+108)
GUC UGC AUC CAG GAA CAU




GGG UC


 


93
H21A(+08+31)
GUU GAA GAU CUG AUA GCC




GGU UGA


 


94
H21D(+18−07)
UAC UUA CUG UCU GUA GCU




CUU UCU


 


95
H22A(+22+45)
CAC UCA UGG UCU CCU GAU




AGC GCA


 


96
H22A(+125+106)
CUG CAA UUC CCC GAG UCU




CUG C


 


97
H22A(+47+69)
ACU GCU GGA CCC AUG UCC




UGA UG


 


98
H22A(+80+101)
CUA AGU UGA GGU AUG GAG




AGU


 


99
H22D(+13−11)
UAU UCA CAG ACC UGC AAU




UCC CC


 


100
H23A(+34+59)
ACA GUG GUG CUG AGA UAG




UAU AGG CC


 


101
H23A(+18+39)
UAG GCC ACU UUG UUG CUC




UUG C


 


102
H23A(+72+90)
UUC AGA GGG CGC UUU CUU C


 


103
H24A(+48+70)
GGG CAG GCC AUU CCU CCU




UCA GA


 


104
H24A(−02+22)
UCU UCA GGG UUU GUA UGU




GAU UCU


 


105
H25A(+9+36)
CUG GGC UGA AUU GUC UGA




AUA UCA CUG


 


106
H25A(+131+156)
CUG UUG GCA CAU GUG AUC




CCA CUG AG


 


107
H25D(+16−08)
GUC UAU ACC UGU UGG CAC




AUG UGA


 


108
H26A(+132+156)
UGC UUU CUG UAA UUC AUC




UGG AGU U


 


109
H26A(−07+19)
CCU CCU UUC UGG CAU AGA




CCU UCC AC


 


110
H26A(+68+92)
UGU GUC AUC CAU UCG UGC




AUC UCU G


 


111
H27A(+82+106)
UUA AGG CCU CUU GUG CUA




CAG GUG G


 


112
H27A(−4+19)
GGG CCU CUU CUU UAG CUC




UCU GA


 


113
H27D(+19−03)
GAC UUC CAA AGU CUU GCA




UUU C


 


114
H28A(−05+19)
GCC AAC AUG CCC AAA CUU




CCU AAG


 


115
H28A(+99+124)
CAG AGA UUU CCU CAG CUC




CGC CAG GA


 


116
H28D(+16−05)
CUU ACA UCU AGC ACC UCA




GAG


 


117
H29A(+57+81)
UCC GCC AUC UGU UAG GGU




CUG UGC C


 


118
H29A(+18+42)
AUU UGG GUU AUC CUC UGA




AUG UCG C


 


119
H29D(+17−05)
CAU ACC UCU UCA UGU AGU




UCU C


 


120
H30A(+122+147)
CAU UUG AGC UGC GUC CAC




CUU GUC UG


 


121
H30A(+25+50)
UCC UGG GCA GAC UGG AUG




CUC UGU UC


 


122
H30D(+19−04)
UUG CCU GGG CUU CCU GAG




GCA UU


 


123
H31D(+06−18)
UUC UGA AAU AAC AUA UAC




CUG UGC


 


124
H31D(+03−22)
UAG UUU CUG AAA UAA CAU




AUA CCU G


 


125
H31A(+05+25)
GAC UUG UCA AAU CAG AUU




GGA


 


126
H31D(+04−20)
GUU UCU GAA AUA ACA UAU




ACC UGU


 


127
H32D(+04−16)
CAC CAG AAA UAC AUA CCA CA


 


128
H32A(+151+170)
CAA UGA UUU AGC UGU GAC UG


 


129
H32A(+10+32)
CGA AAC UUC AUG GAG ACA




UCU UG


 


130
H32A(+49+73)
CUU GUA GAC GCU GCU CAA




AAU UGG C


 


131
H33D(+09−11)
CAU GCA CAC ACC UUU GCU CC


 


132
H33A(+53+76)
UCU GUA CAA UCU GAC GUC




CAG UCU


 


133
H33A(+30+56)
GUC UUU AUC ACC AUU UCC




ACU UCA GAC


 


134
H33A(+64+88)
CCG UCU GCU UUU UCU GUA




CAA UCU G


 


135
H34A(+83+104)
UCC AUA UCU GUA GCU GCC




AGC C


 


136
H34A(+143+165)
CCA GGC AAC UUC AGA AUC




CAA AU


 


137
H34A(−20+10)
UUU CUG UUA CCU GAA AAG




AAU UAU AAU GAA


 


138
H34A(+46+70)
CAU UCA UUU CCU UUC GCA




UCU UAC G


 


139
H34A(+95+120)
UGA UCU CUU UGU CAA UUC




CAU AUC UG


 


140
H34D(+10−20)
UUC AGU GAU AUA GGU UUU




ACC UUU CCC CAG


 


141
H34A(+72+96)
CUG UAG CUG CCA GCC AUU




CUG UCA AG


 


142
H35A(+141+161)
UCU UCU GCU CGG GAG GUG




ACA


 


143
H35A(+116+135)
CCA GUU ACU AUU CAG AAG AC


 


144
H35A(+24+43)
UCU UCA GGU GCA CCU UCU GU


 


145
H36A(+26+50)
UGU GAU GUG GUC CAC AUU




CUG GUC A


 


146
H36A(−02+18)
CCA UGU GUU UCU GGU AUU CC


 


147
H37A(+26+50)
CGU GUA GAG UCC ACC UUU




GGG CGU A


 


148
H37A(+82+105)
UAC UAA UUU CCU GCA GUG




GUC ACC


 


149
H37A(+134+157)
UUC UGU GUG AAA UGG CUG




CAA AUC


 


150
H38A(−01+19)
CCU UCA AAG GAA UGG AGG CC


 


151
H38A(+59+83)
UGC UGA AUU UCA GCC UCC




AGU GGU U


 


152
H38A(+88+112)
UGA AGU CUU CCU CUU UCA




GAU UCA C


 


153
H39A(+62+85)
CUG GCU UUC UCU CAU CUG




UGA UUC


 


154
H39A(+39+58)
GUU GUA AGU UGU CUC CUC UU


 


155
H39A(+102+121)
UUG UCU GUA ACA GCU GCU GU


 


156
H39D(+10−10)
GCU CUA AUA CCU UGA GAG CA


 


157
H40A(−05+17)
CUU UGA GAC CUC AAA UCC




UGU U


 


158
H40A(+129+153)
CUU UAU UUU CCU UUC AUC




UCU GGG C


 


159
H42A(−04+23)
AUC GUU UCU UCA CGG ACA




GUG UGC UGG


 


160
H42A(+86+109)
GGG CUU GUG AGA CAU GAG




UGA UUU


 


161
H42D(+19−02)
A CCU UCA GAG GAC UCC UCU




UGC


 


162
H43D(+10−15)
UAU GUG UUA CCU ACC CUU




GUC GGU C


 


163
H43A(+101+120)
GGA GAG AGC UUC CUG UAG CU


 


164
H43A(+78+100)
UCA CCC UUU CCA CAG GCG




UUG CA


 


165
H44A(+85+104)
UUU GUG UCU UUC UGA GAA AC


 


166
H44D(+10−10)
AAA GAC UUA CCU UAA GAU AC


 


167
H44A(−06+14)
AUC UGU CAA AUC GCC UGC AG


 


168
H46D(+16−04)
UUA CCU UGA CUU GCU CAA GC


 


169
H46A(+90+109)
UCC AGG UUC AAG UGG GAU AC


 


170
H47A(+76+100)
GCU CUU CUG GGC UUA UGG




GAG CAC U


 


171
H47D(+25−02)
ACC UUU AUC CAC UGG AGA




UUU GUC UGC


 


172
H47A(−9+12)
UUC CAC CAG UAA CUG AAA




CAG


 


173
H50A(+02+30)
CCA CUC AGA GCU CAG AUC




UUC UAA CUU CC


 


174
H50A(+07+33)
CUU CCA CUC AGA GCU CAG




AUC UUC UAA


 


175
H50D(+07−18)
GGG AUC CAG UAU ACU UAC




AGG CUC C


 


176
H51A(−01+25)
ACC AGA GUA ACA GUC UGA




GUA GGA GC


 


177
H51D(+16−07)
CUC AUA CCU UCU GCU UGA




UGA UC


 


178
H51A(+111+134)
UUC UGU CCA AGC CCG GUU




GAA AUC


 


179
H51A(+61+90)
ACA UCA AGG AAG AUG GCA




UUU CUA GUU UGG


 


180
H51A(+66+90)
ACA UCA AGG AAG AUG GCA




UUU CUA G


 


181
H51A(+66+95)
CUC CAA CAU CAA GGA AGA




UGG CAU UUC UAG


 


182
H51D(+08−17)
AUC AUU UUU UCU CAU ACC




UUC UGC U


 


183
H51A/D(+08−17) &
AUC AUU UUU UCU CAU ACC



(−15+)
UUC UGC UAG GAG CUA AAA


 


184
H51A(+175+195)
CAC CCA CCA UCA CCC UCU




GUG


 


185
H51A(+199+220)
AUC AUC UCG UUG AUA UCC




UCA A


 


186
H52A(−07+14)
UCC UGC AUU GUU GCC UGU




AAG


 


187
H52A(+12+41)
UCC AAC UGG GGA CGC CUC




UGU UCC AAA UCC


 


188
H52A(+17+37)
ACU GGG GAC GCC UCU GUU




CCA


 


189
H52A(+93+112)
CCG UAA UGA UUG UUC UAG CC


 


190
H52D(+05−15)
UGU UAA AAA ACU UAC UUC GA


 


191
H53A(+45+69)
CAU UCA ACU GUU GCC UCC




GGU UCU G


 


192
H53A(+39+62)
CUG UUG CCU CCG GUU CUG




AAG GUG


 


193
H53A(+39+69)
CAU UCA ACU GUU GCC UCC




GGU UCU GAA GGU G


 


194
H53D(+14−07)
UAC UAA CCU UGG UUU CUG




UGA


 


195
H53A(+23+47)
CUG AAG GUG UUC UUG UAC




UUC AUC C


 


196
H53A(+150+176)
UGU AUA GGG ACC CUC CUU




CCA UGA CUC


 


197
H53D(+20−05)
CUA ACC UUG GUU UCU GUG




AUU UUC U


 


198
H53D(+09−18)
GGU AUC UUU GAU ACU AAC




CUU GGU UUC


 


199
H53A(−12+10)
AUU CUU UCA ACU AGA AUA




AAA G


 


200
H53A(−07+18)
GAU UCU GAA UUC UUU CAA




CUA GAA U


 


201
H53A(+07+26)
AUC CCA CUG AUU CUG AAU UC


 


202
H53A(+124+145)
UUG GCU CUG GCC UGU CCU




AAG A


 


203
H46A(+86+315)
CUC UUU UCC AGG UUC AAG




UGG GAU ACU AGC


 


204
H46A(+107+137)
CAA GCU UUU CUU UUA GUU




GCU GCU CUU UUC C


 


205
H46A(−10+20)
UAU UCU UUU GUU CUU CUA




GCC UGG AGA AAG


 


206
H46A(+50+77)
CUG CUU CCU CCA ACC AUA




AAA CAA AUU C


 


207
H45A(−06+20)
CCA AUG CCA UCC UGG AGU




UCC UGU AA


 


208
H45A(+91+110)
UCC UGU AGA AUA CUG GCA UC


 


209
H45A(+125+151)
UGC AGA CCU CCU GCC ACC




GCA GAU UCA


 


210
H45D(+16−04)
CUA CCU CUU UUU UCU GUC UG


 


211
H45A(+71+90)
UGU UUU UGA GGA UUG CUG AA





Description of 2′-O-methyl phosphorothioate antisense oligonucleotides that have been used to date to study induced exon skipping during the processing of the dystrophin pre-mRNA. Since these 2′-O-methyl antisense oligonucleotides are more RNA-like, U represents uracil. With other antisense chemistries such as peptide nucleic acids or morpholinos, these U bases may be shown as “T”.















TABLE 1B





SEQ ID
SEQUENCE
NUCLEOTIDE SEQUENCE (5′-3′)

















81
H20A(+44+71)
CUG GCA GAA UUC GAU CCA CCG




GCU GUU C


82
H20A(+147+168)
CAG CAG UAG UUG UCA UCU GCU




C


 


80
H19A(+35+65)
GCC UGA GCU GAU CUG CUG GCA




UCU UGC AGU U


81
H20A(+44+71)
CUG GCA GAA UUC GAU CCA CCG




GCU GUU C


82
H20A(+147+168)
CAG CAG UAG UUG UCA UCU GCU




C


 


194
H53D(+14−07)
UAC UAA CCU UGG UUU CUG UGA


195
H53A(+23+47)
CUG AAG GUG UUC UUG UAC UUC




AUC C


196
H53A(+150+175)
UGU AUA GGG ACC CUC CUU CCA




UGA CUC





Description of a cocktail of 2′-O-methyl phosphorothioate antisense oligonucleotides that have been used to date to study induced exon skipping during the processing of the dystrophin pre-mRNA.















TABLE 1C





SEQ ID
SEQUENCE
NUCELOTIDE SEQUENCE (5′-3′)

















81
H20A(+44+71)-
CUG GCA GAA UUC GAU CCA CCG




GCU GUU C-


82
H20A(+147+168)
CAG CAG UAG UUG UCA UCU GCU




C


 


80
H19A(+35+65)-
GCC UGA GCU GAU CUG CUG GCA




UCU UGC AGU U


88
H20A(+44+63)-
-AUU CGA UCC ACC GGC UGU UC-


79
H20A(+149+168)
CUG CUG GCA UCU UGC AGU U


 


80
H19A(+35+65)-
GCC UGA GCU GAU CUG CUG GCA




UCU UGC AGU U


88
H20A(+44+63)
-AUU CGA UCC ACC GGC UGU UC-


 


80
H19A(+35+65)-
GCC UGA GCU GAU CUG CUG GCA




UCU UGC AGU U


79
H20A(+149+168)
CUG CUG GCA UCU UGC AGU U


 


138
H34A(+46+70)-
CAU UCA UUU CCU UUC GCA UCU




UAC G-


139
H34A(+94+120)
UGA UCU CUU UGU CAA UUC CAU




AUC UG


 


124
H31D(+03−22)-
UAG UUU CUG AAA UAA CAU AUA



UU-
CCU G-UU-


144
H35A(+24+43)
UCU UCA GGU GCA CCU UCU GU


 


195
H53A(+23+47)-
CUG AAG GUG UUC UUG UAC UUC



AA-
AUC C-


196
H53A(+150+175)-
UGU AUA GGG ACC CUC CUU CCA




UGA CUC-


 


194
AA-
AA-



H53D(+14−07)
UAC UAA CCU UGG UUU CUG UGA


 


—
Aimed at exons
CAG CAG UAG UUG UCA UCU GCU


212
19/20/20
CAA CUG GCA GAA UUC GAU CCA




CCG GCU GUU CAA GCC UGA GCU




GAU CUG CUC GCA UCU UGC AGU





Description of a “weasel” of 2′-O-methyl phosphorothioate antisense oligonucleotides that have been used to date to study induced exon skipping during the processing of the dystrophin pre-mRNA.









DETAILED DESCRIPTION OF THE INVENTION
General
Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variation and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in the specification, individually or collectively and any and all combinations or any two or more of the steps or features.
The present invention is not to be limited in scope by the specific embodiments described herein, which are intended for the purpose of exemplification only. Functionally equivalent products, compositions and methods are clearly within the scope of the invention as described herein.
Sequence identity numbers (SEQ ID NO:) containing nucleotide and amino acid sequence information included in this specification are collected at the end of the description and have been prepared using the programme Patent In Version 3.0. Each nucleotide or amino acid sequence is identified in the sequence listing by the numeric indicator <210> followed by the sequence identifier (e.g. <210>1, <210>2, etc.). The length, type of sequence and source organism for each nucleotide or amino acid sequence are indicated by information provided in the numeric indicator fields <211>, <212> and <213>, respectively. Nucleotide and amino acid sequences referred to in the specification are defined by the information provided in numeric indicator field <400> followed by the sequence identifier (e.g. <400>1, <400>2, etc.).
An antisense molecules nomenclature system was proposed and published to distinguish between the different antisense molecules (see Mann et al., (2002) J Gen Med 4, 644-654). This nomenclature became especially relevant when testing several slightly different antisense molecules, all directed at the same target region, as shown below:

H#A/D(x:y).

The first letter designates the species (e.g. H: human, M: murine, C: canine) “#” designates target dystrophin exon number.
“A/D” indicates acceptor or donor splice site at the beginning and end of the exon, respectively.
(x y) represents the annealing coordinates where “−” or “+” indicate intronic or exonic sequences respectively. As an example, A(−6+18) would indicate the last 6 bases of the intron preceding the target exon and the first 18 bases of the target exon. The closest splice site would be the acceptor so these coordinates would be preceded with an “A”. Describing annealing coordinates at the donor splice site could be D(+2−18) where the last 2 exonic bases and the first 18 intronic bases correspond to the annealing site of the antisense molecule. Entirely exonic annealing coordinates that would be represented by A(+65+85), that is the site between the 65th and 85th nucleotide from the start of that exon.
The entire disclosures of all publications (including patents, patent applications, journal articles, laboratory manuals, books, or other documents) cited herein are hereby incorporated by reference. No admission is made that any of the references constitute prior art or are part of the common general knowledge of those working in the field to which this invention relates.
As used necessarily herein the term “derived” and “derived from” shall be taken to indicate that a specific integer may be obtained from a particular source albeit not directly from that source.
Throughout this specification, unless the context requires otherwise, the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.
Other definitions for selected terms used herein may be found within the detailed description of the invention and apply throughout. Unless otherwise defined, all other scientific and technical terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which the invention belongs.
DESCRIPTION OF THE PREFERRED EMBODIMENT
When antisense molecule(s) are targeted to nucleotide sequences involved in splicing in exons within pre-mRNA sequences, normal splicing of the exon may be inhibited causing the splicing machinery to by-pass the entire mutated exon from the mature mRNA. The concept of antisense oligonucleotide induced exon skipping is shown in FIG. 2. In many genes, deletion of an entire exon would lead to the production of a non-functional protein through the loss of important functional domains or the disruption of the reading frame. In some proteins, however, it is possible to shorten the protein by deleting one or more exons, without disrupting the reading frame, from within the protein without seriously altering the biological activity of the protein. Typically, such proteins have a structural role and or possess functional domains at their ends. The present invention describes antisense molecules capable of binding to specified dystrophin pre-mRNA targets and re-directing processing of that gene.
Antisense Molecules
According to a first aspect of the invention, there is provided antisense molecules capable of binding to a selected target to induce exon skipping. To induce exon skipping in exons of the Dystrophin gene transcript, the antisense molecules are preferably selected from the group of compounds shown in Table 1A. There is also provided a combination or “cocktail” of two or more antisense oligonucleotides capable of binding to a selected target to induce exon skipping. To induce exon skipping in exons of the Dystrophin gene transcript, the antisense molecules in a “cocktail” are preferably selected from the group of compounds shown in Table 1B. Alternatively, exon skipping may be induced by antisense oligonucleotides joined together “weasels” preferably selected from the group of compounds shown in Table 1C.
Designing antisense molecules to completely mask consensus splice sites may not necessarily generate any skipping of the targeted exon. Furthermore, the inventors have discovered that size or length of the antisense oligonucleotide itself is not always a primary factor when designing antisense molecules. With some targets such as exon 19, antisense oligonucleotides as short as 12 bases were able to induce exon skipping, albeit not as efficiently as longer (20-31 bases) oligonucleotides. In some other targets, such as murine dystrophin exon 23, antisense oligonucleotides only 17 residues long were able to induce more efficient skipping than another overlapping compound of 25 nucleotides.
The inventors have also discovered that there does not appear to be any standard motif that can be blocked or masked by antisense molecules to redirect splicing. In some exons, such as mouse dystrophin exon 23, the donor splice site was the most amenable to target to re-direct skipping of that exon. It should be noted that designing and testing a series of exon 23 specific antisense molecules to anneal to overlapping regions of the donor splice site showed considerable variation in the efficacy of induced exon skipping. As reported in Mann et al., (2002) there was a significant variation in the efficiency of bypassing the nonsense mutation depending upon antisense oligonucleotide annealing (“Improved antisense oligonucleotide induced exon skipping in the mdx mouse model of muscular dystrophy”. J Gen Med 4: 644-654). Targeting the acceptor site of exon 23 or several internal domains was not found to induce any consistent exon 23 skipping.
In other exons targeted for removal, masking the donor splice site did not induce any exon skipping. However, by directing antisense molecules to the acceptor splice site (human exon 8 as discussed below), strong and sustained exon skipping was induced. It should be noted that removal of human exon 8 was tightly linked with the co-removal of exon 9. There is no strong sequence homology between the exon 8 antisense oligonucleotides and corresponding regions of exon 9 so it does not appear to be a matter of cross reaction. Rather the splicing of these two exons is inextricably linked. This is not an isolated instance as the same effect is observed in canine cells where targeting exon 8 for removal also resulted in the skipping of exon 9. Targeting exon 23 for removal in the mouse dystrophin pre-mRNA also results in the frequent removal of exon 22 as well. This effect occurs in a dose dependent manner and also indicates close coordinated processing of 2 adjacent exons.
In other targeted exons, antisense molecules directed at the donor or acceptor splice sites did not induce exon skipping while annealing antisense molecules to intra-exonic regions (i.e. exon splicing enhancers within human dystrophin exon 6) was most efficient at inducing exon skipping. Some exons, both mouse and human exon 19 for example, are readily skipped by targeting antisense molecules to a variety of motifs. That is, targeted exon skipping is induced after using antisense oligonucleotides to mask donor and acceptor splice sites or exon splicing enhancers.
To identify and select antisense oligonucleotides suitable for use in the modulation of exon skipping, a nucleic acid sequence whose function is to be modulated must first be identified. This may be, for example, a gene (or mRNA transcribed form the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent. Within the context of the present invention, preferred target site(s) are those involved in mRNA splicing (i.e. splice donor sites, splice acceptor sites, or exonic splicing enhancer elements). Splicing branch points and exon recognition sequences or splice enhancers are also potential target sites for modulation of mRNA splicing.
Preferably, the present invention aims to provide antisense molecules capable of binding to a selected target in the dystrophin pre-mRNA to induce efficient and consistent exon skipping. Duchenne muscular dystrophy arises from mutations that preclude the synthesis of a functional dystrophin gene product. These Duchenne muscular dystrophy gene defects are typically nonsense mutations or genomic rearrangements such as deletions, duplications or micro-deletions or insertions that disrupt the reading frame. As the human dystrophin gene is a large and complex gene with the 79 exons being spliced together to generate a mature mRNA with an open reading frame of approximately 11,000 bases, there are many positions where these mutations can occur. Consequently, a comprehensive antisense oligonucleotide based therapy to address many of the different disease-causing mutations in the dystrophin gene will require that many exons can be targeted for removal during the splicing process.
Within the context of the present invention, preferred target site(s) are those involved in mRNA splicing (i.e. splice donor sites, splice acceptor sites or exonic splicing enhancer elements). Splicing branch points and exon recognition sequences or splice enhancers are also potential target sites for modulation of mRNA splicing.
The oligonucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides which can hydrogen bond with each other. Thus, “specifically hybridisable” and “complementary” are terms which are used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the oligonucleotide and the DNA or RNA target. It is understood in the art that the sequence of an antisense molecule need not be 100% complementary to that of its target sequence to be specifically hybridisable. An antisense molecule is specifically hybridisable when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.
While the above method may be used to select antisense molecules capable of deleting any exon from within a protein that is capable of being shortened without affecting its biological function, the exon deletion should not lead to a reading frame shift in the shortened transcribed mRNA. Thus, if in a linear sequence of three exons the end of the first exon encodes two of three nucleotides in a codon and the next exon is deleted then the third exon in the linear sequence must start with a single nucleotide that is capable of completing the nucleotide triplet for a codon. If the third exon does not commence with a single nucleotide there will be a reading frame shift that would lead to the generation of truncated or a non-functional protein.
It will be appreciated that the codon arrangements at the end of exons in structural proteins may not always break at the end of a codon, consequently there may be a need to delete more than one exon from the pre-mRNA to ensure in-frame reading of the mRNA. In such circumstances, a plurality of antisense oligonucleotides may need to be selected by the method of the invention wherein each is directed to a different region responsible for inducing splicing in the exons that are to be deleted.
The length of an antisense molecule may vary so long as it is capable of binding selectively to the intended location within the pre-mRNA molecule. The length of such sequences can be determined in accordance with selection procedures described herein. Generally, the antisense molecule will be from about 10 nucleotides in length up to about 50 nucleotides in length. It will be appreciated however that any length of nucleotides within this range may be used in the method. Preferably, the length of the antisense molecule is between 17 to 30 nucleotides in length.
In order to determine which exons can be connected in a dystrophin gene, reference should be made to an exon boundary map. Connection of one exon with another is based on the exons possessing the same number at the 3′ border as is present at the 5′ border of the exon to which it is being connected. Therefore, if exon 7 were deleted, exon 6 must connect to either exons 12 or 18 to maintain the reading frame. Thus, antisense oligonucleotides would need to be selected which redirected splicing for exons 7 to 11 in the first instance or exons 7 to 17 in the second instance. Another and somewhat simpler approach to restore the reading frame around an exon 7 deletion would be to remove the two flanking exons. Induction of exons 6 and 8 skipping should result in an in-frame transcript with the splicing of exons 5 to 9. In practise however, targeting exon 8 for removal from the pre-mRNA results in the co-removal of exon 9 so the resultant transcript would have exon 5 joined to exon 10. The inclusion or exclusion of exon 9 does not alter the reading frame. Once the antisense molecules to be tested have been identified, they are prepared according to standard techniques known in the art. The most common method for producing antisense molecules is the methylation of the 2′ hydroxyribose position and the incorporation of a phosphorothioate backbone produces molecules that superficially resemble RNA but that are much more resistant to nuclease degradation.
To avoid degradation of pre-mRNA during duplex formation with the antisense molecules, the antisense molecules used in the method may be adapted to minimise or prevent cleavage by endogenous RNase H. This property is highly preferred as the treatment of the RNA with the unmethylated oligonucleotides either intracellularly or in crude extracts that contain RNase H leads to degradation of the pre-mRNA: antisense oligonucleotide duplexes. Any form of modified antisense molecules that is capable of by-passing or not inducing such degradation may be used in the present method. An example of antisense molecules which when duplexed with RNA are not cleaved by cellular RNase H is 2′-O-methyl derivatives. 2′-O-methyl-oligoribonucleotides are very stable in a cellular environment and in animal tissues, and their duplexes with RNA have higher Tm values than their ribo- or deoxyribo-counterparts.
Antisense molecules that do not activate RNase H can be made in accordance with known techniques (see, e.g., U.S. Pat. No. 5,149,797). Such antisense molecules, which may be deoxyribonucleotide or ribonucleotide sequences, simply contain any structural modification which sterically hinders or prevents binding of RNase H to a duplex molecule containing the oligonucleotide as one member thereof, which structural modification does not substantially hinder or disrupt duplex formation. Because the portions of the oligonucleotide involved in duplex formation are substantially different from those portions involved in RNase H binding thereto, numerous antisense molecules that do not activate RNase H are available. For example, such antisense molecules may be oligonucleotides wherein at least one, or all, of the inter-nucleotide bridging phosphate residues are modified phosphates, such as methyl phosphonates, methyl phosphorothioates, phosphoromorpholidates, phosphoropiperazidates and phosphoramidates. For example, every other one of the internucleotide bridging phosphate residues may be modified as described. In another non-limiting example, such antisense molecules are molecules wherein at least one, or all, of the nucleotides contain a 2′ lower alkyl moiety (e.g., C1-C4, linear or branched, saturated or unsaturated alkyl, such as methyl, ethyl, ethenyl, propyl, 1-propenyl, 2-propenyl, and isopropyl). For example, every other one of the nucleotides may be modified as described.
While antisense oligonucleotides are a preferred form of the antisense molecules, the present invention comprehends other oligomeric antisense molecules, including but not limited to oligonucleotide mimetics such as are described below.
Specific examples of preferred antisense compounds useful in this invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. As defined in this specification, oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
In other preferred oligonucleotide mimetics, both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethyiglycine backbone. The nucleo-bases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
Modified oligonucleotides may also contain one or more substituted sugar moieties. Oligonucleotides may also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. Certain nucleo-bases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.
Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.
It is not necessary for all positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide. The present invention also includes antisense compounds that are chimeric compounds. “Chimeric” antisense compounds or “chimeras,” in the context of this invention, are antisense molecules, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound. These oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the increased resistance to nuclease degradation, increased cellular uptake, and an additional region for increased binding affinity for the target nucleic acid.
Methods of Manufacturing Antisense Molecules
The antisense molecules used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). One method for synthesising oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,066.
Any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives. In one such automated embodiment, diethyl-phosphoramidites are used as starting materials and may be synthesized as described by Beaucage, et al., (1981) Tetrahedron Letters, 22:1859-1862.
The antisense molecules of the invention are synthesised in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules. The molecules of the invention may also be mixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as for example, liposomes, receptor targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption.
Therapeutic Agents
The present invention also can be used as a prophylactic or therapeutic, which may be utilised for the purpose of treatment of a genetic disease.
Accordingly, in one embodiment the present invention provides antisense molecules that bind to a selected target in the dystrophin pre-mRNA to induce efficient and consistent exon skipping described herein in a therapeutically effective amount admixed with a pharmaceutically acceptable carrier, diluent, or excipient.
The phrase “pharmaceutically acceptable” refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similarly untoward reaction, such as gastric upset and the like, when administered to a patient. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water or saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, particularly for injectable solutions. Suitable pharmaceutical carriers are described in Martin, Remington's Pharmaceutical Sciences, 18th Ed., Mack Publishing Co., Easton, Pa., (1990).
In a more specific form of the invention there are provided pharmaceutical compositions comprising therapeutically effective amounts of an antisense molecule together with pharmaceutically acceptable diluents, preservatives, solubilizers, emulsifiers, adjuvants and/or carriers. Such compositions include diluents of various buffer content (e.g., Tris-HCl, acetate, phosphate), pH and ionic strength and additives such as detergents and solubilizing agents (e.g., Tween 80, Polysorbate 80), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), preservatives (e.g., Thimersol, benzyl alcohol) and bulking substances (e.g., lactose, mannitol). The material may be incorporated into particulate preparations of polymeric compounds such as polylactic acid, polyglycolic acid, etc. or into liposomes. Hylauronic acid may also be used. Such compositions may influence the physical state, stability, rate of in vivo release, and rate of in vivo clearance of the present proteins and derivatives. See, e.g., Martin, Remington's Pharmaceutical Sciences, 18th Ed. (1990, Mack Publishing Co., Easton, Pa. 18042) pages 1435-1712 that are herein incorporated by reference. The compositions may be prepared in liquid form, or may be in dried powder, such as lyophilised form.
It will be appreciated that pharmaceutical compositions provided according to the present invention may be administered by any means known in the art. Preferably, the pharmaceutical compositions for administration are administered by injection, orally, or by the pulmonary, or nasal route. The antisense molecules are more preferably delivered by intravenous, intra-arterial, intraperitoneal, intramuscular, or subcutaneous routes of administration.
Antisense Molecule Based Therapy
Also addressed by the present invention is the use of antisense molecules of the present invention, for manufacture of a medicament for modulation of a genetic disease.
The delivery of a therapeutically useful amount of antisense molecules may be achieved by methods previously published. For example, intracellular delivery of the antisense molecule may be via a composition comprising an admixture of the antisense molecule and an effective amount of a block copolymer. An example of this method is described in US patent application US 20040248833.
Other methods of delivery of antisense molecules to the nucleus are described in Mann C J et al., (2001) [“Antisense-induced exon skipping and the synthesis of dystrophin in the mdx mouse”. Proc., Natl. Acad. Science, 98(1) 42-47] and in Gebski et al., (2003). Human Molecular Genetics, 12(15): 1801-1811.
A method for introducing a nucleic acid molecule into a cell by way of an expression vector either as naked DNA or complexed to lipid carriers, is described in U.S. Pat. No. 6,806,084.
It may be desirable to deliver the antisense molecule in a colloidal dispersion system. Colloidal dispersion systems include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes or liposome formulations.
Liposomes are artificial membrane vesicles which are useful as delivery vehicles in vitro and in vivo. These formulations may have net cationic, anionic or neutral charge characteristics and are useful characteristics with in vitro, in vivo and ex vivo delivery methods. It has been shown that large unilamellar vesicles (LUV), which range in size from 0.2-4.0 .PHI.m can encapsulate a substantial percentage of an aqueous buffer containing large macromolecules. RNA, and DNA can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley, et al., Trends Biochem. Sci., 6:77, 1981).
In order for a liposome to be an efficient gene transfer vehicle, the following characteristics should be present: (1) encapsulation of the antisense molecule of interest at high efficiency while not compromising their biological activity; (2) preferential and substantial binding to a target cell in comparison to non-target cells; (3) delivery of the aqueous contents of the vesicle to the target cell cytoplasm at high efficiency; and (4) accurate and effective expression of genetic information (Mannino, et al., Biotechniques, 6:682, 1988).
The composition of the liposome is usually a combination of phospholipids, particularly high-phase-transition-temperature phospholipids, usually in combination with steroids, especially cholesterol. Other phospholipids or other lipids may also be used. The physical characteristics of liposomes depend on pH, ionic strength, and the presence of divalent cations.
Alternatively, the antisense construct may be combined with other pharmaceutically acceptable carriers or diluents to produce a pharmaceutical composition. Suitable carriers and diluents include isotonic saline solutions, for example phosphate-buffered saline. The composition may be formulated for parenteral, intramuscular, intravenous, subcutaneous, intraocular, oral or transdermal administration.
The routes of administration described are intended only as a guide since a skilled practitioner will be able to determine readily the optimum route of administration and any dosage for any particular animal and condition. Multiple approaches for introducing functional new genetic material into cells, both in vitro and in vivo have been attempted (Friedmann (1989) Science, 244:1275-1280).
These approaches include integration of the gene to be expressed into modified retroviruses (Friedmann (1989) supra; Rosenberg (1991) Cancer Research 51(18), suppl.: 5074S-5079S); integration into non-retrovirus vectors (Rosenfeld, et al. (1992) Cell, 68:143-155; Rosenfeld, et al. (1991) Science, 252:431-434); or delivery of a transgene linked to a heterologous promoter-enhancer element via liposomes (Friedmann (1989), supra; Brigham, et al. (1989) Am. J. Med. Sci., 298:278-281; Nabel, et al. (1990) Science, 249:1285-1288; Hazinski, et al. (1991) Am. J. Resp. Cell Molec. Biol., 4:206-209; and Wang and Huang (1987) Proc. Natl. Acad. Sci. (USA), 84:7851-7855); coupled to ligand-specific, cation-based transport systems (Wu and Wu (1988) J. Biol. Chem., 263:14621-14624) or the use of naked DNA, expression vectors (Nabel et al. (1990), supra); Wolff et al. (1990) Science, 247:1465-1468). Direct injection of transgenes into tissue produces only localized expression (Rosenfeld (1992) supra); Rosenfeld et al. (1991) supra; Brigham et al. (1989) supra; Nabel (1990) supra; and Hazinski et al. (1991) supra). The Brigham et al. group (Am. J. Med. Sci. (1989) 298:278-281 and Clinical Research (1991) 39 (abstract)) have reported in vivo transfection only of lungs of mice following either intravenous or intratracheal administration of a DNA liposome complex. An example of a review article of human gene therapy procedures is: Anderson, Science (1992) 256:808-813.
The antisense molecules of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to prodrugs and pharmaceutically acceptable salts of the compounds of the invention, pharmaceutically acceptable salts of such pro-drugs, and other bioequivalents.
The term “pharmaceutically acceptable salts” refers to physiologically and pharmaceutically acceptable salts of the compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.
For oligonucleotides, preferred examples of pharmaceutically acceptable salts include but are not limited to (a) salts formed with cations such as sodium, potassium, ammonium, magnesium, calcium, polyamines such as spermine and spermidine, etc.; (b) acid addition salts formed with inorganic acids, for example hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid and the like; (c) salts formed with organic acids such as, for example, acetic acid, oxalic acid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconic acid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-toluenesulfonic acid, naphthalenedisulfonic acid, polygalacturonic acid, and the like; and (d) salts formed from elemental anions such as chlorine, bromine, and iodine. The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, (including by nebulizer, intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intra-arterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Oligonucleotides with at least one 2′-O-methoxyethyl modification are believed to be particularly useful for oral administration.
The pharmaceutical formulations of the present invention, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.
Kits of the Invention
The invention also provides kits for treatment of a patient with a genetic disease which kit comprises at least an antisense molecule, packaged in a suitable container, together with instructions for its use.
In a preferred embodiment, the kits will contain at least one antisense molecule as shown in Table 1A, or a cocktail of antisense molecules as shown in Table 1B or a “weasel” compound as shown in Table 1C. The kits may also contain peripheral reagents such as buffers, stabilizers, etc.
Those of ordinary skill in the field should appreciate that applications of the above method has wide application for identifying antisense molecules suitable for use in the treatment of many other diseases.
EXAMPLES
The following Examples serve to more fully describe the manner of using the above-described invention, as well as to set forth the best modes contemplated for carrying out various aspects of the invention. It is understood that these Examples in no way serve to limit the true scope of this invention, but rather are presented for illustrative purposes. The references cited herein are expressly incorporated by reference.
Methods of molecular cloning, immunology and protein chemistry, which are not explicitly described in the following examples, are reported in the literature and are known by those skilled in the art. General texts that described conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art, included, for example: Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989); Glover ed., DNA Cloning: A Practical Approach, Volumes I and II, MRL Press, Ltd., Oxford, U.K. (1985); and Ausubel, F., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., Struhl, K. Current Protocols in Molecular Biology. Greene Publishing Associates/Wiley Intersciences, New York (2002).
Determining Induced Exon Skipping in Human Muscle Cells
Attempts by the inventors to develop a rational approach in antisense molecules design were not completely successful as there did not appear to be a consistent trend that could be applied to all exons. As such, the identification of the most effective and therefore most therapeutic antisense molecules compounds has been the result of empirical studies.
These empirical studies involved the use of computer programs to identify motifs potentially involved in the splicing process. Other computer programs were also used to identify regions of the pre-mRNA which may not have had extensive secondary structure and therefore potential sites for annealing of antisense molecules. Neither of these approaches proved completely reliable in designing antisense oligonucleotides for reliable and efficient induction of exon skipping.
Annealing sites on the human dystrophin pre-mRNA were selected for examination, initially based upon known or predicted motifs or regions involved in splicing. 2OMe antisense oligonucleotides were designed to be complementary to the target sequences under investigation and were synthesised on an Expedite 8909 Nucleic Acid Synthesiser. Upon completion of synthesis, the oligonucleotides were cleaved from the support column and de-protected in ammonium hydroxide before being desalted. The quality of the oligonucleotide synthesis was monitored by the intensity of the trityl signals upon each deprotection step during the synthesis as detected in the synthesis log. The concentration of the antisense oligonucleotide was estimated by measuring the absorbance of a diluted aliquot at 260 nm.
Specified amounts of the antisense molecules were then tested for their ability to induce exon skipping in an in vitro assay, as described below.
Briefly, normal primary myoblast cultures were prepared from human muscle biopsies obtained after informed consent. The cells were propagated and allowed to differentiate into myotubes using standard culturing techniques. The cells were then transfected with the antisense oligonucleotides by delivery of the oligonucleotides to the cells as cationic lipoplexes, mixtures of antisense molecules or cationic liposome preparations.
The cells were then allowed to grow for another 24 hours, after which total RNA was extracted and molecular analysis commenced. Reverse transcriptase amplification (RT-PCR) was undertaken to study the targeted regions of the dystrophin pre-mRNA or induced exonic re-arrangements.
For example, in the testing of an antisense molecule for inducing exon 19 skipping the RT-PCR test scanned several exons to detect involvement of any adjacent exons. For example, when inducing skipping of exon 19, RT-PCR was carried out with primers that amplified across exons 17 and 21. Amplifications of even larger products in this area (i.e. exons 13-26) were also carried out to ensure that there was minimal amplification bias for the shorter induced skipped transcript. Shorter or exon skipped products tend to be amplified more efficiently and may bias the estimated of the normal and induced transcript.
The sizes of the amplification reaction products were estimated on an agarose gel and compared against appropriate size standards. The final confirmation of identity of these products was carried out by direct DNA sequencing to establish that the correct or expected exon junctions have been maintained.
Once efficient exon skipping had been induced with one antisense molecule, subsequent overlapping antisense molecules may be synthesized and then evaluated in the assay as described above. Our definition of an efficient antisense molecule is one that induces strong and sustained exon skipping at transfection concentrations in the order of 300 nM or less.
Antisense Oligonucleotides Directed at Exon 8
Antisense oligonucleotides directed at exon 8 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 3 shows differing efficiencies of two antisense molecules directed at exon 8 acceptor splice site. H8A(−06+18) [SEQ ID NO:1], which anneals to the last 6 bases of intron 7 and the first 18 bases of exon 8, induces substantial exon 8 and 9 skipping when delivered into cells at a concentration of 20 nM. The shorter antisense molecule, H8A(−06+14) [SEQ ID NO: 4] was only able to induce exon 8 and 9 skipping at 300 nM, a concentration some 15 fold higher than H8A(−06+18), which is the preferred antisense molecule.
This data shows that some particular antisense molecules induce efficient exon skipping while another antisense molecule, which targets a near-by or overlapping region, can be much less efficient. Titration studies show one compound is able to induce targeted exon skipping at 20 nM while the less efficient antisense molecules only induced exon skipping at concentrations of 300 nM and above. Therefore, we have shown that targeting of the antisense molecules to motifs involved in the splicing process plays a crucial role in the overall efficacy of that compound.
Efficacy refers to the ability to induce consistent skipping of a target exon. However, sometimes skipping of the target exons is consistently associated with a flanking exon. That is, we have found that the splicing of some exons is tightly linked. For example, in targeting exon 23 in the mouse model of muscular dystrophy with antisense molecules directed at the donor site of that exon, dystrophin transcripts missing exons 22 and 23 are frequently detected. As another example, when using an antisense molecule directed to exon 8 of the human dystrophin gene, all induced transcripts are missing both exons 8 and 9. Dystrophin transcripts missing only exon 8 are not observed.







TABLE 2







(SEQ ID NOS 1-5, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H8A(−06+18)
5′-GAU AGG UGG UAU CAA
Very strong



CAU CUG UAA
to 20 nM


 


H8A(−03+18)
5′-GAU AGG UGG UAU CAA
Very strong



CAU CUG
skipping to




40 nM


 


H8A(−07+18)
5′-GAU AGG UGG UAU CAA
Strong



CAU CUG UAA G
skipping to




40 nM


 


H8A(−06+14)
5′-GGU GGU AUC AAC AUC
Skipping to



UGU AA
300 nM


 


H8A(−10+10)
5′-GUA UCA ACA UCU GUAA
Patchy/weak



GC AC
skipping to




100 nm









Antisense Oligonucleotides Directed at Exon 7
Antisense oligonucleotides directed at exon 7 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 4 shows the preferred antisense molecule, H7A(+45+67) [SEQ ID NO: 6], and another antisense molecule, H7A(+2+26) [SEQ ID NO: 7], inducing exon 7 skipping. Nested amplification products span exons 3 to 9. Additional products above the induced transcript missing exon 7 arise from amplification from carry-over outer primers from the RT-PCR as well as heteroduplex formation.







TABLE 3







(SEQ ID NOS 6-9, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H7A(+45+67)
5′-UGC AUG UUC CAG
Strong



UCG UUG UGU GG
skipping to




20 nM


 


H7A(+02+26)
5′-CAC UAU UCC AGU
Weak



CAA AUA GGU CUG G
skipping




at 100 nM


 


H7D(+15−10)
5′-AUU UAC CAA CCU
Weak



UCA GGA UCG AGU A
skipping




to 300 nM


 


H7A(−18+03)
5′-GGC CUA AAA CAC
Weak



AUA CAC AUA
skipping




to 300 nM









Antisense Oligonucleotides Directed at Exon 6
Antisense oligonucleotides directed at exon 6 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 5 shows an example of two non-preferred antisense molecules inducing very low levels of exon 6 skipping in cultured human cells. Targeting this exon for specific removal was first undertaken during a study of the canine model using the oligonucleotides as listed in Table 4, below. Some of the human specific oligonucleotides were also evaluated, as shown in FIG. 5. In this example, both antisense molecules target the donor splice site and only induced low levels of exon 6 skipping. Both H6D(+4−21) [SEQ ID NO: 17] and H6D(+18−4) [SEQ ID NO: 18] would be regarded as non-preferred antisense molecules.
One antisense oligonucleotide that induced very efficient exon 6 skipping in the canine model, C6A(+69+91) [SEQ ID NO: 14], would anneal perfectly to the corresponding region in human dystrophin exon 6. This compound was evaluated, found to be highly efficient at inducing skipping of that target exon, as shown in FIG. 6 and is regarded as the preferred compound for induced exon 6 skipping. Table 4 below discloses antisense molecule sequences for induced exon 6 skipping.







TABLE 4







(SEQ ID NOS 10-18, respectively, in order of


appearance)









Antisense

Ability to


Oligo

induce


name
Sequence
skipping





C6A(−10+10)
5′ CAU UUU UGA CCU ACA
No skipping



UGU GG



 


C6A(−14+06)
5′ UUU GAC CUA CAU GUG
No skipping



GAA AG



 


C6A(−14+12)
5′ UAC AUU UUU GAC CUA
No skipping



CAU GUG GAA AG



 


C6A(−13+09)
5′ AUU UUU GAC CUA CAU
No skipping



GGG AAA G



 


CH6A(+69+91)
5′ UAC GAG UUG AUU GUC
Strong



GGA CCC AG
skipping




to 20 nM


 


C6D(+12−13)
5′ GUG GUC UCC UUA CCU
Weak skipping



AUG ACU GUG G
at 300 nM


 


C6D(+06−11)
5′ GGU CUC CUU ACC UAU
No skipping



GA



 


H6D(+04−21)
5′ UGU CUC AGU AAU CUU
Weak skipping



CUU ACC UAU
to 50 nM


 


H6D(+18−04)
5′ UCU UAC CUA UGA CUA
Very weak



UGG AUG AGA
skipping




to 300 nM









Antisense Oligonucleotides Directed at Exon 4
Antisense oligonucleotides directed at exon 4 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 7 shows an example of a preferred antisense molecule inducing skipping of exon 4 skipping in cultured human cells. In this example, one preferred antisense compound, H4A(+13+32) [SEQ ID NO:19], which targeted a presumed exonic splicing enhancer induced efficient exon skipping at a concentration of 20 nM while other non-preferred antisense oligonucleotides failed to induce even low levels of exon 4 skipping. Another preferred antisense molecule inducing skipping of exon 4 was H4A(+111+40) [SEQ ID NO:22], which induced efficient exon skipping at a concentration of 20 nM.







TABLE 5







(SEQ ID NOS 19, 22, 20, and 21, respectively,


in order of appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H4A(+13+32)
5′ GCA UGA ACU CUU
Skipping to



GUG GAU CC
20 nM


 


H4A(+11+40)
5′ UGU UCA GGG CAU
Skipping to



GAA CUC UUG UGG AUC
20 nM



CUU



 


H4D(+04−16)
5′ CCA GGG UAC UAC
No skipping



UUA CAU UA



 


H4D(−24−44)
5′ AUC GUG UGU CAC
No skipping



AGC AUC CAG









Antisense Oligonucleotides Directed at Exon 3
Antisense oligonucleotides directed at exon 3 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H3A(+30+60) [SEQ ID NO:23] induced substantial exon 3 skipping when delivered into cells at a concentration of 20 nM to 600 nM. The antisense molecule, H3A(+35+65) [SEQ ID NO: 24] induced exon skipping at 300 nM.







TABLE 6







(SEQ ID NOS 23-30, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H3A(+30+60)
UAG GAG GCG CCU CCC AUC
Moderate



CUG UAG GUC ACU G
skipping




to 20 to




600 nM


 


H3A(+35+65)
AGG UCU AGG AGG CGC CUC
Working to



CCA UCC UGU AGG U
300 nM


 


H3A(+30+54)
GCG CCU CCC AUC CUG UAG
Moderate



GUC ACU G
100-600 nM


 


H3D(+46−21)
CUU CGA GGA GGU CUA GGA
No skipping



GGC GCC UC



 


H3A(+30+50)
CUC CCA UCC UGU AGG UCA
Moderate 



CUG
20-600 nM


 


H3D(+19−03)
UAC CAG UUU UUG CCC UGU
No skipping



CAG G



 


H3A(−06+20)
UCA AUA UGC UGC UUCCCA
No skipping



AAC UGA AA



 


H3A(+37+61)
CUA GGA GGC GCC UCC CAU
No skipping



CCU GUA G









Antisense Oligonucleotides Directed at Exon 5
Antisense oligonucleotides directed at exon 5 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H5A(+20+50) [SEQ ID NO:31] induces substantial exon 5 skipping when delivered into cells at a concentration of 100 nM. Table 7 below shows other antisense molecules tested. The majority of these antisense molecules were not as effective at exon skipping as H5A(+20+50). However, H5A(+15+45) [SEQ ID NO: 40] was able to induce exon 5 skipping at 300 nM.







TABLE 7







(SEQ ID NOS 31-40, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H5A(+20+50)
UUA UGA UUU CCA UCU
Working to



ACG AUG UCA GUA CUU C
100 nM


 


H5D(+25−05)
CUU ACC UGC CAG UGG
No skipping



AGG AUU AUA UUC CAA A



 


H5D(+10−15)
CAU CAG GAU UCU UAC
Inconsistent



CUG CCA GUG G
at 300 nM


 


H5A(+10+34)
CGA UGU CAG UAC UUC
Very weak



CAA UAU UCA C



 


H5D(−04−21)
ACC AUU CAU CAG GAU
No skipping



UCU



 


H5D(+16−02)
ACC UGC CAG UGG AGG
No skipping



AUU



 


H5A(−07+20)
CCA AUA UUC ACU AAA
No skipping



UCA ACC UGU UAA



 


H5D(+18−12)
CAG GAU UCU UAC CUG
No skipping



CCA GUG GAG GAU UAU



 


H5A(+05+35)
ACG AUG UCA GUA CUU
No skipping



CCA AUA UUC ACU AAA U



 


H5A(+15+45)
AUU UCC AUC UAC GAU
Working to



GUC AGU ACU UCC AAU A
300 nM









Antisense Oligonucleotides Directed at Exon 10
Antisense oligonucleotides directed at exon 10 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H10A(−05+16) [SEQ ID NO:41] induced substantial exon 10 skipping when delivered into cells. Table 8 below shows other antisense molecules tested. The antisense molecules ability to induce exon skipping was variable. Table 8 below discloses antisense molecule sequences that induce exon 10 skipping.







TABLE 8







(SEQ ID NOS 41-45, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H10A(−05+16)
CAG GAG CUU CCA AAU GCU
Not tested



GCA



 


H10A(−05+24)
CUU GUC UUC AGG AGC UUC
Not tested



CAA AUG CUG CA



 


H10A(+98+119)
UCC UCA GCA GAA AGA AGC
Not tested



CAC G



 


H10A(+130+149)
UUA GAA AUC UCU CCU UGU
No skipping



GC



 


H10A(−33−14)
UAA AUU GGG UGU UAC ACA
No skipping



AU









Antisense Oligonucleotides Directed at Exon 11
Antisense oligonucleotides directed at exon 11 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 8B shows an example of H11A(+75+97) [SEQ ID NO:49] antisense molecule inducing exon 11 skipping in cultured human cells. H11A(+75+97) induced substantial exon 11 skipping when delivered into cells at a concentration of 5 nM. Table 9 below shows other antisense molecules tested. The antisense molecules ability to induce exon skipping was observed at 100 nM.







TABLE 9







(SEQ ID NOS 46-49 and 46, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H11D(+26+49)
CCC UGA GGC AUU CCC AUC
Skipping at



UUG AAU
100 nM


 


H11D(+11−09)
AGG ACU UAC UUG CUU UGU
Skipping at



UU
100 nM


 


H11A(+118+140)
CUU GAA UUU AGG AGA UUC
Skipping at



AUC UG
100 nM


 


H11A(+75+97)
CAU CUU CUG AUA AUU UUC
Skipping at



CUG UU
100 nM


 


H11D(+26+49)
CCC UGA GGC AUU CCC AUC
Skipping at



UUG AAU
5 nM









Antisense Oligonucleotides Directed at Exon 12
Antisense oligonucleotides directed at exon 12 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H12A(+52+75) [SEQ ID NO:50] induced substantial exon 12 skipping when delivered into cells at a concentration of 5 nM, as shown in FIG. 8A. Table 10 below shows other antisense molecules tested at a concentration range of 5, 25, 50, 100, 200 and 300 nM. The antisense molecules ability to induce exon skipping was variable.







TABLE 10







(SEQ ID NOS 50-52, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H12A(+52+75)
UCU UCU GUU UUU GUU AGC
Skipping at



CAG UCA
5 nM


 


H12A(−10+10)
UCU AUG UAA ACU GAA AAU
Skipping at



UU
100 nM


 


H12A(+11+30)
UUC UGG AGA UCC AUU AAA
No skipping



AC









Antisense Oligonucleotides Directed at Exon 13
Antisense oligonucleotides directed at exon 13 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H13A(+77+100) [SEQ ID NO:53] induced substantial exon 13 skipping when delivered into cells at a concentration of 5 nM. Table 11 below includes two other antisense molecules tested at a concentration range of 5, 25, 50, 100, 200 and 300 nM. These other antisense molecules were unable to induce exon skipping.







TABLE 11







(SEQ ID NOS 53-55, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence 
skipping





H13A(+77+100)
CAG CAG UUG CGU GAU CUC
Skipping at



CAC UAG
5 nM


 


H13A(+55+75)
UUC AUC AAC UAC CAC CAC
No skipping



CAU



 


H13D(+06−19)
CUA AGC AAA AUA AUC UGA
No skipping



CCU UAA G









Antisense Oligonucleotides Directed at Exon 14
Antisense oligonucleotides directed at exon 14 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H14A(+37+64) [SEQ ID NO:56] induced weak exon 14 skipping when delivered into cells at a concentration of 100 nM. Table 12 below includes other antisense molecules tested at a concentration range of 5, 25, 50, 100, 200 and 300 nM. The other antisense molecules were unable to induce exon skipping at any of the concentrations tested.







TABLE 12







(SEQ ID NOS 56-62, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H14A(+37+64)
CUU GUA AAA GAA CCC AGC
Skipping at



GGU CUU CUG U
100 nM


 


H14A(+14+35)
CAU CUA CAG AUG UUU GCC
No skipping



CAU C



 


H14A(+51+73)
GAA GGA UGU CUU GUA AAA
No skipping



GAA CC



 


H14D(−02+18)
ACC UGU UCU UCA GUA AGA
No skipping



CG



 


H14D(+14−10)
CAU GAC ACA CCU GUU CUU
No skipping



CAG UAA



 


H14A(+61+80)
CAU UUG AGA AGG AUG UCU
No skipping



UG



 


H14A(−12+12)
AUC UCC CAA UAC CUG GAG
No skipping



AAG AGA









Antisense Oligonucleotides Directed at Exon 15
Antisense oligonucleotides directed at exon 15 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H15A(−12+19) [SEQ ID NO:63] and H15A(+48+71) [SEQ ID NO:64] induced substantial exon 15 skipping when delivered into cells at a concentration of 10 Nm, as shown in FIG. 9A. Table 13 below includes other antisense molecules tested at a concentration range of 5, 25, 50, 100, 200 and 300 Nm. These other antisense molecules were unable to induce exon skipping at any of the concentrations tested.







TABLE 13







(SEQ ID NOS 63-65, 63, and 66, respectively,


in order of appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H15A(−12+19)
GCC AUG CAC UAA AAA GGC
Skipping at



ACU GCA AGA CAU U
5 Nm


 


H15A(+48+71)
UCU UUA AAG CCA GUU GUG
Skipping at



UGA AUC
5 Nm


 


H15A(+08+28)
UUU CUG AAA GCC AUG CAC
No skipping



UAA



 


H15A(−12+19)
GCC AUG CAC UAA AAA GGC
No skipping



ACU GCA AGA CAU U



 


H15D(+17−08)
GUA CAU ACG GCC AGU UUU
No skipping



UGA AGA C









Antisense Oligonucleotides Directed at Exon 16
Antisense oligonucleotides directed at exon 16 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H16A(−12+19) [SEQ ID NO:67] and H16A(−06+25) [SEQ ID NO:68] induced substantial exon 16 skipping when delivered into cells at a concentration of 10 nM, as shown in FIG. 9B. Table 14 below includes other antisense molecules tested. H16A(−06+19) [SEQ ID NO:69] and H16A(+87+109) [SEQ ID NO:70] were tested at a concentration range of 5, 25, 50, 100, 200 and 300 nM. These two antisense molecules were able to induce exon skipping at 25 nM and 100 nM, respectively. Additional antisense molecules were tested at 100, 200 and 300 nM and did not result in any exon skipping.







TABLE 14







(SEQ ID NOS 67-78, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H16A(−12+19)
CUA GAU CCG CUU UUA AAA
Skipping at



CCU GUU AAA ACA A
5 nM


 


H16A(−06+25)
UCU UUU CUA GAU CCG CUU
Skipping at



UUA AAA CCU GUU A
5 nM


 


H16A(−06+19)
CUA GAU CCG CUU UUA AAA
Skipping at



CCU GUU A
25 nM


 


H16A(+87+109)
CCG UCU UCU GGG UCA CUG
Skipping at



ACU UA
100 nM


 


H16A(−07+19)
CUA GAU CCG CUU UUA AAA
No skipping



CCU GUU AA



 


H16A(−07+13)
CCG CUU UUA AAA CCU GUU
No skipping



AA



 


H16A(+12+37)
UGG AUU GCU UUU UCU UUU
No skipping



CUA GAU CC



 


H16A(+92+116)
CAU GCU UCC GUC UUC UGG
No skipping



GUC ACU G



 


H16A(+45+67)
G AUC UUG UUU GAG UGA
No skipping



AUA CAG U



 


H16A(+105+126)
GUU AUC CAG CCA UGC UUC
No skipping



CGU C



 


H16D(+05−20)
UGA UAA UUG GUA UCA CUA
No skipping



ACC UGU G



 


H16D(+12−11)
GUA UCA CUA ACC UGU GCU
No skipping



GUA C









Antisense Oligonucleotides Directed at Exon 19
Antisense oligonucleotides directed at exon 19 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H19A(+35+65) [SEQ ID NO:79] induced substantial exon 19 skipping when delivered into cells at a concentration of 10 nM. This antisense molecule also showed very strong exon skipping at concentrations of 25, 50, 100, 300 and 600 nM.
FIG. 10 illustrates exon 19 and 20 skipping using a “cocktail” of antisense oligonucleotides, as tested using gel electrophoresis. It is interesting to note that it was not easy to induce exon 20 skipping using single antisense oligonucleotides H20A(+44+71) [SEQ ID NO:81] or H20A(+149+170) [SEQ ID NO:82], as illustrated in sections 2 and 3 of the gel shown in FIG. 10. Whereas, a “cocktail” of antisense oligonucleotides was more efficient as can be seen in section 4 of FIG. 10 using a “cocktail” of antisense oligonucleotides H20A(+44+71) and H20A(+149+170). When the cocktail was used to target exon 19, skipping was even stronger (see section 5, FIG. 10).
FIG. 11 illustrates gel electrophoresis results of exon 19/20 skipping using “weasels” The “weasels” were effective in skipping exons 19 and 20 at concentrations of 25, 50, 100, 300 and 600 nM. A further “weasel” sequence is shown in the last row of Table 3C. This compound should give good results.
Antisense Oligonucleotides Directed at Exon 20
Antisense oligonucleotides directed at exon 20 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
None of the antisense oligonucleotides tested induced exon 20 skipping when delivered into cells at a concentration of 10, 25, 50, 300 or 600 nM (see Table 15). Antisense molecules H20A(−11+17) [SEQ ID NO:86] and H20D(+08−20) [SEQ ID NO:87] are yet to be tested.
However, a combination or “cocktail” of H20A(+44+71) [SEQ ID NO: 81] and H20(+149+170) [SEQ ID NO:82] in a ratio of 1:1, exhibited very strong exon skipping at a concentration of 100 nM and 600 nM. Further, a combination of antisense molecules H19A(+35+65) [SEQ ID NO:79], H20A(+44+71) [SEQ ID NO:81] and H20A(+149+170) [SEQ ID NO:82] in a ratio of 2:1:1, induced very strong exon skipping at a concentration ranging from 10 nM to 600 nM.







TABLE 15







(SEQ ID NOS 81-87, 81-82, and 80-82,  


respectively, in order of appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H20A(+44+71)
CUG GCA GAA UUC GAU CCA
No skipping



CCG GCU GUU C



 


H20A(+147+168)
CAG CAG UAG UUG UCA UCU
No skipping



GCU C



 


H20A(+185+203)
UGA UGG GGU GGU GGG UUG
No skipping



G



 


H20A(−08+17)
AUC UGC AUU AAC ACC CUC
No skipping



UAG AAA G



 


H20A(+30+53)
CCG GCU GUU CAG UUG UUC
No skipping



UGA GGC



 


H20A(−11+17)
AUC UGC AUU AAC ACC CUC
Not tested



UAG AAA GAA A
yet


 


H20D(+08−20)
GAA GGA GAA GAG AUU CUU
Not tested



ACC UUA CAA A
yet


 


H20A(+44+71) &
CUG GCA GAA UUC GAU CCA
Very strong



CCG GCU GUU C
skipping


H20A(+147+168)
CAG CAG UAG UUG UCA UCU




GCU C



 


H19A(+35+65);
GCC UGA GCU GAU CUG CUG
Very strong



GCA UCU UGC AGU U;  
skipping


H20A(+44+71);
CUG GCA GAA UUC GAU CCA




CCG GCU GUU C;



H20A(+147+168)
CAG CAG UAG UUG UCA UCU




GCU C









Antisense Oligonucleotides Directed at Exon 21
Antisense oligonucleotides directed at exon 21 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H21A(+85+108) [SEQ ID NO:92] and H21A(+85+106) [SEQ ID NO:91] induced exon 21 skipping when delivered into cells at a concentration of 50 nM. Table 16 below includes other antisense molecules tested at a concentration range of 5, 25, 50, 100, 200 and 300 nM. These antisense molecules showed a variable ability to induce exon skipping







TABLE 16







(SEQ ID NOS 90-94, respectively, in order of


appearance)









Antisense

Ability to


Oligonucleotide

induce


name
Sequence
skipping





H21A(−06+16)
GCC GGU UGA CUU CAU CCU
Skips at



GUG C
600 nM


 


H21A(+85+106) 
CUG CAU CCA GGA ACA UGG
Skips at 50



GUC C
nM


 


H21A(+85+108)
GUC UGC AUC CAG GAA CAU
Skips at 50



GGG UC
nM


 


H21A(+08+31)
GUU GAA GAU CUG AUA GCC
Skips faintly



GGU UGA
to


 


H21D(+18−07)
UAC UUA CUG UCU GUA GCU
No skipping



CUU UCU









Antisense Oligonucleotides Directed at Exon 22
Antisense oligonucleotides directed at exon 22 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 12 illustrates differing efficiencies of two antisense molecules directed at exon 22 acceptor splice site. H22A(+125+106) [SEQ ID NO:96] and H22A(+80+101) [SEQ ID NO: 98] induce strong exon 22 skipping from 50 nM to 600 nM concentration.
H22A(+125+146) [SEQ ID NO:96] and H22A(+80+101) [SEQ ID NO:98] induced exon 22 skipping when delivered into cells at a concentration of 50 nM. Table 17 below shows other antisense molecules tested at a concentration range of 50, 100, 300 and 600 nM. These antisense molecules showed a variable ability to induce exon skipping.







TABLE 17







(SEQ ID NOS 95-99, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H22A(+22+45)
CAC UCA UGG UCU CCU GAU
No skipping



AGC GCA



 


H22A(+125+146)
CUG CAA UUC CCC GAG UCU
Skipping to



CUG C
50 nM


 


H22A(+47+69)
ACU GCU GGA CCC AUG UCC
Skipping to



UGA UG 
300 nM


 


H22A(+80+101)
CUA AGU UGA GGU AUG GAG
Skipping to



AGU
50 nM


 


H22D(+13−11)
UAU UCA CAG ACC UGC AAU
No skipping



UCC CC









Antisense Oligonucleotides Directed at Exon 23
Antisense oligonucleotides directed at exon 23 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
Table 18 below shows antisense molecules tested at a concentration range of 25, 50, 100, 300 and 600 nM. These antisense molecules showed no ability to induce exon skipping or are yet to be tested.







TABLE 18







(SEQ ID NOS 100-102, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H23A(+34+59)
ACA GUG GUG CUG AGA UAG
No skipping



UAU AGG CC



 


H23A(+18+39)
UAG GCC ACU UUG UUG CUC
No Skipping



UUG C



 


H23A(+72+90)
UUC AGA GGG CGC UUU CUU
No Skipping



C









Antisense Oligonucleotides Directed at Exon 24
Antisense oligonucleotides directed at exon 24 were prepared using similar methods as described above. Table 19 below outlines the antisense oligonucleotides directed at exon 24 that are yet to be tested for their ability to induce exon 24 skipping.







TABLE 19







(SEQ ID NOS 103-104, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H24A(+48+70)
GGG CAG GCC AUU CCU CCU
Needs



UCA GA
testing


 


H24A(−02+22)
UCU UCA GGG UUU GUA UGU
Needs



GAU UCU
testing









Antisense Oligonucleotides Directed at Exon 25
Antisense oligonucleotides directed at exon 25 were prepared using similar methods as described above. Table 20 below shows the antisense oligonucleotides directed at exon 25 that are yet to be tested for their ability to induce exon 25 skipping.







TABLE 20







(SEQ ID NOS 105-107, respectively, in order of


appearance)









Antisense

Ability to 


oligonucleotide

induce


name
Sequence
skipping





H25A(+9+36)
CUG GGC UGA AUU GUC UGA
Needs



AUA UCA CUG
testing


 


H25A(+131+156)
CUG UUG GCA CAU GUG AUC
Needs



CCA CUG AG
testing


 


H25D(+16−08)
GUC UAU ACC UGU UGG CAC
Needs



AUG UGA
testing









Antisense Oligonucleotides Directed at Exon 26
Antisense oligonucleotides directed at exon 26 were prepared using similar methods as described above. Table 21 below outlines the antisense oligonucleotides directed at exon 26 that are yet to be tested for their ability to induce exon 26 skipping.







TABLE 21







(SEQ ID NOS 108-110, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H26A(+132+156)
UGC UUU CUG UAA UUC
Needs testing



AUC UGG AGU U



 


H26A(−07+19)
CCU CCU UUC UGG CAU
Needs testing



AGA CCU UCC AC



 


H26A(+68+92)
UGU GUC AUC CAU UCG
Faint skipping



UGC AUC UCU G
at 600 nM









Antisense Oligonucleotides Directed at Exon 27
Antisense oligonucleotides directed at exon 27 were prepared using similar methods as described above. Table 22 below outlines the antisense oligonucleotides directed at exon 27 that are yet to be tested for their ability to induce exon 27 skipping.







TABLE 22







(SEQ ID NOS 111-113, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H27A(+82+106)
UUA AGG CCU CUU GUG
Needs testing



CUA CAG GUG G



 


H27A(−4+19)
GGG CCU CUU CUU UAG
Faint skipping



CUC UCU GA
at 600 and




300 nM


 


H27D(+19−03)
GAC UUC CAA AGU CUU
v. strong



GCA UUU C
skipping at




600 and 300 nM









Antisense Oligonucleotides Directed at Exon 28
Antisense oligonucleotides directed at exon 28 were prepared using similar methods as described above. Table 23 below outlines the antisense oligonucleotides directed at exon 28 that are yet to be tested for their ability to induce exon 28 skipping.







TABLE 23







(SEQ ID NOS 114-116, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H28A(−05+19)
GCC AAC AUG CCC AAA
v. strong



CUU CCU AAG
skipping at




600 and 300 nM


 


H28A(+99+124)
CAG AGA UUU CCU CAG
Needs testing



CUC CGC CAG GA



 


H28D(+16−05)
CUU ACA UCU AGC ACC
v. strong



UCA GAG
skipping at




600 and 300 nM









Antisense Oligonucleotides Directed at Exon 29
Antisense oligonucleotides directed at exon 29 were prepared using similar methods as described above. Table 24 below outlines the antisense oligonucleotides directed at exon 29 that are yet to be tested for their ability to induce exon 29 skipping.







TABLE 24







(SEQ ID NOS 117-119, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H29A(+57+81)
UCC GCC AUC UGU UAG
Needs testing



GGU CUG UGC C



 


H29A(+18+42)
AUU UGG GUU AUC CUC
v. strong



UGA AUG UCG C
skipping at




600 and 300 nM


 


H29D(+17−05)
CAU ACC UCU UCA UGU
v. strong



AGU UCC C
skipping at




600 and 300 nM









Antisense Oligonucleotides Directed at Exon 30
Antisense oligonucleotides directed at exon 30 were prepared using similar methods as described above. Table 25 below outlines the antisense oligonucleotides directed at exon 30 that are yet to be tested for their ability to induce exon 30 skipping.







TABLE 25







(SEQ ID NOS 120-122, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H30A(+122+147)
CAU UUG AGC UGC GUC CAC
Needs testing



CUU GUC UG



 


H30A(+25+50)
UCC UGG GCA GAC UGG AUG
Very strong



CUC UGU UC
skipping at




600 and 300




nM.


 


H30D(+19−04)
UUG CCU GGG CUU CCU GAG
Very strong



GCA UU
skipping at




600 and 300




nM.









Antisense Oligonucleotides Directed at Exon 31
Antisense oligonucleotides directed at exon 31 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 13 illustrates differing efficiencies of two antisense molecules directed at exon 31 acceptor splice site and a “cocktail” of exon 31 antisense oligonucleotides at varying concentrations. H31D(+03−22) [SEQ ID NO:124] substantially induced exon 31 skipping when delivered into cells at a concentration of 20 nM. Table 26 below also includes other antisense molecules tested at a concentration of 100 and 300 nM. These antisense molecules showed a variable ability to induce exon skipping.







TABLE 26







(SEQ ID NOS 123-126, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H31D(+06−18)
UUC UGA AAU AAC AUA UAC
Skipping to



CUG UGC
300 nM


 


H31D(+03−22)
UAG UUU CUG AAA UAA CAU
Skipping to



AUA CCU G
20 nM


 


H31A(+05+25)
GAC UUG UCA AAU CAG AUU
No skipping



GGA



 


H31D(+04−20)
GUU UCU GAA AUA ACA UAU
Skipping to



ACC UGU
300 nM









Antisense Oligonucleotides Directed at Exon 32
Antisense oligonucleotides directed at exon 32 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H32D(+04−16) [SEQ ID NO:127] and H32A(+49+73) [SEQ ID NO:130] induced exon 32 skipping when delivered into cells at a concentration of 300 nM. Table 27 below also shows other antisense molecules tested at a concentration of 100 and 300 nM. These antisense molecules did not show an ability to induce exon skipping.







TABLE 27







(SEQ ID NOS 127-130, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H32D(+04−16)
CAC CAG AAA UAC AUA CCA
Skipping to



CA
300 nM


 


H32A(+151+170)
CAA UGA UUU AGC UGU GAC
No skipping



UG



 


H32A(+10+32)
CGA AAC UUC AUG GAG ACA
No skipping



UCU UG



 


H32A(+49+73)
CUU GUA GAC GCU GCU CAA
Skipping to



AAU UGG C
300 nM









Antisense Oligonucleotides Directed at Exon 33
Antisense oligonucleotides directed at exon 33 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 14 shows differing efficiencies of two antisense molecules directed at exon 33 acceptor splice site. H33A(+64+88) [SEQ ID NO:134] substantially induced exon 33 skipping when delivered into cells at a concentration of 10 nM. Table 28 below includes other antisense molecules tested at a concentration of 100, 200 and 300 nM. These antisense molecules showed a variable ability to induce exon skipping.







TABLE 28







(SEQ ID NOS 131-134, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H33D(+09−11)
CAU GCA CAC ACC UUU GCU
No skipping



CC



 


H33A(+53+76)
UCU GUA CAA UCU GAC GUC
Skipping to



CAG UCU
200 nM


 


H33A(+30+56)
GUC UUU AUC ACC AUU UCC
Skipping to



ACU UCA GAC
200 nM


 


H33A(+64+88)
CCG UCU GCU UUU UCU GUA
Skipping to



CAA UCU G
10 nM









Antisense Oligonucleotides Directed at Exon 34
Antisense oligonucleotides directed at exon 34 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
Table 29 below includes antisense molecules tested at a concentration of 100 and 300 nM. These antisense molecules showed a variable ability to induce exon skipping.







TABLE 29







(SEQ ID NOS 135-141, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H34A(+83+104)
UCC AUA UCU GUA GCU GCC
No skipping



AGC C



 


H34A(+143+165)
CCA GGC AAC UUC AGA AUC
No skipping



CAA AU



 


H34A(−20+10)
UUU CUG UUA CCU GAA AAG
Not tested



AAU UAU AAU GAA



 


H34A(+46+70)
CAU UCA UUU CCU UUC GCA
Skipping to



UCU UAC G
300 nM


 


H34A(+95+120)
UGA UCU CUU UGU CAA UUC
Skipping to 



CAU AUC UG
300 nM


 


H34D(+10−20)
UUC AGU GAU AUA GGU UUU
Not tested



ACC UUU CCC CAG



 


H34A(+72+96)
CUG UAG CUG CCA GCC AUU
No skipping



CUG UCA AG









Antisense Oligonucleotides Directed at Exon 35
Antisense oligonucleotides directed at exon 35 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 15 shows differing efficiencies of antisense molecules directed at exon 35 acceptor splice site. H35A(+24+43) [SEQ ID NO:144] substantially induced exon 35 skipping when delivered into cells at a concentration of 20 nM. Table 30 below also includes other antisense molecules tested at a concentration of 100 and 300 nM. These antisense molecules showed no ability to induce exon skipping.







TABLE 30







(SEQ ID NOS 142-144, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H35A(+141+161)
UCU UCU GCU CGG GAG GUG
Skipping to



ACA
20 nM


 


H35A(+116+135)
CCA GUU ACU AUU CAG AAG
No skipping



AC



 


H35A(+24+43)
UCU UCA GGU GCA CCU UCU
No skipping



GU









Antisense Oligonucleotides Directed at Exon 36
Antisense oligonucleotides directed at exon 36 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
Antisense molecule H36A(+26+50) [SEQ ID NO:145] induced exon 36 skipping when delivered into cells at a concentration of 300 nM, as shown in FIG. 16.
Antisense Oligonucleotides Directed at Exon 37
Antisense oligonucleotides directed at exon 37 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 17 shows differing efficiencies of two antisense molecules directed at exon 37 acceptor splice site. H37A(+82+105) [SEQ ID NO:148] and H37A(+134+157) [SEQ ID NO:149] substantially induced exon 37 skipping when delivered into cells at a concentration of 10 nM. Table 31 below shows the antisense molecules tested.







TABLE 31







(SEQ ID NOS 147-149, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H37A(+26+50)
CGU GUA GAG UCC ACC UUU
No skipping



GGG CGU A



 


H37A(+82+105)
UAC UAA UUU CCU GCA GUG
Skipping to



GUC ACC
10 nM


 


H37A(+134+157)
UUC UGU GUG AAA UGG CUG
Skipping to



CAA AUC
10 nM









Antisense Oligonucleotides Directed at Exon 38
Antisense oligonucleotides directed at exon 38 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 18 illustrates antisense molecule H38A(+88+112) [SEQ ID NO:152], directed at exon 38 acceptor splice site. H38A(+88+112) substantially induced exon 38 skipping when delivered into cells at a concentration of 10 nM. Table 32 below shows the antisense molecules tested and their ability to induce exon skipping.







TABLE 32







(SEQ ID NOS 150-152, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H38A(−01+19)
CCU UCA AAG GAA UGG AGG
No skipping



CC



 


H38A(+59+83)
UGC UGA AUU UCA GCC UCC
Skipping to



AGU GGU U
10 nM


 


H38A(+88+112)
UGA AGU CUU CCU CUU UCA
Skipping to



GAU UCA C
10 nM









Antisense Oligonucleotides Directed at Exon 39
Antisense oligonucleotides directed at exon 39 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H39A(+62+85) [SEQ ID NO:153] induced exon 39 skipping when delivered into cells at a concentration of 100 nM. Table 33 below shows the antisense molecules tested and their ability to induce exon skipping.







TABLE 33







(SEQ ID NOS 153-156, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H39A(+62+85)
CUG GCU UUC UCU CAU CUG
Skipping to



UGA UUC
100 nM


 


H39A(+39+58)
GUU GUA AGU UGU CUC CUC
No skipping



UU



 


H39A(+102+121)
UUG UCU GUA ACA GCU GCU
No skipping



GU



 


H39D(+10−10)
GCU CUA AUA CCU UGA GAG
Skipping to



CA
300 nM









Antisense Oligonucleotides Directed at Exon 40
Antisense oligonucleotides directed at exon 40 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 19 illustrates antisense molecule H40A(−05+17) [SEQ ID NO:157] directed at exon 40 acceptor splice site. H40A(−05+17) and H40A(+129+153) [SEQ ID NO:158] both substantially induced exon 40 skipping when delivered into cells at a concentration of 5 nM.
Antisense Oligonucleotides Directed at Exon 42
Antisense oligonucleotides directed at exon 42 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 20 illustrates antisense molecule H42A(−04+23) [SEQ ID NO:159], directed at exon 42 acceptor splice site. H42A(−4+23) and H42D(+19−02) [SEQ ID NO:161] both induced exon 42 skipping when delivered into cells at a concentration of 5 nM. Table 34 below shows the antisense molecules tested and their ability to induce exon 42 skipping.







TABLE 34







(SEQ ID NOS 159-160, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H42A(−4+23)
AUC GUU UCU UCA CGG ACA
Skipping to



GUG UGC UGG
5 nM


 


H42A(+86+109)
GGG CUU GUG AGA CAU GAG
Skipping to



UGA UUU
100 nM


 


H42D(+19−02)
A CCU UCA GAG GAC UCC
Skipping to



UCU UGC
5 nM









Antisense Oligonucleotides Directed at Exon 43
Antisense oligonucleotides directed at exon 43 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H43A(+101+120) [SEQ ID NO:163] induced exon 43 skipping when delivered into cells at a concentration of 25 nM. Table 35 below includes the antisense molecules tested and their ability to induce exon 43 skipping.







TABLE 35







(SEQ ID NOS 162-164, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H43D(+10−15)
UAU GUG UUA CCU ACC CUU
Skipping to



GUC GGU C
100 nM


 


H43A(+101+120)
GGA GAG AGC UUC CUG UAG
Skipping to



CU
25 nM


 


H43A(+78+100)
UCA CCC UUU CCA CAG GCG
Skipping to



UUG CA
200 nM









Antisense Oligonucleotides Directed at Exon 44
Antisense oligonucleotides directed at exon 44 were prepared using similar methods as described above. Testing for the ability of these antisense molecules to induce exon 44 skipping is still in progress. The antisense molecules under review are shown as SEQ ID Nos: 165 to 167 in Table 1A.
Antisense Oligonucleotides Directed at Exon 45
Antisense oligonucleotides directed at exon 45 were prepared using similar methods as described above. Testing for the ability of these antisense molecules to induce exon 45 skipping is still in progress. The antisense molecules under review are shown as SEQ ID Nos: 207 to 211 in Table 1A.
Antisense Oligonucleotides Directed at Exon 46
Antisense oligonucleotides directed at exon 46 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 21 illustrates the efficiency of one antisense molecule directed at exon 46 acceptor splice site. Antisense oligonucleotide H46A(+86+115) [SEQ ID NO:203] showed very strong ability to induce exon 46 skipping. Table 36 below includes antisense molecules tested. These antisense molecules showed varying ability to induce exon 46 skipping.







TABLE 36







(SEQ ID NOS 168-169 and 203-206, respectively,


in order of appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H46D(+16−04)
UUA CCU UGA CUU GCU CAA
No skipping



GC



 


H46A(+90+109)
UCC AGG UUC AAG UGG GAU
No skipping



AC



 


H46A(+86+115)
CUC UUU UCC AGG UUC AAG
Good skipping



UGG GAU ACU AGC
to 100 nM


 


H46A(+107+137)
CAA GCU UUU CUU UUA GUU
Good skipping



GCU GCU CUU UUC C
to 100 nM


 


H46A(−10+20)
UAU UCU UUU GUU CUU CUA
Weak skipping



GCC UGG AGA AAG



 


H46A(+50+77)
CUG CUU CCU CCA ACC AUA
Weak skipping



AAA CAA AUU C









Antisense Oligonucleotides Directed at Exon 47
Antisense oligonucleotides directed at exon 47 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
H47A(+76+100) [SEQ ID NO:170] and H47A(−09+12) [SEQ ID NO:172] both induced exon 47 skipping when delivered into cells at a concentration of 200 nM. H47D(+25−02) [SEQ ID NO: 171] is yet to be prepared and tested.
Antisense Oligonucleotides Directed at Exon 50
Antisense oligonucleotides directed at exon 50 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
Antisense oligonucleotide molecule H50(+02+30) [SEQ ID NO: 173] was a strong inducer of exon skipping. Further, H50A(+07+33) [SEQ ID NO:174] and H50D(+07−18) [SEQ ID NO:175] both induced exon 50 skipping when delivered into cells at a concentration of 100 nM.
Antisense Oligonucleotides Directed at Exon 51
Antisense oligonucleotides directed at exon 51 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 22 illustrates differing efficiencies of two antisense molecules directed at exon 51 acceptor splice site. Antisense oligonucleotide H51A(+66+90) [SEQ ID NO:180] showed the stronger ability to induce exon 51 skipping. Table 37 below includes antisense molecules tested at a concentration range of 25, 50, 100, 300 and 600 nM. These antisense molecules showed varying ability to induce exon skipping. The strongest inducers of exon skipping were antisense oligonucleotide H51A(+61+90) [SEQ ID NO: 179] and H51A(+66+95) [SEQ ID NO: 179].







TABLE 37







(SEQ ID NOS 176-185, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H51A(−01+25)
ACC AGA GUA ACA GUC UGA
Faint



GUA GGA GC
skipping


 


H51D(+16−07)
CUC AUA CCU UCU GCU UGA
Skipping at



UGA UC
300 nM


 


H51A(+111+134)
UUC UGU CCA AGC CCG GUU
Needs re-



GAA AUC
testing


 


H51A(+61+90)
ACA UCA AGG AAG AUG GCA
Very strong



UUU CUA GUU UGG
skipping


 


H51A(+66+90)
ACA UCA AGG AAG AUG GCA
skipping



UUU CUA G



 


H51A(+66+95)
CUC CAA CAU CAA GGA AGA
Very strong



UGG CAU UUC UAG
skipping


 


H51D(+08−17)
AUC AUU UUU UCU CAU ACC
No skipping



UUC UGC U



 


H51A/D(+08−17) &
AUC AUU UUU UCU CAU ACC
No skipping


(−15+?)
UUC UGC UAG GAG CUA AAA



 


H51A(+175+195)
CAC CCA CCA UCA CCC UCU
No skipping



GUG



 


H51A(+199+220)
AUC AUC UCG UUG AUA UCC
No skipping



UCA A









Antisense Oligonucleotides Directed at Exon 52
Antisense oligonucleotides directed at exon 52 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 22 also shows differing efficiencies of four antisense molecules directed at exon 52 acceptor splice site. The most effective antisense oligonucleotide for inducing exon 52 skipping was H52A(+17+37) [SEQ ID NO:188].
Table 38 below shows antisense molecules tested at a concentration range of 50, 100, 300 and 600 nM. These antisense molecules showed varying ability to induce exon 50 skipping. Antisense molecules H52A(+12+41) [SEQ ID NO:187] and H52A(+17+37) [SEQ ID NO:188] showed the strongest exon 50 skipping at a concentration of 50 nM.







TABLE 38







(SEQ ID NOS 186-190, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H52A(−07+14)
UCC UGC AUU GUU GCC UGU
No skipping



AAG



 


H52A(+12+41)
UCC AAC UGG GGA CGC CUC
Very strong



UGU UCC AAA UCC
skipping


 


H52A(+17+37)
ACU GGG GAC GCC UCU GUU
Skipping to



CCA
50 nM


 


H52A(+93+112)
CCG UAA UGA UUG UUC UAG
No skipping



CC



 


H52D(+05−15)
UGU UAA AAA ACU UAC UUC
No skipping



GA









Antisense Oligonucleotides Directed at Exon 53
Antisense oligonucleotides directed at exon 53 were prepared and tested for their ability to induce exon skipping in human muscle cells using similar methods as described above.
FIG. 22 also shows antisense molecule H53A(+39+69) [SEQ ID NO:193] directed at exon 53 acceptor splice site. This antisense oligonucleotide was able to induce exon 53 skipping at 5, 100, 300 and 600 nM. A “cocktail” of three exon 53 antisense oligonucleotides:H53A(+23+47) [SEQ ID NO:195], H53A(+150+175) [SEQ ID NO:196] and H53A(+14-07) [SEQ ID NO:194], was also tested, as shown in FIG. 20 and exhibited an ability to induce exon skipping.
Table 39 below includes other antisense molecules tested at a concentration range of 50, 100, 300 and 600 nM. These antisense molecules showed varying ability to induce exon 53 skipping. Antisense molecule H53A(+39+69) [SEQ ID NO:193] induced the strongest exon 53 skipping.







TABLE 39







(SEQ ID NOS 191-202, respectively, in order of


appearance)









Antisense

Ability to


oligonucleotide

induce


name
Sequence
skipping





H53A(+45+69)
CAU UCA ACU GUU GCC
Faint skipping



UCC GGU UCU G
at 50 nM


 


H53A(+39+62)
CUG UUG CCU CCG GUU
Faint skipping



CUG AAG GUG
at 50 nM


 


H53A(+39+69)
CAU UCA ACU GUU GCC
Strong



UCC GGU UCU GAA GGU G
skipping to




50 nM


 


H53D(+14−07)
UAC UAA CCU UGG UUU
Very faint



CUG UGA
skipping to




50 nM


 


H53A(+23+47)
CUG AAG GUG UUC UUG
Very faint



UAC UUC AUC C
skipping to




50 nM


 


H53A(+150+176)
UGU AUA GGG ACC CUC
Very faint



CUU CCA UGA CUC
skipping to




50 nM


 


H53D(+20−05)
CUA ACC UUG GUU UCU
Not made yet



GUG AUU UUC U



 


H53D(+09−18)
GGU AUC UUU GAU ACU
Faint at



AAC CUU GGU UUC
600 nM


 


H53A(−12+10)
AUU CUU UCA ACU AGA
No skipping



AUA AAA G



 


H53A(−07+18)
GAU UCU GAA UUC UUU
No skipping



CAA CUA GAA U



 


H53A(+07+26)
AUC CCA CUG AUU CUG
No skipping



AAU UC



 


H53A(+124+145)
UUG GCU CUG GCC UGU
No skipping



CCU AAG A

## Claims

1. An isolated antisense oligonucleotide that is specifically hybridizable to an exon 53 target region of the Dystrophin gene designated as annealing site H53A (+23+47), wherein the antisense oligonucleotide consists of the sequence identified as SEQ ID NO: 195, wherein the uracil bases are optionally thymine bases.

2. The antisense oligonucleotide of claim 1, wherein the uracil bases are thymine bases.

3. The antisense oligonucleotide of claim 1, wherein the oligonucleotide does not activate RNase H.

4. The antisense oligonucleotide of claim 1, comprising a non-natural backbone.

5. The antisense oligonucleotide of claim 1, wherein the sugar moieties of the oligonucleotide backbone are replaced with non-natural moieties.

6. The antisense oligonucleotide of claim 5, wherein the non-natural moieties are morpholinos.

7. The antisense oligonucleotide of claim 1, wherein the inter-nucleotide linkages of the oligonucleotide backbone are replaced with non-natural inter-nucleotide linkages.

8. The antisense oligonucleotide of claim 7, wherein the non-natural inter-nucleotide linkages are modified phosphates.

9. The antisense oligonucleotide of claim 1, wherein the sugar moieties of the oligonucleotide backbone are replaced with non-natural moieties and the inter-nucleotide linkages of the oligonucleotide backbone are replaced with non-natural inter-nucleotide linkages.

10. The antisense oligonucleotide of claim 9, wherein the non-natural moieties are morpholinos and the non-natural internucleotide linkages are modified phosphates.

11. The antisense oligonucleotide of claim 10, wherein the modified phosphates are methyl phosphonates, methyl phosphorothioates, phosphoromorpholidates, phosphoropiperazidates or phosphoroamidates.

12. The antisense oligonucleotide of claim 1, wherein the oligonucleotide is a 2′-O-methyl-oligoribonucleotide.

13. The antisense oligonucleotide of claim 1, wherein the oligonucleotide is a peptide nucleic acid.

14. The antisense oligonucleotide of claim 1, wherein the oligonucleotide is chemically linked to one or more moieties or conjugates that enhance the activity, cellular distribution, or cellular uptake of the antisense oligonucleotide.

15. The antisense oligonucleotide of claim 14, wherein the oligonucleotide is chemically linked to a polyethylene glycol molecule.

16. A pharmaceutical composition, comprising an antisense oligonucleotide of claim 1 and a saline solution that includes a phosphate buffer.

17. The antisense oligonucleotide of claim 8, wherein the modified phosphates are methyl phosphonates, methyl phosphorothioates, phosphoromorpholidates, phosphoropiperazidates or phosphoroamidates.

18. The antisense oligonucleotide of claim 17, wherein the modified phosphates are phosphoramidates.

19. The antisense oligonucleotide of claim 17, wherein the modified phosphates are phosphoromornpholidates.

20. A method of inducing exon-skipping of a dystrophin exon 53, comprising delivering an antisense oligonucleotide that is specifically hybridizable to an exon 53 target region of the dystrophin gene designated as annealing site H53A (+23+47), wherein the antisense oligonucleotide consists of the sequence identified as SEQ ID NO: 195, wherein the uracil bases are optionally thymine bases, thereby inducing exon-skipping of the dystrophin exon.

21. The method of claim 20, wherein the cell is a human muscle cell.

22. The method of claim 21, wherein the human muscle cell is in a patient.

23. The method of claim 11, wherein the patient has muscular dystrophy.

24. The method of claim 23, wherein the muscular dystrophy is Duchenne Muscular Dystrophy.

25. The method of claim 20, wherein the uracil bases are thymine bases.