NZ749395A - Antisense oligonucleotides for modulating htra1 expression - Google Patents
Antisense oligonucleotides for modulating htra1 expressionInfo
- Publication number
- NZ749395A NZ749395A NZ749395A NZ74939517A NZ749395A NZ 749395 A NZ749395 A NZ 749395A NZ 749395 A NZ749395 A NZ 749395A NZ 74939517 A NZ74939517 A NZ 74939517A NZ 749395 A NZ749395 A NZ 749395A
- Authority
- NZ
- New Zealand
- Prior art keywords
- oligonucleotide
- htra1
- nucleosides
- seq
- lna
- Prior art date
Links
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Abstract
The present invention relates to antisense oligonucleotides (oligomers) that are complementary to HTRA1, leading to modulation of the expression of HTRA1. Modulation of HTRA expression is beneficial for a range of medical disorders, such as macular degeneration, e.g. age-related macular degeneration. .
Description
P33710-WO
ANTISENSE OLIGONUCLEOTIDES FOR MODULATING HTRA1 EXPRESSION
FIELD OF INVENTION
The present invention relates to antisense oligonucleotides (oligomers) that are complementary
to HTRA1, leading to modulation of the expression of HTRA1. Modulation of HTRA1
expression is beneficial for a range of medical disorders, such as macular degeneration, e.g.
age-related macular degeneration.
BACKGROUND
The human high temperature requirement A (HTRA) family of serine proteases are ubiquitously
expressed PDZ-proteases that are involved in maintaining protein homeostasis in extracellular
compartments by combining the dual functions of a protease and a chaperone. HTRA
housekeeping proteases are implicated in organization of the extracellular matrix, cell
proliferation and ageing. Modulation of HTRA activity is connected with severe diseases,
including Duchenne muscular dystrophy (Bakay et al. 2002, Neuromuscul. Disord. 12: 125-141),
arthritis, such as osteoarthritis (Grau et al. 2006, JBC 281: 6124-6129), cancer, familial
ischemic cerebral small-vessel disease and age-related macular degeneration, as well as
Parkinson's disease and Alzheimer's disease. The human HTRA1 contains an insulin-like
growth factor (IGF) binding domain. It has been proposed to regulate IGF availability and cell
growth (Zumbrunn and Trueb, 1996, FEES Letters 398:189-192) and to exhibit tumor
suppressor properties. HTRA1 expression is down-regulated in metastatic melanoma, and may
thus indicate the degree of melanoma progression. Overexpression of HTRA1 in a metastatic
melanoma cell line reduced proliferation and invasion in vitro, and reduced tumor growth in a
xenograft mouse model (Baldi et al., 2002, Oncogene 21:6684-6688). HTRA1 expression is
also down-regulated in ovarian cancer. In ovarian cancer cell lines, HTRA1 overexpression
induces cell death, while antisense HTRA1 expression promoted anchorage-independent
growth (Chien et al., 2004, Oncogene 23:1636-1644).
In addition to its effect on the IGF pathway, HTRA1 also inhibits signaling by the TGF β family of
growth factors (Oka et al., 2004, Development 131:1041-1053). HTRA1 can cleave amyloid
precursor protein (APP), and HTRA1 inhibitors cause the accumulation of A β peptide in cultured
cells. Thus, HTRA1 is also implicated in Alzheimer's disease (Grau et al.,2005, Proc. Nat. Acad.
Sci. USA. 102:6021-6026).
On the other hand HTRA1 upregulation has been observed and seems to be associated to
Duchenne muscular dystrophy (Bakay et al. 2002, Neuromuscul. Disord. 12: 125-141) and
osteoarthritis (Grau et al. 2006, JBC 281: 6124-6129) and AMD (Fritsche, et al. Nat Gen 2013
45(4):433-9.)
P33710-WO
A single nucleotide polymorphism (SNP) in the HTRA1 promoter region (rs11200638) is
associated with a 10 fold increased the risk of developing age-related macular degeneration
(AMD). Moreover the HTRA1 SNPs are in linkage disequilibrium with the ARMS2 SNP
(rs10490924) associated with increased risk of developing age-related macular degeneration
(AMD). The risk allele is associated with 2-3 fold increased HTRA1 mRNA and protein
expression, and HTRA1 is present in drusen in patients with AMD (Dewan et al., 2006, Science
314:989-992; Yang et al., 2006, Science 314:992-993). Different animal models have
confirmed that over-expression of HtrA1 Induces AMD-like phenotype in mice. The hHTRA
transgenic mouse (Veierkottn, PlosOne 2011) reveals degradation of the elastic lamina of
Bruch’s membrane, determines choroidal vascular abnormalities (Jones, PNAS 2011) and
increases the Polypoidal choroidal vasculopathy (PCV) lesions (Kumar, IOVS 2014).
Additionally it has been reported Bruch’s membrane damage in hHTRA1 Tg mice, which
determines upon exposure to cigarette smoke 3 fold increases CNV (Nakayama, IOVS 2014)
Age-related macular degeneration (AMD) is the leading cause of irreversible loss of vision in
people over the age of 65. With onset of AMD there is gradual loss of the light sensitive
photoreceptor cells in the back of the eye, the underlying pigment epithelial cells that support
them metabolically, and the sharp central vision they provide. Age is the major risk factor for the
onset of AMD: the likelihood of developing AMD triples after age 55. Smoking, light iris color,
gender (women are at greater risk), obesity, and repeated exposure to UV radiation also
increase the risk of AMD. There are two forms of AMD: dry AMD and wet AMD. In dry AMD,
drusen appear in the macula of the eye, the cells in the macula die, and vision becomes blurry.
Dry AMD can progress in three stages: 1) early, 2) intermediate, and 3) advanced dry AMD. Dry
AMD can also progress into wet AMD during any of these stages. Wet AMD (also known as
exudative AMD), is associated with pathologic posterior segment neovascularization. The
posterior segment neovascularization (PSNV) found in exudative AMD is characterized as
pathologic choroidal neovascularization. Leakage from abnormal blood vessels forming in this
process damages the macula and impairs vision, eventually leading to blindness. Treatment
strategies for wet AMD are few and palliative at best. There is therefore an unmet medical need
in the provision of effective drugs to treat macular degenerative conditions such as wet and dry
AMD. claims a composition for treating a subject suffering from age related
macular degeneration comprising a nucleic acid molecules comprising an antisense sequence
that hybridizes to HTRA1 gene or mRNA: No antisense molecules are disclosed.
WO2009/006460 provides siRNAs targeting HTRA1 and their use in treating AMD.
OBJECTIVE OF THE INVENTION
The present invention provides antisense oligonucleotides which modulate HTRA1 in vivo or in
vitro. The invention identified cryptic target sequence motifs present in the human HTRA1
mRNA (including pre-mRNA) which may be targeted by antisense oligonucleotides to give
P33710-WO
effective HTRA1 inhibition. The invention also provides effective antisense oligonucleotide
sequences and compounds which are capable of inhibiting HTRA1, and their use in treatment of
diseases or disorders where HTRA1 is indicated.
SUMMARY OF INVENTION
The present invention relates to oligonucleotides targeting a mammalian HTRA1 nucleic acid,
i.e. are capable of inhibiting the expression of HTRA1 and to treat or prevent diseases related to
the functioning of the HTRA1. The oligonucleotides targeting HTRA1 are antisense
oligonucleotides, i.e. are complementary to their HTRA1 nucleic acid target.
The oligonucleotide of the invention may be in the form of a pharmaceutically acceptable salt,
such as a sodium salt or a potassium salt.
Accordingly, the invention provides antisense oligonucleotides which comprise a contiguous
nucleotide sequence of 10 - 30 nucleotides in length with at least 90% complementarity, such
as fully complementary to a mammalian HTRA1 nucleic acid, such as SEQ ID NO 1, SEQ ID
NO 2, SEQ ID NO 3 or SEQ ID NO 4.
In a further aspect, the invention provides pharmaceutical compositions comprising the
oligonucleotides of the invention and pharmaceutically acceptable diluents, carriers, salts and/or
adjuvants.
The invention provides LNA antisense oligonucleotides, such as LNA gapmer oligonucleotides,
which comprise a contiguous nucleotide sequence of 10 - 30 nucleotides in length with at least
90% complementarity, such as fully complementary to a HTRA1 nucleic acid, such as a
sequence selected from the group consisting of SEQ ID NO 1, SEQ ID NO 2, SEQ ID NO 3 or
SEQ ID NO 4.
The invention provides for an antisense oligonucleotide comprising a contiguous nucleotide
region of 10 – 22, such as 12 - 22 nucleotides which are at least 90% such as 100%
complementarity to SEQ ID NO 147:
SEQ ID NO 147: 5’ CCAACAACCAGGTAAATATTTG 3’
The invention provides for an antisense oligonucleotide comprising a contiguous nucleotide
region of 10 – 17, such as 11, 12, 13, 14, 15, 16, such as 12 – 16 or 12 - 17 nucleotides which
are complementarity to a sequence selected from the group consisting of SEQ ID NO 148 -
155.
The invention provides for an antisense oligonucleotide comprising a contiguous nucleotide
region of 10 – 17, such as 11, 12, 13, 14, 15, 16, such as 12 – 16 or 12 - 17 nucleotides which
are complementarity to SEQ ID NO 148 or 155.
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The invention provides for an antisense oligonucleotide of 10 – 30 nucleotides in length,
wherein said antisense oligonucleotide comprises a contiguous nucleotide region of 10 – 22
nucleotides which are at least 90% such as 100% complementarity to SEQ ID NO 147:
SEQ ID NO 147: 5’ CCAACAACCAGGTAAATATTTG 3’
The invention provides for an antisense oligonucleotide of 10 – 30 nucleotides in length,
wherein said antisense oligonucleotide comprises a contiguous nucleotide region of at least 10,
such as at least 12 contiguous nucleotides which are complementary to a sequence present in
a sequence selected from SEQ ID NO 148 – 155.
The invention provides for an antisense oligonucleotide of at least 12 nucleotides in length,
wherein said antisense oligonucleotide comprises the contiguous sequence of SEQ ID NO 146
SEQ ID NO 146: 5’ TTTACCTGGTT 3’.
The invention provides for the oligonucleotides provided in the examples. The invention
provides for the oligonucleotide, such as an antisense oligonucleotide, which comprises at least
, such as at least 12, present in a sequence selected from the group consisting of SEQ ID NO
5 – 145.
The invention provides for a conjugate comprising the oligonucleotide according to the
invention, and at least one conjugate moiety covalently attached to said oligonucleotide.
The invention provides for a pharmaceutically acceptable salt of the oligonucleotide or
conjugate of the invention.
In a further aspect, the invention provides methods for in vivo or in vitro method for modulation
of HTRA1 expression in a cell which is expressing HTRA1, by administering an oligonucleotide,
conjugate or composition of the invention in an effective amount to said cell.
In a further aspect the invention provides methods for treating or preventing a disease, disorder
or dysfunction associated with in vivo activity of HTRA1 comprising administering a
therapeutically or prophylactically effective amount of the oligonucleotide of the invention, or
conjugate thereof, to a subject suffering from or susceptible to the disease, disorder or
dysfunction.
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In a further aspect the oligonucleotide or composition of the invention is used for the treatment
or prevention of macular degeneration, and other disorders where HTRA1 is implicated.
The invention provides for the oligonucleotide or conjugate of the invention, for use in the
treatment of a disease or disorder selected from the list comprising of Duchenne muscular
dystrophy, arthritis, such as osteoarthritis, familial ischemic cerebral small-vessel disease,
Alzhiemer’s disease and Parkinson's disease.
The invention provides for the oligonucleotide or conjugate of the invention, for use in the
treatment of macular degeneration, such as wet or dry age related macular degeneration (e.g.
wAMD, dAMD, geographic atrophy, intermediate dAMD) or diabetic retinopathy.
The invention provides for the use of the oligonucleotide, conjugate or composition of the
invention, for the manufacture of a medicament for the treatment of macular degeneration, such
as wet or dry age related macular degeneration (e.g. wAMD, dAMD, geographic atrophy,
intermediate dAMD) or diabetic retinopathy.
The invention provides for the use of the oligonucleotide, conjugate or composition of the
invention, for the manufacture of a medicament for the treatment of a disease or disorder
selected from the group consisting of Duchenne muscular dystrophy, arthritis, such as
osteoarthritis, familial ischemic cerebral small-vessel disease, Alzhiemer’s disease and
Parkinson's disease.
The invention provides for a method of treatment of a subject suffering from a disease or
disorder selected from the group consisting of Duchenne muscular dystrophy, arthritis, such as
osteoarthritis, familial ischemic cerebral small-vessel disease, Alzhiemer’s disease and
Parkinson's disease, said method comprising the step of administering an effective amount of
the oligonucleotide, conjugate or composition of the invention to the subject.
The invention provides for a method of treatment of a subject suffering from an ocular disease,
such as macular degeneration, such as wet or dry age related macular degeneration (e.g.
wAMD, dAMD, geographic atrophy, intermediate dAMD) or diabetic retinopathy, said method
comprising the step of administering an effective amount of the oligonucleotide, conjugate or
composition of the invention to the subject.
The invention provides for a method of treatment of a subject suffering from an ocular disease,
such as macular degeneration, such as wet or dry age related macular degeneration (e.g.
wAMD, dAMD, geographic atrophy, intermediate dAMD) or diabetic retinopathy, said method
comprising administering at least two dosages of the oligonucleotide of the invention, or
pharmaceutically acceptable salt thereof, in an intraocular injection in a dosage of from about
10µg - 200 µg, wherein the dosage interval between administration consecutive is at least 4
weeks or at least monthly.
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BRIEF DESCRIPTION OF FIGURES
Figure 1. A library of n=129 HTRA1 LNA oligonucleotides were screened in U251 and ARPE19
cell lines at 25 µM. Read out: HTRA1 qPCR. n=6 oligos located between position 33042 –
33064 were relatively active.
Figure 2. A library of n=116 HTRA1 LNA oligonucleotides in the 33042 – 33064 hot spot were
screened in U251 and ARPE19 cell lines at 5 and 25 µM, respectively. n=7 oligos were selected
for further analysis. Read out: HTRA1 qPCR.
Figure 3. Dose response of HTRA1 mRNA level upon treatment of human primary RPE cells
with LNA oligonucleotide 139,1 and 143,1.
Figure 5. Rat in vivo efficacy study, 7 days of treatment, IVT administration, dose response.
Retina samples from rat eyes treated with PBS, 140.1 or 143.1 were analyzed. Htra1 ISH
RNAscope was performed, in A) representative samples and in B) an overview table of results
are shown. GFAP IHC was also performed, GFAP is a marker for reactive gliosis and reticular
fibrosis. C) Retina samples subjected to Htra1 qPCR. RE: right eye, LE: left eye. D) Oligo
content bioanalysis was performed and dose response curves for bioanalysis plotted versus
relative mRNA expression is shown. EC determinations was made in Graph Pad Prims. For
PBS treated samples, the oligo content were set to 0.01µg/g tissue.
Figure 6. Poc study, Blue light-induced retinal degeneration in albino rats A) Recovery of
electroretinogram a-wave and b-wave amplitudes 14 days after blue light exposure (%).The
bars indicate group means and 95% CI. Each data point indicates mean of right and left eye
values for each study animal. B) ISH RNA scope, examples from 2 different areas of the retina.
C) Htra1 qPCR of retina samples. D) PK PD correlation.
Figure 7. Rat in vivo efficacy kinetic study, IVT administration, 50µg/eye, 3, 7, 14 days of
treatment. A) HTRA1 mRNA level measured in the retina by qPCR. B) HTRA1 mRNA level
quantified by ISH. The residual HTRA1 mRNA expression level is shown as % of control (PBS-
treated cells) in A and B & C) Dose response curves of oligo content vs. qPCR data for
individual time points.
Figure 8. Non Human Primate (NHP) PK/PD study, IVT administration, 25µg/eye. A) HTRA1
mRNA level measured in the retina by qPCR. B) HTRA1 mRNA level illustrated by ISH. C-D)
Quantification of HTRA1 protein level in retina and vitreous, respectively, by IP-MS. Dots show
data for individual animals. Error bars show standard deviations for technical replicates (n=3).
Figure 9. A Compound of the invention (Compound ID NO 143,1). The compound may be in
the form of a pharmaceutical salt, such as a sodium salt or a potassium salt.
Figure 10. A Compound of the invention (Compound ID No 145,3). The compound may be in
the form of a pharmaceutical salt, such as a sodium salt or a potassium salt.
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Figure 11. An example of a pharmaceutical salt of compound 143.1. M+ is a suitable cation,
typically a positive metal ion, such as a sodium or potassium ion. The stoichiometric ratio of the
cation to the oligonucleotide anion will depend on the charge of the cation used. Suitably,
+ ++ +++
cations with one, two or three positive charge (M , M , or M , may be used). For illustrative
purpose, twice as many single + charged cations (monovalent), such as Na or K are needed
as compared to a divalent cation such as Ca
Figure 12. An example of a pharmaceutical salt of compound 145.3. See the figure legend for
figure 11 for the description of the cation M .
DEFINITIONS
Oligonucleotide
The term “oligonucleotide” as used herein is defined as it is generally understood by the skilled
person as a molecule comprising two or more covalently linked nucleosides. Such covalently
bound nucleosides may also be referred to as nucleic acid molecules or oligomers.
Oligonucleotides are commonly made in the laboratory by solid-phase chemical synthesis
followed by purification. When referring to a sequence of the oligonucleotide, reference is made
to the sequence or order of nucleobase moieties, or modifications thereof, of the covalently
linked nucleotides or nucleosides. The oligonucleotide of the invention is man-made, and is
chemically synthesized, and is typically purified or isolated. The oligonucleotide of the invention
may comprise one or more modified nucleosides or nucleotides.
Antisense oligonucleotides
The term “Antisense oligonucleotide” as used herein is defined as oligonucleotides capable of
modulating expression of a target gene by hybridizing to a target nucleic acid, in particular to a
contiguous sequence on a target nucleic acid. The antisense oligonucleotides are not
essentially double stranded and are therefore not siRNAs. Preferably, the antisense
oligonucleotides of the present invention are single stranded.
Contiguous Nucleotide Region
The term “contiguous nucleotide region” refers to the region of the oligonucleotide which is
complementary to the target nucleic acid. The term may be used interchangeably herein with
the term “contiguous nucleotide sequence” or “contiguous nucleobase sequence” and the term
“oligonucleotide motif sequence”. In some embodiments all the nucleotides of the
oligonucleotide are present in the contiguous nucleotide region. In some embodiments the
oligonucleotide comprises the contiguous nucleotide region and may, optionally comprise
further nucleotide(s), for example a nucleotide linker region which may be used to attach a
functional group to the contiguous nucleotide sequence. The nucleotide linker region may or
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may not be complementary to the target nucleic acid. In some embodiments the
internucleoside linkages present between the nucleotides of the contiguous nucleotide region
are all phosphorothioate internucleoside linkages. In some embodiments, the contiguous
nucleotide region comprises one or more sugar modified nucleosides.
Nucleotides
Nucleotides are the building blocks of oligonucleotides and polynucleotides, and for the
purposes of the present invention include both naturally occurring and non-naturally occurring
nucleotides. In nature, nucleotides, such as DNA and RNA nucleotides comprise a ribose sugar
moiety, a nucleobase moiety and one or more phosphate groups (which is absent in
nucleosides). Nucleosides and nucleotides may also interchangeably be referred to as “units” or
“monomers”.
Modified nucleoside
The term “modified nucleoside” or “nucleoside modification” as used herein refers to
nucleosides modified as compared to the equivalent DNA or RNA nucleoside by the introduction
of one or more modifications of the sugar moiety or the (nucleo)base moiety. In a preferred
embodiment the modified nucleoside comprise a modified sugar moiety. The term modified
nucleoside may also be used herein interchangeably with the term “nucleoside analogue” or
modified “units” or modified “monomers”.
Modified internucleoside linkage
The term “modified internucleoside linkage” is defined as generally understood by the skilled
person as linkages other than phosphodiester (PO) linkages, that covalently couples two
nucleosides together. Nucleotides with modified internucleoside linkage are also termed
“modified nucleotides”. In some embodiments, the modified internucleoside linkage increases
the nuclease resistance of the oligonucleotide compared to a phosphodiester linkage. For
naturally occurring oligonucleotides, the internucleoside linkage includes phosphate groups
creating a phosphodiester bond between adjacent nucleosides. Modified internucleoside
linkages are particularly useful in stabilizing oligonucleotides for in vivo use, and may serve to
protect against nuclease cleavage at regions of DNA or RNA nucleosides in the oligonucleotide
of the invention, for example within the gap region of a gapmer oligonucleotide, as well as in
regions of modified nucleosides.
In an embodiment, the oligonucleotide comprises one or more internucleoside linkages modified
from the natural phosphodiester to a linkage that is for example more resistant to nuclease
attack. Nuclease resistance may be determined by incubating the oligonucleotide in blood
serum or by using a nuclease resistance assay (e.g. snake venom phosphodiesterase (SVPD)),
both are well known in the art. Internucleoside linkages which are capable of enhancing the
nuclease resistance of an oligonucleotide are referred to as nuclease resistant internucleoside
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linkages. In some embodiments all of the internucleoside linkages of the oligonucleotide, or
contiguous nucleotide sequence thereof, are modified. It will be recognized that, in some
embodiments the nucleosides which link the oligonucleotide of the invention to a non-nucleotide
functional group, such as a conjugate, may be phosphodiester. In some embodiments all of the
internucleoside linkages of the oligonucleotide, or contiguous nucleotide sequence thereof, are
nuclease resistant internucleoside linkages.
In some embodiments the modified internucleoside linkages may be phosphorothioate
internucleoside linkages. In some embodiments, the modified internucleoside linkages are
compatible with the RNaseH recruitment of the oligonucleotide of the invention, for example
phosphorothioate.
In some embodiments the internucleoside linkage comprises sulphur (S), such as a
phosphorothioate internucleoside linkage.
A phosphorothioate internucleoside linkage is particularly useful due to nuclease resistance,
beneficial pharmakokinetics and ease of manufacture. In some embodiments all of the
internucleoside linkages of the oligonucleotide, or contiguous nucleotide sequence thereof, are
phosphorothioate.
Nucleobase
The term nucleobase includes the purine (e.g. adenine and guanine) and pyrimidine (e.g. uracil,
thymine and cytosine) moiety present in nucleosides and nucleotides which form hydrogen
bonds in nucleic acid hybridization. In the context of the present invention the term nucleobase
also encompasses modified nucleobases which may differ from naturally occurring
nucleobases, but are functional during nucleic acid hybridization. In this context “nucleobase”
refers to both naturally occurring nucleobases such as adenine, guanine, cytosine, thymidine,
uracil, xanthine and hypoxanthine, as well as non-naturally occurring variants. Such variants are
for example described in Hirao et al (2012) Accounts of Chemical Research vol 45 page 2055
and Bergstrom (2009) Current Protocols in Nucleic Acid Chemistry Suppl. 37 1.4.1.
In a some embodiments the nucleobase moiety is modified by changing the purine or pyrimidine
into a modified purine or pyrimidine, such as substituted purine or substituted pyrimidine, such
as a nucleobased selected from isocytosine, pseudoisocytosine, 5-methyl cytosine, 5-thiozolo-
cytosine, 5-propynyl-cytosine, 5-propynyl-uracil, 5-bromouracil 5-thiazolo-uracil, 2-thio-uracil,
2’thio-thymine, inosine, diaminopurine, 6-aminopurine, 2-aminopurine, 2,6-diaminopurine and 2-
chloroaminopurine.
The nucleobase moieties may be indicated by the letter code for each corresponding
nucleobase, e.g. A, T, G, C or U, wherein each letter may optionally include modified
nucleobases of equivalent function. For example, in the exemplified oligonucleotides, the
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nucleobase moieties are selected from A, T, G, C, and 5-methyl cytosine. Optionally, for LNA
gapmers, 5-methyl cytosine LNA nucleosides may be used. In some embodiments, the
cytosine nucleobases in a 5’cg3’ motif is 5-methyl cytosine.
Modified oligonucleotide
The term modified oligonucleotide describes an oligonucleotide comprising one or more sugar-
modified nucleosides and/or modified internucleoside linkages. The term chimeric”
oligonucleotide is a term that has been used in the literature to describe oligonucleotides with
modified nucleosides.
Complementarity
The term complementarity describes the capacity for Watson-Crick base-pairing of
nucleosides/nucleotides. Watson-Crick base pairs are guanine (G)-cytosine (C) and adenine
(A) - thymine (T)/uracil (U). It will be understood that oligonucleotides may comprise
nucleosides with modified nucleobases, for example 5-methyl cytosine is often used in place of
cytosine, and as such the term complementarity encompasses Watson Crick base-paring
between non-modified and modified nucleobases (see for example Hirao et al (2012) Accounts
of Chemical Research vol 45 page 2055 and Bergstrom (2009) Current Protocols in Nucleic
Acid Chemistry Suppl. 37 1.4.1).
The term “% complementary” as used herein, refers to the number of nucleotides in percent of
a contiguous nucleotide region or sequence in a nucleic acid molecule (e.g. oligonucleotide)
which, at a given position, are complementary to (i.e. form Watson Crick base pairs with) a
contiguous nucleotide sequence, at a given position of a separate nucleic acid molecule (e.g.
the target nucleic acid). The percentage is calculated by counting the number of aligned bases
that form pairs between the two sequences, dividing by the total number of nucleotides in the
oligonucleotide and multiplying by 100. In such a comparison a nucleobase/nucleotide which
does not align (form a base pair) is termed a mismatch.
It will be understood that when referring to complementarity between two sequences, the
determination of complementarity is measured across the length of the shorter of the two
sequences, such as the length of the contiguous nucleotide region or sequence.
The term “fully complementary”, refers to 100% complementarity. In the absence of a % term
value or indication of a mismatch, complementary means fully complementary.
Identity
The term “Identity” as used herein, refers to the number of nucleotides in percent of a
contiguous nucleotide sequence in a nucleic acid molecule (e.g. oligonucleotide) which, at a
given position, are identical to (i.e. in their ability to form Watson Crick base pairs with the
complementary nucleoside) a contiguous nucleotide sequence, at a given position of a separate
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nucleic acid molecule (e.g. the target nucleic acid). The percentage is calculated by counting
the number of aligned bases that are identical between the two sequences, including gaps,
dividing by the total number of nucleotides in the oligonucleotide and multiplying by 100.
Percent Identity = (Matches x 100)/Length of aligned region (with gaps).
When determining the identity of the contiguous nucleotide region of an oligonucleotide, the
identity is calculated across the length of the contiguous nucleotide region. In embodiments
where the entire contiguous nucleotide sequence of the oligonucleotide is the contiguous
nucleotide region, identity is therefore calculated across the length of the nucleotide sequence
of the oligonucleotide. In this respect the contiguous nucleotide region may be identical to a
region of the reference nucleic acid sequence, or in some embodiments may be identical to the
entire reference nucleic acid. Unless otherwise indicated a sequence which has 100% identity
to a reference sequence is referred to as being identical. For example, the reference sequence
may be selected from the group consisting of any one of SEQ ID NOs 5 – 146 and 156.
However, if the oligonucleotide comprises additional nucleotide(s) flanking the contiguous
nucleotide region, for example region D’ or D’’, these additional flanking nucleotides may be
disregarded when determining identity. In some embodiments, identity may be calculated
across the entire oligonucleotide sequence.
In some embodiments, the antisense oligonucleotide oligonucleotide of the invention comprises
a contiguous nucleotide region of 10 – 22 contiguous nucleotides which are identical to SEQ ID
NO 156:
SEQ ID NO 156: 5’ CAAATATTTACCTGGTTGTTGG 3’
In some embodiments, the contiguous nucleotide region consists or comprises of at least 10
contiguous nucleotides, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, contiguous
nucleotides, such as from 12-22, such as from 14-18 contiguous nucleotides of SEQ ID NO
156. In some embodiments, the entire contiguous sequence of the oligonucleotide consists or
comprises of at least 10 contiguous nucleotides, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, contiguous nucleotides, such as from 12-22, such as from 14-18 contiguous nucleotides
of SEQ ID NO 156.
In some embodiments, the contiguous nucleotide region is at least 12 contiguous nucleotides of
SEQ ID NO 156. In some embodiments, the contiguous nucleotide region is at least 14
contiguous nucleotides of SEQ ID NO 156. In some embodiments, the contiguous nucleotide
region is at least 16 contiguous nucleotides SEQ ID NO 156.
In some embodiments, the contiguous nucleotide region is at least 10, 12, 14 or 16 contiguous
nucleotides which are identical to SEQ ID NO 143.
In some embodiments, the contiguous nucleotide region is at least 10, 12, 14 or 16 contiguous
nucleotides which are identical to SEQ ID NO 145.
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In some embodiments, the contiguous nucleotide region is at least 10, 11, 12, 13, 14, 15 or 16
contiguous nucleotides which are identical to SEQ ID NO 143.
In some embodiments, the contiguous nucleotide region is at least 10, 11, 12, 13, 14, 15, 16 or
17 contiguous nucleotides which are identical to SEQ ID NO 145.
In some embodiments, the contiguous nucleotide consists or comprises SEQ ID NO 143.
In some embodiments, the contiguous nucleotide region consists or comprises SEQ ID NO 145.
In some embodiments, the contiguous nucleotide region is at least 10, 12, 14 or 16 contiguous
nucleotides which are identical to a sequence selected from the group consisting of SEQ ID NO
138, 139, 140, 141, 142, 143, 144 and 145. In some embodiments, the contiguous nucleotide
region comprises or consists of a sequence selected from the group consisting of SEQ ID NO
138, 139, 140, 141, 142, 143, 144 and 145.
In some embodiments the contiguous nucleotide region comprises the sequence SEQ ID NO
146: TTTACCTGGTT.
The invention provides for an antisense oligonucleotide 11 – 30 nucleotides in length, such as
12 – 20 nucleotides in length, which comprises the sequence SEQ ID NO 146:
TTTACCTGGTT.
Hybridization
The term “hybridizing” or “hybridizes” as used herein is to be understood as two nucleic acid
strands (e.g. an oligonucleotide and a target nucleic acid) forming hydrogen bonds between
base pairs on opposite strands thereby forming a duplex. The affinity of the binding between
two nucleic acid strands is the strength of the hybridization. It is often described in terms of the
melting temperature (T ) defined as the temperature at which half of the oligonucleotides are
duplexed with the target nucleic acid. At physiological conditions T is not strictly proportional to
the affinity (Mergny and Lacroix, 2003,Oligonucleotides 13:515–537). The standard state Gibbs
free energy ΔG° is a more accurate representation of binding affinity and is related to the
dissociation constant (K ) of the reaction by ΔG°=-RTln(K ), where R is the gas constant and T
is the absolute temperature. Therefore, a very low ΔG° of the reaction between an
oligonucleotide and the target nucleic acid reflects a strong hybridization between the
oligonucleotide and target nucleic acid. ΔG° is the energy associated with a reaction where
aqueous concentrations are 1M, the pH is 7, and the temperature is 37°C. The hybridization of
oligonucleotides to a target nucleic acid is a spontaneous reaction and for spontaneous
reactions ΔG° is less than zero. ΔG° can be measured experimentally, for example, by use of
the isothermal titration calorimetry (ITC) method as described in Hansen et al., 1965,Chem.
Comm. 36–38 and Holdgate et al., 2005, Drug Discov Today. The skilled person will know that
commercial equipment is available for ΔG° measurements. ΔG° can also be estimated
numerically by using the nearest neighbor model as described by SantaLucia, 1998, Proc Natl
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Acad Sci USA. 95: 1460–1465 using appropriately derived thermodynamic parameters
described by Sugimoto et al., 1995, Biochemistry 34:11211–11216 and McTigue et al., 2004,
Biochemistry 43:5388–5405. In order to have the possibility of modulating its intended nucleic
acid target by hybridization, oligonucleotides of the present invention hybridize to a target
nucleic acid with estimated ΔG° values below -10 kcal for oligonucleotides that are 10-30
nucleotides in length. In some embodiments the degree or strength of hybridization is measured
by the standard state Gibbs free energy ΔG°. The oligonucleotides may hybridize to a target
nucleic acid with estimated ΔG° values below the range of -10 kcal, such as below -15 kcal,
such as below -20 kcal and such as below -25 kcal for oligonucleotides that are 8-30
nucleotides in length. In some embodiments the oligonucleotides hybridize to a target nucleic
acid with an estimated ΔG° value of -10 to -60 kcal, such as -12 to -40, such as from -15 to -30
kcal or-16 to -27 kcal such as -18 to -25 kcal.
Target Sequence
The oligonucleotide comprises a contiguous nucleotide region which is complementary to or
hybridizes to a sub-sequence of the target nucleic acid molecule. The term “target sequence”
as used herein refers to a sequence of nucleotides present in the target nucleic acid which
comprises the nucleobase sequence which is complementary to the contiguous nucleotide
region or sequence of the oligonucleotide of the invention. In some embodiments, the target
sequence consists of a region on the target nucleic acid which is complementary to the
contiguous nucleotide region or sequence of the oligonucleotide of the invention. In some
embodiments the target sequence is longer than the complementary sequence of a single
oligonucleotide, and may, for example represent a preferred region of the target nucleic acid
which may be targeted by several oligonucleotides of the invention.
The oligonucleotide of the invention comprises a contiguous nucleotide region which is
complementary to the target nucleic acid, such as a target sequence.
The oligonucleotide comprises a contiguous nucleotide region of at least 10 nucleotides which
is complementary to or hybridizes to a target sequence present in the target nucleic acid
molecule. The contiguous nucleotide region (and therefore the target sequence) comprises of
at least 10 contiguous nucleotides, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
contiguous nucleotides, such as from 12-22, such as from 14-18 contiguous nucleotides.
In some embodiments the target sequence is, or is present within SEQ ID NO 147.
In some embodiments the target sequence is selected from the group consisting of
SEQ ID NO 148, 149, 150, 151, 152, 153, 154 and 155:
SEQ ID NO 148: AACAACCAGGTAAATA
SEQ ID NO 149: CAACCAGGTAAATATTTG
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SEQ ID NO 150: CCAACAACCAGGTAAA
SEQ ID NO 151: AACCAGGTAAATATTTGG
SEQ ID NO 152: ACAACCAGGTAAATATTTGG
SEQ ID NO 153: CAACAACCAGGTAAATAT
SEQ ID NO 154: ACAACCAGGTAAATAT
SEQ ID NO 155: AACAACCAGGTAAATAT
The invention provides for an antisense oligonucleotide of 10 – 30 nucleotides in length,
wherein said antisense oligonucleotide comprises a contiguous nucleotide region of at least 10,
contiguous nucleotides which are complementary to a sequence present in a sequence
selected from SEQ ID NO 147 & 148 – 155.
The invention provides for an antisense oligonucleotide of 12 – 30 nucleotides in length,
wherein said antisense oligonucleotide comprises a contiguous nucleotide region of at least 12
contiguous nucleotides which are complementary to a sequence present in a sequence
selected from SEQ ID NO 147 & 148 – 155.
The invention provides for an antisense oligonucleotide of 14 – 30 nucleotides in length,
wherein said antisense oligonucleotide comprises a contiguous nucleotide region of at least 14
contiguous nucleotides which are complementary to a sequence present in a sequence
selected from SEQ ID NO 147 & 148 – 155.
The invention provides for an antisense oligonucleotide which consists or comprises a
contiguous nucleotide region which is complementary to a sequence selected from SEQ ID NO
148 – 155.
The target sequence may be a sub-sequence of the target nucleic acid. In some embodiments
the oligonucleotide or contiguous nucleotide region is fully complementary to, or only comprises
one or two mismatches to an HTRA1 sub-sequence, such as a sequence selected from the
group consisting of SEQ ID NO 148 - 154. In some embodiments the oligonucleotide or
contiguous nucleotide region is fully complementary to, or only comprises one or two
mismatches to an HTRA1 sub-sequence SEQ ID NO 147.
Target Cell
The term a target cell as used herein refers to a cell which is expressing the target nucleic acid.
In some embodiments the target cell may be in vivo or in vitro. In some embodiments the target
cell is a mammalian cell such as a rodent cell, such as a mouse cell, or a rat cell, or a primate
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cell such as a monkey cell or a human cell. In some embodiments, the cell may be a pig cell, a
dog cell or a rabbit cell. In some embodiments the target cell may be a retinal cell, such as a
retinal pigment epithelium (PRE) cell. In some embodiments the cell is selected from the group
consisting of RPE cells, Bipolar Cell, Amacrine cells, Endothelial cells, Ganglion cells and
Microglia cells. For in vitro assessment, the target cell may be a primary cell or an established
cell line, such as U251, ARPE19, HEK293, or rat C6 cells.
Target nucleic acid
According to the present invention, the target nucleic acid is a nucleic acid which encodes
mammalian HTRA1 and may for example be a gene, a RNA, a mRNA, and pre-mRNA, a
mature mRNA or a cDNA sequence. The target may therefore be referred to as an HTRA1
target nucleic acid.
Suitably, the target nucleic acid encodes an HTRA1 protein, in particular mammalian HTRA1,
such as human HTRA1 (See for example tables 1 & 2 which provides the mRNA and pre-
mRNA sequences for human and rat HTRA1).
In some embodiments, the target nucleic acid is selected from the group consisting of SEQ ID
NO: 1, 2, 3, and 4, or naturally occurring variants thereof (e.g. sequences encoding a
mammalian HTRA1 protein.
A target cell is a cell which is expressing the HTRA1 target nucleic acid. In preferred
embodiments the target nucleic acid is the HTRA1 mRNA, such as the HTRA1 pre-mRNA or
HTRA1 mature mRNA. The poly A tail of HTRA1 mRNA is typically disregarded for antisense
oligonucleotide targeting.
If employing the oligonucleotide of the invention in research or diagnostics the target nucleic
acid may be a cDNA or a synthetic nucleic acid derived from DNA or RNA.
The target sequence may be a sub-sequence of the target nucleic acid. In some embodiments
the oligonucleotide or contiguous nucleotide region is fully complementary to, or only comprises
one or two mismatches to an HTRA1 sub-sequence, such as a sequence selected from the
group consisting of SEQ ID NO 148, 149, 150, 151, 152, 153, 154 and 155.
Complementarity to the target or sub-sequence thereof is measured over the length of the
oligonucleotide, or contiguous nucleotide region thereof.
For in vivo or in vitro application, the oligonucleotide of the invention is typically capable of
inhibiting the expression of the HTRA1 target nucleic acid in a cell which is expressing the
HTRA1 target nucleic acid. The contiguous sequence of nucleobases of the oligonucleotide of
the invention is typically complementary to the HTRA1 target nucleic acid, as measured across
the length of the oligonucleotide, optionally with the exception of one or two mismatches, and
optionally excluding nucleotide based linker regions which may link the oligonucleotide to an
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optional functional group such as a conjugate, or other non-complementary terminal nucleotides
(e.g. region D). The target nucleic acid may, in some embodiments, be a RNA or DNA, such as
a messenger RNA, such as a mature mRNA or a pre-mRNA. In some embodiments the target
nucleic acid is a RNA or DNA which encodes mammalian HTRA1 protein, such as human
HTRA1, e.g. the human HTRA1 mRNA sequence, such as that disclosed as SEQ ID NO 1
(NM_002775.4, GI:190014575). Further information on exemplary target nucleic acids is
provided in tables 1 & 2.
Table 1. Genome and assembly information for human and rat HTRA1.
Species Chr. Strand Genomic coordinates Assembly NCBI reference
Start End sequence* accession
number for mRNA
Human 10 fwd 122461525 122514908 GRCh38.p2 release NM_002775.4
Rat 1 fwd 201499067 201548508 Rnor_6.0 release NM_031721.1
Fwd = forward strand. The genome coordinates provide the pre-mRNA sequence (genomic sequence).
The NCBI reference provides the mRNA sequence (cDNA sequence).
*The National Center for Biotechnology Information reference sequence database is a comprehensive,
integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and
protein. It is hosted at www.ncbi.nlm.nih.gov/refseq.
Table 2. Sequence details for human and rat HTRA1.
Species RNA type Length SEQ ID
(nt) NO
Human mRNA 2138 1
Human premRNA 53384 2
Rat mRNA 2012 3
Rat premRNA 49442 4
Naturally occurring variant
The term “naturally occurring variant” refers to variants of HTRA1 gene or transcripts which
originate from the same genetic loci as the target nucleic acid, but may differ for example, by
virtue of degeneracy of the genetic code causing a multiplicity of codons encoding the same
amino acid, or due to alternative splicing of pre-mRNA, or the presence of polymorphisms, such
as single nucleotide polymorphisms, and allelic variants. Based on the presence of the
sufficient complementary sequence to the oligonucleotide, the oligonucleotide of the invention
may therefore target the target nucleic acid and naturally occurring variants thereof. In some
embodiments, the naturally occurring variants have at least 95% such as at least 98% or at
least 99% homology to a mammalian HTRA1 target nucleic acid, such as a target nucleic acid
selected form the group consisting of SEQ ID NO 1, 2, 3, or 4.
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Modulation of expression
The term “modulation of expression” as used herein is to be understood as an overall term for
an oligonucleotide’s ability to alter the amount of HTRA1 when compared to the amount of
HTRA1 before administration of the oligonucleotide. Alternatively modulation of expression may
be determined by reference to a control experiment where the oligonucleotide of the invention is
not administered. One type of modulation is an oligonucleotide’s ability to inhibit, down-
regulate, reduce, suppress, remove, stop, block, prevent, lessen, lower, avoid or terminate
expression of HTRA1, e.g. by degradation of mRNA or blockage of transcription. The antisense
oligonucleotide of the invention are capable of inhibiting, down-regulating, reduce, suppress,
remove, stop, block, prevent, lessen, lower, avoid or terminate expression of HTRA1.
High affinity modified nucleosides
A high affinity modified nucleoside is a modified nucleotide which, when incorporated into the
oligonucleotide enhances the affinity of the oligonucleotide for its complementary target, for
example as measured by the melting temperature (T ). A high affinity modified nucleoside of
the present invention preferably result in an increase in melting temperature between +0.5 to
o o o
+12 C, more preferably between +1.5 to +10 C and most preferably between+3 to +8 C per
modified nucleoside. Numerous high affinity modified nucleosides are known in the art and
include for example, many 2’ substituted nucleosides as well as locked nucleic acids (LNA) (see
e.g. Freier & Altmann; Nucl. Acid Res., 1997, 25, 4429-4443 and Uhlmann; Curr. Opinion in
Drug Development, 2000, 3(2), 293-213).
Sugar modifications
The oligomer of the invention may comprise one or more nucleosides which have a modified
sugar moiety, i.e. a modification of the sugar moiety when compared to the ribose sugar moiety
found in DNA and RNA.
Numerous nucleosides with modification of the ribose sugar moiety have been made, primarily
with the aim of improving certain properties of oligonucleotides, such as affinity and/or nuclease
resistance.
Such modifications include those where the ribose ring structure is modified, e.g. by
replacement with a hexose ring (HNA), or a bicyclic ring, which typically have a biradicle bridge
between the C2 and C4 carbons on the ribose ring (LNA), or an unlinked ribose ring which
typically lacks a bond between the C2 and C3 carbons (e.g. UNA). Other sugar modified
nucleosides include, for example, bicyclohexose nucleic acids (WO2011/017521) or tricyclic
nucleic acids (WO2013/154798). Modified nucleosides also include nucleosides where the
sugar moiety is replaced with a non-sugar moiety, for example in the case of peptide nucleic
acids (PNA), or morpholino nucleic acids.
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Sugar modifications also include modifications made via altering the substituent groups on the
ribose ring to groups other than hydrogen, or the 2’-OH group naturally found in DNA and RNA
nucleosides. Substituents may, for example be introduced at the 2’, 3’, 4’ or 5’ positions.
Nucleosides with modified sugar moieties also include 2’ modified nucleosides, such as 2’
substituted nucleosides. Indeed, much focus has been spent on developing 2’ substituted
nucleosides, and numerous 2’ substituted nucleosides have been found to have beneficial
properties when incorporated into oligonucleotides, such as enhanced nucleoside resistance
and enhanced affinity.
2’ modified nucleosides.
A 2’ sugar modified nucleoside is a nucleoside which has a substituent other than H or –OH at
the 2’ position (2’ substituted nucleoside) or comprises a 2’ linked biradicle, and includes 2’
substituted nucleosides and LNA (2’ – 4’ biradicle bridged) nucleosides. For example, the 2’
modified sugar may provide enhanced binding affinity and/or increased nuclease resistance to
the oligonucleotide. Examples of 2’ substituted modified nucleosides are 2’-O-alkyl-RNA, 2’-O-
methyl-RNA, 2’-alkoxy-RNA, 2’-O-methoxyethyl-RNA (MOE), 2’-amino-DNA, 2’-Fluoro-RNA,
and 2’-F-ANA nucleoside. For further examples, please see e.g. Freier & Altmann; Nucl. Acid
Res., 1997, 25, 4429-4443 and Uhlmann; Curr. Opinion in Drug Development, 2000, 3(2), 293-
213, and Deleavey and Damha, Chemistry and Biology 2012, 19, 937. Below are illustrations of
some 2’ substituted modified nucleosides.
Locked Nucleic Acid Nucleosides (LNA).
LNA nucleosides are modified nucleosides which comprise a linker group (referred to as a
biradicle or a bridge) between C2’ and C4’ of the ribose sugar ring of a nucleotide. These
nucleosides are also termed bridged nucleic acid or bicyclic nucleic acid (BNA) in the literature.
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In some embodiments, the modified nucleoside or the LNA nucleosides of the oligomer of the
invention has a general structure of the formula I or II:
beta-D alpha-L
Formula I Formula II
a a b
wherein W is selected from -O-, -S-, -N(R )-, -C(R R )-, such as, in some embodiments –O-;
B designates a nucleobase moiety;
Z designates an internucleoside linkage to an adjacent nucleoside, or a 5'-terminal group;
Z* designates an internucleoside linkage to an adjacent nucleoside, or a 3'-terminal group;
a b a b
X designates a group selected from the list consisting of -C(R R )-, -C(R )=C(R )-, -
a a a
C(R )=N-, -O-, -Si(R ) -, -S-, -SO -, -N(R )-, and >C=Z
In some embodiments, X is selected from the group consisting of: –O-, -S-, NH-, NR R , -CH -,
a b a b
CR R , -C(=CH )-, and -C(=CR R )-
In some embodiments, X is -O-
a b a b
Y designates a group selected from the group consisting of -C(R R )-, -C(R )=C(R )-, -
a a a
C(R )=N-, -O-, -Si(R ) -, -S-, -SO -, -N(R )-, and >C=Z
In some embodiments, Y is selected from the group consisting of: –CH -, -C(R R )-, –CH CH -,
2 2 2
a b a b a b a b a b a b a
-C(R R )-C(R R )-, –CH CH CH -, -C(R R )C(R R )C(R R )-, -C(R )=C(R )-, and -C(R )=N-
2 2 2
In some embodiments, Y is selected from the group consisting of: -CH2-, -CHR -, -CHCH3-,
CR R -
or -X-Y- together designate a bivalent linker group (also referred to as a radicle) together
designate a bivalent linker group consisting of 1, 2, or 3 groups/atoms selected from the group
a b a b a a a
consisting of -C(R R )-, -C(R )=C(R )-, -C(R )=N-, -O-, -Si(R )2-, -S-, -SO2-, -N(R )-, and >C=Z,
In some embodiments, -X-Y- designates a biradicle selected from the groups consisting of: -X-
a b a- -
CH -, -X-CR R -, -X-CHR , -X-C(HCH ) , -O-Y-, -O-CH -, -S-CH -, -NH-CH -, -O-CHCH -, -CH -
2 3 2 2 2 3 2
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O-CH , -O-CH(CH CH )-, -O-CH -CH -, OCH -CH -CH -,-O-CH OCH -, -O-NCH -, -C(=CH )-
2 3 3 2 2 2 2 2 2 2 2 2
a a b a
CH -, -NR -CH -, N-O-CH , -S-CR R - and -S-CHR -.
2 2 2
In some embodiments –X-Y- designates –O-CH - or –O-CH(CH )-.
wherein Z is selected from -O-, -S-, and -N(R )-,
and R and, when present R , each is independently selected from hydrogen, optionally
substituted C -alkyl, optionally substituted C -alkenyl, optionally substituted C -alkynyl,
1-6 2-6 2-6
hydroxy, optionally substituted C -alkoxy, C -alkoxyalkyl, C -alkenyloxy, carboxy, C -
1-6 2-6 2-6 1-6
alkoxycarbonyl, C -alkylcarbonyl, formyl, aryl, aryloxy-carbonyl, aryloxy, arylcarbonyl,
heteroaryl, heteroaryloxy-carbonyl, heteroaryloxy, heteroarylcarbonyl, amino, mono- and di(C1
alkyl)amino, carbamoyl, mono- and di(C -alkyl)-amino-carbonyl, amino-C -alkyl-
1-6 1-6
aminocarbonyl, mono- and di(C -alkyl)amino-C -alkyl-aminocarbonyl, C -alkyl-
1-6 1-6 1-6
carbonylamino, carbamido, C -alkanoyloxy, sulphono, C -alkylsulphonyloxy, nitro, azido,
1-6 1-6
sulphanyl, C -alkylthio, halogen, where aryl and heteroaryl may be optionally substituted and
where two geminal substituents R and R together may designate optionally substituted
methylene (=CH ), wherein for all chiral centers, asymmetric groups may be found in either R or
S orientation.
1 2 3 5 5*
wherein R , R , R , R and R are independently selected from the group consisting of:
hydrogen, optionally substituted C -alkyl, optionally substituted C -alkenyl, optionally
1-6 2-6
substituted C2alkynyl, hydroxy, C1alkoxy, C2alkoxyalkyl, C2alkenyloxy, carboxy, C1
alkoxycarbonyl, C -alkylcarbonyl, formyl, aryl, aryloxy-carbonyl, aryloxy, arylcarbonyl,
heteroaryl, heteroaryloxy-carbonyl, heteroaryloxy, heteroarylcarbonyl, amino, mono- and di(C -
alkyl)amino, carbamoyl, mono- and di(C -alkyl)-amino-carbonyl, amino-C -alkyl-
1-6 1-6
aminocarbonyl, mono- and di(C -alkyl)amino-C -alkyl-aminocarbonyl, C -alkyl-
1-6 1-6 1-6
carbonylamino, carbamido, C -alkanoyloxy, sulphono, C -alkylsulphonyloxy, nitro, azido,
1-6 1-6
sulphanyl, C1alkylthio, halogen, where aryl and heteroaryl may be optionally substituted, and
where two geminal substituents together may designate oxo, thioxo, imino, or optionally
substituted methylene.
1 2 3 5 5*
In some embodiments R , R , R , R and R are independently selected from C alkyl, such as
methyl, and hydrogen.
1 2 3 5 5*
In some embodiments R , R , R , R and R are all hydrogen.
1 2 3 5 5*
In some embodiments R , R , R , are all hydrogen, and either R and R is also hydrogen and
5*
the other of R and R is other than hydrogen, such as C alkyl such as methyl.
In some embodiments, R is either hydrogen or methyl. In some embodiments, when present,
R is either hydrogen or methyl.
In some embodiments, one or both of R and R is hydrogen
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In some embodiments, one of R and R is hydrogen and the other is other than hydrogen
In some embodiments, one of R and R is methyl and the other is hydrogen
In some embodiments, both of R and R are methyl.
1 2 3 5 5*
In some embodiments, the biradicle –X-Y- is –O-CH -, W is O, and all of R , R , R , R and R
are all hydrogen. Such LNA nucleosides are disclosed in WO99/014226, WO00/66604,
WO98/039352 and WO2004/046160 which are all hereby incorporated by reference, and
include what are commonly known as beta-D-oxy LNA and alpha-L-oxy LNA nucleosides.
1 2 3 5 5*
In some embodiments, the biradicle –X-Y- is –S-CH -, W is O, and all of R , R , R , R and R
are all hydrogen. Such thio LNA nucleosides are disclosed in WO99/014226 and
WO2004/046160 which are hereby incorporated by reference.
1 2 3 5 5*
In some embodiments, the biradicle –X-Y- is –NH-CH -, W is O, and all of R , R , R , R and R
are all hydrogen. Such amino LNA nucleosides are disclosed in WO99/014226 and
WO2004/046160 which are hereby incorporated by reference.
In some embodiments, the biradicle –X-Y- is –O-CH -CH - or –O-CH -CH - CH -, W is O, and
2 2 2 2 2
1 2 3 5 5*
all of R , R , R , R and R are all hydrogen. Such LNA nucleosides are disclosed in
WO00/047599 and Morita et al, Bioorganic & Med.Chem. Lett. 12 73-76, which are hereby
incorporated by reference, and include what are commonly known as 2’-O-4’C-ethylene bridged
nucleic acids (ENA).
1 2 3
In some embodiments, the biradicle –X-Y- is –O-CH2-, W is O, and all of R , R , R , and one of
5* 5 5*
R and R are hydrogen, and the other of R and R is other than hydrogen such as C alkyl,
such as methyl. Such 5’ substituted LNA nucleosides are disclosed in WO2007/134181 which is
hereby incorporated by reference.
a b a b
In some embodiments, the biradicle –X-Y- is –O-CR R -, wherein one or both of R and R are
1 2 3 5 5*
other than hydrogen, such as methyl, W is O, and all of R , R , R , and one of R and R are
5*
hydrogen, and the other of R and R is other than hydrogen such as C alkyl, such as methyl.
Such bis modified LNA nucleosides are disclosed in WO2010/077578 which is hereby
incorporated by reference.
In some embodiments, the biradicle –X-Y- designate the bivalent linker group –O-
CH(CH OCH )- (2’ O-methoxyethyl bicyclic nucleic acid - Seth at al., 2010, J. Org. Chem. Vol
75(5) pp. 1569-81). In some embodiments, the biradicle –X-Y- designate the bivalent linker
group –O-CH(CH CH )- (2’O-ethyl bicyclic nucleic acid - Seth at al., 2010, J. Org. Chem. Vol
75(5) pp. 1569-81). In some embodiments, the biradicle –X-Y- is –O-CHR -, W is O, and all of
1 2 3 5 5*
R , R , R , R and R are all hydrogen. Such 6’ substituted LNA nucleosides are disclosed in
WO10036698 and WO07090071 which are both hereby incorporated by reference.
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1 2 3
In some embodiments, the biradicle –X-Y- is –O-CH(CH OCH )-, W is O, and all of R , R , R ,
5*
R and R are all hydrogen. Such LNA nucleosides are also known as cyclic MOEs in the art
(cMOE) and are disclosed in WO07090071.
In some embodiments, the biradicle –X-Y- designate the bivalent linker group –O-CH(CH )-. – in
either the R- or S- configuration. In some embodiments, the biradicle –X-Y- together designate
the bivalent linker group –O-CH -O-CH - (Seth at al., 2010, J. Org. Chem). In some
1 2 3 5 5*
embodiments, the biradicle –X-Y- is –O-CH(CH )-, W is O, and all of R , R , R , R and R are
all hydrogen. Such 6’ methyl LNA nucleosides are also known as cET nucleosides in the art,
and may be either (S)cET or (R)cET stereoisomers, as disclosed in WO07090071 (beta-D) and
WO2010/036698 (alpha-L) which are both hereby incorporated by reference).
a b a b
In some embodiments, the biradicle –X-Y- is –O-CR R -, wherein in neither R or R is
1 2 3 5 5* a
hydrogen, W is O, and all of R , R , R , R and R are all hydrogen. In some embodiments, R
and R are both methyl. Such 6’ di-substituted LNA nucleosides are disclosed in WO
2009006478 which is hereby incorporated by reference.
a 1 2 3 5 5*
In some embodiments, the biradicle –X-Y- is –S-CHR -, W is O, and all of R , R , R , R and R
are all hydrogen. Such 6’ substituted thio LNA nucleosides are disclosed in WO11156202
which is hereby incorporated by reference. In some 6’ substituted thio LNA embodiments R is
methyl.
In some embodiments, the biradicle –X-Y- is –C(=CH2)-C(R R )-, such as –C(=CH2)-CH2- , or –
1 2 3 5 5*
C(=CH )-CH(CH )-W is O, and all of R , R , R , R and R are all hydrogen. Such vinyl carbo
LNA nucleosides are disclosed in WO08154401 and WO09067647 which are both hereby
incorporated by reference.
a 1 2 3 5 5*
In some embodiments the biradicle –X-Y- is –N(-OR )-, W is O, and all of R , R , R , R and R
are all hydrogen. In some embodiments R is C alkyl such as methyl. Such LNA nucleosides
are also known as N substituted LNAs and are disclosed in WO2008/150729 which is hereby
incorporated by reference. In some embodiments, the biradicle –X-Y- together designate the
bivalent linker group –O-NR -CH - (Seth at al., 2010, J. Org. Chem). In some embodiments the
a 1 2 3 5 5*
biradicle –X-Y- is –N(R )-, W is O, and all of R , R , R , R and R are all hydrogen. In some
embodiments R is C alkyl such as methyl.
5*
In some embodiments, one or both of R and R is hydrogen and, when substituted the other of
5* 1 2 3
R and R is C alkyl such as methyl. In such an embodiment, R , R , R , may all be
hydrogen, and the biradicle –X-Y- may be selected from –O-CH2- or –O-C(HCR )-, such as –O-
C(HCH3)-.
a b a b
In some embodiments, the biradicle is –CR R -O-CR R -, such as CH -O-CH -, W is O and all
1 2 3 5 5* a
of R , R , R , R and R are all hydrogen. In some embodiments R is C alkyl such as methyl.
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Such LNA nucleosides are also known as conformationally restricted nucleotides (CRNs) and
are disclosed in WO2013036868 which is hereby incorporated by reference.
a b a b
In some embodiments, the biradicle is –O-CR R -O-CR R -, such as O-CH -O-CH -, W is O
1 2 3 5 5* a
and all of R , R , R , R and R are all hydrogen. In some embodiments R is C alkyl such as
methyl. Such LNA nucleosides are also known as COC nucleotides and are disclosed in
Mitsuoka et al., Nucleic Acids Research 2009 37(4), 1225-1238, which is hereby incorporated
by reference.
It will be recognized than, unless specified, the LNA nucleosides may be in the beta-D or alpha-
L stereoisoform.
Examples of LNA nucleosides are presented in Scheme 1.
Scheme 1
As illustrated in the examples, in some embodiments of the invention the LNA nucleosides in
the oligonucleotides are beta-D-oxy-LNA nucleosides.
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Nuclease mediated degradation
Nuclease mediated degradation refers to an oligonucleotide capable of mediating degradation
of a complementary nucleotide sequence when forming a duplex with such a sequence.
In some embodiments, the oligonucleotide may function via nuclease mediated degradation of
the target nucleic acid, where the oligonucleotides of the invention are capable of recruiting a
nuclease, particularly and endonuclease, preferably endoribonuclease (RNase), such as RNase
H. Examples of oligonucleotide designs which operate via nuclease mediated mechanisms are
oligonucleotides which typically comprise a region of at least 5 or 6 DNA nucleosides and are
flanked on one side or both sides by affinity enhancing nucleosides, for example gapmers,
headmers and tailmers.
RNase H Activity and Recruitment
The RNase H activity of an antisense oligonucleotide refers to its ability to recruit RNase H
when in a duplex with a complementary RNA molecule. WO01/23613 provides in vitro methods
for determining RNaseH activity, which may be used to determine the ability to recruit RNaseH.
Typically an oligonucleotide is deemed capable of recruiting RNase H if it, when provided with a
complementary target nucleic acid sequence, has an initial rate, as measured in pmol/l/min, of
at least 5%, such as at least 10% or more than 20% of the of the initial rate determined when
using a oligonucleotide having the same base sequence as the modified oligonucleotide being
tested, but containing only DNA monomers, with phosphorothioate linkages between all
monomers in the oligonucleotide, and using the methodology provided by Example 91 - 95 of
WO01/23613 (hereby incorporated by reference).
Gapmer
The term gapmer as used herein refers to an antisense oligonucleotide which comprises a
region of RNase H recruiting oligonucleotides (gap) which is flanked 5’ and 3’ by regions which
comprise one or more affinity enhancing modified nucleosides (flanks or wings). Various
gapmer designs are described herein. Headmers and tailmers are oligonucleotides capable of
recruiting RNase H where one of the flanks is missing, i.e. only one of the ends of the
oligonucleotide comprises affinity enhancing modified nucleosides. For headmers the 3’ flank is
missing (i.e. the 5’ flank comprises affinity enhancing modified nucleosides) and for tailmers the
5’ flank is missing (i.e. the 3’ flank comprises affinity enhancing modified nucleosides).
LNA Gapmer
The term LNA gapmer is a gapmer oligonucleotide wherein at least one of the affinity enhancing
modified nucleosides is an LNA nucleoside.
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Mixed Wing Gapmer
The term mixed wing gapmer refers to a LNA gapmer wherein the flank regions comprise at
least one LNA nucleoside and at least one non-LNA modified nucleoside, such as at least one
DNA nucleoside or at least one 2’ substituted modified nucleoside, such as, for example, 2’-O-
alkyl-RNA, 2’-O-methyl-RNA, 2’-alkoxy-RNA, 2’-O-methoxyethyl-RNA (MOE), 2’-amino-DNA, 2’-
Fluoro-RNA and 2’-F-ANA nucleoside(s). In some embodiments the mixed wing gapmer has
one flank which comprises LNA nucleosides (e.g. 5’ or 3’) and the other flank (3’ or 5’
respectfully) comprises 2’ substituted modified nucleoside(s).
Conjugate
The term conjugate as used herein refers to an oligonucleotide which is covalently linked to a
non-nucleotide moiety (conjugate moiety or region C or third region).
The term conjugate as used herein refers to an oligonucleotide which is covalently linked to a
non-nucleotide moiety (conjugate moiety or region C or third region).
In some embodiments, the non-nucleotide moiety selected from the group consisting of a
protein, such as an enzyme, an antibody or an antibody fragment or a peptide; a lipophilic
moiety such as a lipid, a phospholipid, a sterol; a polymer, such as polyethyleneglycol or
polypropylene glycol; a receptor ligand; a small molecule; a reporter molecule; and a non-
nucleosidic carbohydrate.
Linkers
A linkage or linker is a connection between two atoms that links one chemical group or segment
of interest to another chemical group or segment of interest via one or more covalent bonds.
Conjugate moieties can be attached to the oligonucleotide directly or through a linking moiety
(e.g. linker or tether). Linkers serve to covalently connect a third region, e.g. a conjugate moiety
to an oligonucleotide (e.g. the termini of region A or C).
In some embodiments of the invention the conjugate or oligonucleotide conjugate of the
invention may optionally, comprise a linker region which is positioned between the
oligonucleotide and the conjugate moiety. In some embodiments, the linker between the
conjugate and oligonucleotide is biocleavable.
Biocleavable linkers comprising or consisting of a physiologically labile bond that is cleavable
under conditions normally encountered or analogous to those encountered within a mammalian
body. Conditions under which physiologically labile linkers undergo chemical transformation
(e.g., cleavage) include chemical conditions such as pH, temperature, oxidative or reductive
conditions or agents, and salt concentration found in or analogous to those encountered in
mammalian cells. Mammalian intracellular conditions also include the presence of enzymatic
activity normally present in a mammalian cell such as from proteolytic enzymes or hydrolytic
enzymes or nucleases. In one embodiment the biocleavable linker is susceptible to S1 nuclease
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cleavage. In a preferred embodiment the nuclease susceptible linker comprises between 1 and
nucleosides, such as 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleosides, more preferably between 2
and 6 nucleosides and most preferably between 2 and 4 linked nucleosides comprising at least
two consecutive phosphodiester linkages, such as at least 3 or 4 or 5 consecutive
phosphodiester linkages. Preferably the nucleosides are DNA or RNA. Phosphodiester
containing biocleavable linkers are described in more detail in (hereby
incorporated by reference), and may be refered to as region D herein.
Conjugates may also be linked to the oligonucleotide via non biocleavable linkers, or in some
embodiments the conjugate may comprise a non-cleavable linker which is covalently attached
to the biocleavable linker. Linkers that are not necessarily biocleavable but primarily serve to
covalently connect a conjugate moiety to an oligonucleotide or biocleavable linker. Such
linkers may comprise a chain structure or an oligomer of repeating units such as ethylene
glycol, amino acid units or amino alkyl groups. In some embodiments the linker (region Y) is an
amino alkyl, such as a C – C amino alkyl group, including, for example C to C amino alkyl
2 36 6 12
groups. In some embodiments the linker (region Y) is a C6 amino alkyl group. Conjugate linker
groups may be routinely attached to an oligonucleotide via use of an amino modified
oligonucleotide, and an activated ester group on the conjugate group.
Treatment
The term ’treatment’ as used herein refers to both treatment of an existing disease (e.g. a
disease or disorder as herein referred to), or prevention of a disease, i.e. prophylaxis. It will
therefore be recognized that treatment as referred to herein may, in some embodiments, be
prophylactic.
DETAILED DESCRIPTION OF THE INVENTION
The Oligonucleotides of the Invention
The invention relates to oligonucleotides capable of inhibiting the expression of HTRA1. The
modulation is may achieved by hybridizing to a target nucleic acid encoding HTRA1 or which is
involved in the regulation of HTRA1. The target nucleic acid may be a mammalian HTRA 1
sequence, such as a sequence selected from the group consisting of SEQ ID 1, 2, 3 or 4.
The oligonucleotide of the invention is an antisense oligonucleotide which targets HTRA1, such
as a mammalian HTRA1.
In some embodiments the antisense oligonucleotide of the invention is capable of modulating
the expression of the target by inhibiting or down-regulating it. Preferably, such modulation
produces an inhibition of expression of at least 20% compared to the normal expression level of
the target, such as at least 30%, 40%, 50%, 60%, 70%, 80%, or 90% inhibition compared to the
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normal expression level of the target. In some embodiments compounds of the invention may
be capable of inhibiting expression levels of HTRA1 mRNA by at least 60% or 70% in vitro
using ARPE-19 cells. In some embodiments compounds of the invention may be capable of
inhibiting expression levels of HTRA1 mRNA by at least 60% or 70% in vitro using ARPE-19
cells. In some embodiments compounds of the invention may be capable of inhibiting
expression levels of HTRA1 protein by at least 50% in vitro using ARPE-19 cells. Suitably, the
examples provide assays which may be used to measure HTRA1 RNA or protein inhibition (e.g.
example 3). The target modulation is triggered by the hybridization between a contiguous
nucleotide sequence of the oligonucleotide and the target nucleic acid. In some embodiments
the oligonucleotide of the invention comprises mismatches between the oligonucleotide and the
target nucleic acid. Despite mismatches hybridization to the target nucleic acid may still be
sufficient to show a desired modulation of HTRA1 expression. Reduced binding affinity resulting
from mismatches may advantageously be compensated by increased number of nucleotides in
the oligonucleotide and/or an increased number of modified nucleosides capable of increasing
the binding affinity to the target, such as 2’ modified nucleosides, including LNA, present within
the oligonucleotide sequence.
An aspect of the present invention relates to an antisense oligonucleotide which comprises a
contiguous nucleotide region of 10 to 30 nucleotides in length with at least 90%
complementarity to HTRA1 target sequence, such as fully complementary to an HTRA1 target
sequence, e.g. a nucleic acid selected from the group consisting SEQ ID NO 1, 2, 3 & 4.
In some embodiments, the oligonucleotide comprises a contiguous sequence which is at least
90% complementary, such as at least 91%, such as at least 92%, such as at least 93%, such as
at least 94%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least
98%, or 100% complementary with a region of the target nucleic acid.
In some embodiments, the oligonucleotide of the invention, or a contiguous nucleotide
sequence thereof is fully complementary (100% complementary) to a region of the target
nucleic acid, or in some embodiments may comprise one or two mismatches between the
oligonucleotide and the target nucleic acid.
In some embodiments the oligonucleotide, or a contiguous nucleotide sequence of at least 12
nucleotides thereof, is at least 90% complementary, such as fully (or 100%) complementary to a
region of SEQ ID NO 147.
In some embodiments the oligonucleotide, or a contiguous nucleotide sequence of at least 12
nucleotides thereof, is at least 90% complementary, such as fully (or 100%) complementary to a
region of a sequence selected from the group consisting of SEQ ID NOs 148, 149, 150, 151,
152, 153, 154 and 155.
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In some embodiments the oligonucleotide, or a contiguous nucleotide sequence of at least 14
nucleotides thereof, is fully (or 100%) complementary to SEQ ID 147, or a sequence selected
from the group consisting of SEQ ID NOs 148, 149, 150, 151, 152, 153, 154 and 155.
In some embodiments the oligonucleotide, or a contiguous nucleotide sequence of at least 16
nucleotides thereof, is fully (or 100%) complementary to SEQ ID 147, or a sequence selected
from the group consisting of SEQ ID NOs 148, 149, 150, 151, 152, 153, 154 and 155.
In some embodiments the oligonucleotide, or contiguous nucleotide region thereof is fully (or
100%) complementary to a sequence selected from the group consisting of SEQ ID NOs 148,
149, 150, 151, 152, 153, 154 and 155.
In some embodiments, the oligonucleotide or contiguous nucleotide region thereof comprises or
consists of a sequence selected from the group consisting of SEQ ID NOs 143, 138, 139, 140,
141, 142, 144 and 145:
SEQ ID NO 143: TATTTACCTGGTTGTT
SEQ ID NO 138: CAAATATTTACCTGGTTG
SEQ ID NO 139: TTTACCTGGTTGTTGG
SEQ ID NO 140: CCAAATATTTACCTGGTT
SEQ ID NO 141: CCAAATATTTACCTGGTTGT
SEQ ID NO 142: ATATTTACCTGGTTGTTG
SEQ ID NO 144: ATATTTACCTGGTTGT
SEQ ID NO 145: ATATTTACCTGGTTGTT
It is understood that the oligonucleotide motif sequences can be modified to for example
increase nuclease resistance and/or binding affinity to the target nucleic acid. Modifications are
described in the definitions and in the “Oligonucleotide design” section.
In some embodiments, the oligonucleotide of the invention, or contiguous nucleotide region
thereof is fully complementary (100% complementary) to a region of the target nucleic acid, or
in some embodiments may comprise one or two mismatches between the oligonucleotide and
the target nucleic acid. In some embodiments the oligonucleotide, or contiguous nucleotide
sequence of at least 12 nucleotides thereof, is at least 90% complementary, such as fully (or
100%) complementary to the target nucleic acid sequence.
In some embodiments the oligonucleotide, or a contiguous nucleotide sequence of at least 12
nucleotides thereof, has 100% identity to a sequence selected from the group consisting of SEQ
ID NOs 5 – 107, or SEQ ID NOs 108 – 137.
In some embodiments the oligonucleotide, or a contiguous nucleotide sequence of at least 14
nucleotides thereof, has 100% identity to a sequence selected from the group consisting of SEQ
ID NOs 5 – 107, or SEQ ID NOs 108 – 137.
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In some embodiments the oligonucleotide, or contiguous nucleotide sequence of at least 16
nucleotides thereof, has 100% identity to a sequence selected from the group consisting of SEQ
ID NOs 5 – 107, or SEQ ID NOs 108 – 137.
In some embodiments the oligonucleotide, or contiguous nucleotide region thereof, comprises
or consists of a sequence selected from SEQ ID NOs 5 – 107, or SEQ ID NOs 108 – 137.
In some embodiments the compound of the invention is selected from the group consisting of:
ID Compound
NO ID #
138 138,1 C A A A t a t t t a c c t g G T T G
s s s s s s s s s s s s s s s s s
139 139,1 TsTstsascscstsgsgststsgstsTsGsG
140 140,1 C C A A a t a t t t a c c t g G T T
s s s s s s s s s s s s s s s s s
141 141,1 C C A a a t a t t t a c c t g g t t G T
s s s s s s s s s s s s s s s s s s s
142 142,1 A T A t t t a c c t g g t t g T T G
s s s s s s s s s s s s s s s s s
143 143,1 T A T t t a c c t g g t T G T T
s s s s s s s s s s s s s s s
143 143,2 T A t t t a c c t g G t T g T T
s s s s s s s s s s s s s s s
143 143,3 T A T t t a c c t g g T T g T T
s s s s s s s s s s s s s s s
144 144,1 A T A T t t a c c t g g T T G T
s s s s s s s s s s s s s s s
144 144,2 A t A T T t a c c t g g t T G T
s s s s s s s s s s s s s s s
145 145,1 A t A T t t a c c t g G T T g T T
s s s s s s s s s s s s s s s s
145 145,2 A T A t t t a c c t g G t T g T T
s s s s s s s s s s s s s s s s
145 145,3 A t A T t t a c c t g g t T G T T
s s s s s s s s s s s s s s s s
Wherein capital letters represent beta-D-oxy LNA nucleosides, all LNA cytosines are 5-methyl
cytosine (as indicated by the superscript ), lower case letters represent DNA nucleosides. All
internucleoside linkages are phosphorothioate internucleoside linkages (as indicated by the
subscript ).
Oligonucleotide design
Oligonucleotide design refers to the pattern of nucleoside sugar modifications in the
oligonucleotide sequence. The oligonucleotides of the invention comprise sugar-modified
nucleosides and may also comprise DNA or RNA nucleosides. In some embodiments, the
oligonucleotide comprises sugar-modified nucleosides and DNA nucleosides. Incorporation of
modified nucleosides into the oligonucleotide of the invention may enhance the affinity of the
oligonucleotide for the target nucleic acid. In that case, the modified nucleosides can be referred
to as affinity enhancing modified nucleotides.
In an embodiment, the oligonucleotide comprises at least 1 modified nucleoside, such as at
least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at
least 11, at least 12, at least 13, at least 14, at least 15 or at least 16 modified nucleosides. In
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an embodiment the oligonucleotide comprises from 1 to 10 modified nucleosides, such as from
2 to 9 modified nucleosides, such as from 3 to 8 modified nucleosides, such as from 4 to 7
modified nucleosides, such as 6 or 7 modified nucleosides. In an embodiment, the
oligonucleotide of the invention may comprise modifications, which are independently selected
from these three types of modifications (modified sugar, modified nucleobase and modified
internucleoside linkage) or a combination thereof. Preferably the oligonucleotide comprises one
or more sugar modified nucleosides, such as 2’ sugar modified nucleosides. Preferably the
oligonucleotide of the invention comprise the one or more 2’ sugar modified nucleoside
independently selected from the group consisting of 2’-O-alkyl-RNA, 2’-O-methyl-RNA, 2’-
alkoxy-RNA, 2’-O-methoxyethyl-RNA, 2’-amino-DNA, 2’-fluoro-DNA, arabino nucleic acid (ANA),
2’-fluoro-ANA and LNA nucleosides. Even more preferably the the one or more modified
nucleoside is LNA.
In some embodiments, at least 1 of the modified nucleosides is a locked nucleic acid (LNA),
such as at least 2, such as at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 of
the modified nucleosides are LNA. In a still further embodiment all the modified nucleosides are
LNA.
In a further embodiment the oligonucleotide comprises at least one modified internucleoside
linkage. In a preferred embodiment the the internucleoside linkages within the contiguous
nucleotide sequence are phosphorothioate or boranophosphate internucleoside linkages. In
some embodiments all the internucleotide linkages in the contiguous sequence of the
oligonucleotide are phosphorothioate linkages.
In some embodiments, the oligonucleotide of the invention comprise at least one modified
nucleoside which is a 2’-MOE-RNA, such as 2, 3, 4, 5, 6, 7, 8, 9 or 10 2’-MOE-RNA nucleoside
units. In some embodiments, at least one of said modified nucleoside is 2’-fluoro DNA, such as
2, 3, 4, 5, 6, 7, 8, 9 or 10 2’-fluoro-DNA nucleoside units.
In some embodiments, the oligonucleotide of the invention comprises at least one LNA unit,
such as 1, 2, 3, 4, 5, 6, 7, or 8 LNA units, such as from 2 to 6 LNA units, such as from 3 to 7
LNA units, 4 to 8 LNA units or 3, 4, 5, 6 or 7 LNA units. In some embodiments, all the modified
nucleosides are LNA nucleosides. In some embodiments, all LNA cytosine units are 5-methyl-
cytosine. In some embodiments the oligonucleotide or contiguous nucleotide region thereof
has at least 1 LNA unit at the 5’ end and at least 2 LNA units at the 3’ end of the nucleotide
sequence. In some embodiments all cytosine nucleobases present in the oligonucleotide of the
invention are 5-methyl-cytosine.
In some embodiments, the oligonucleotide of the invention comprises at least one LNA unit and
at least one 2’ substituted modified nucleoside.
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In some embodiments of the invention, the oligonucleotide comprise both 2’ sugar modified
nucleosides and DNA units.
In an embodiment of the invention the oligonucleotide of the invention is capable of recruiting
RNase H.
In some embodiments, the oligonucleotide of the invention or contiguous nucleotide region
thereof is a gapmers oligonucleotide.
Gapmer design
In some embodiments the oligonucleotide of the invention, or contiguous nucleotide region
thereof, has a gapmer design or structure also referred herein merely as “Gapmer”. In a gapmer
structure the oligonucleotide comprises at least three distinct structural regions a 5’-flank, a gap
and a 3’-flank, F-G-F’ in ‘5 -> 3’ orientation. In this design, flanking regions F and F’ (also
termed wing regions) comprise at least one sugar modified nucleoside which is adjacent to
region G, and may in some embodiments comprise a contiguous stretch of 2 – 7 sugar modified
nucleoside, or a contiguous stretch of sugar modified and DNA nucleosides (mixed wings
comprising both sugar modified and DNA nucleosides). Consequently, the nucleosides of the 5’
flanking region and the 3’ flanking region which are adjacent to the gap region are sugar
modified nucleosides, such as 2’ modified nucleosides. The gap region, G, comprises a
contiguous stretch of nucleotides which are capable of recruiting RNase H, when the
oligonucleotide is in duplex with the HTRA1target nucleic acid. In some embodiments, region G
comprises a contiguous stretch of 5 – 16 DNA nucleosides. The gapmer region F-G-F’ is
complementary to the HTRA1 target nucleic acid, and may therefore be the contiguous
nucleotide region of the oligonucleotide.
Regions F and F’, flanking the 5’ and 3’ ends of region G, may comprise one or more affinity
enhancing modified nucleosides. In some embodiments, the 3’ flank comprises at least one
LNA nucleoside, preferably at least 2 LNA nucleosides. In some embodiments, the 5’ flank
comprises at least one LNA nucleoside. In some embodiments both the 5’ and 3’ flanking
regions comprise a LNA nucleoside. In some embodiments all the nucleosides in the flanking
regions are LNA nucleosides. In other embodiments, the flanking regions may comprise both
LNA nucleosides and other nucleosides (mixed flanks), such as DNA nucleosides and/or non-
LNA modified nucleosides, such as 2’ substituted nucleosides. In this case the gap is defined as
a contiguous sequence of at least 5 RNase H recruiting nucleosides (such as 5 – 16 DNA
nucleosides) flanked at the 5’ and 3’ end by an affinity enhancing modified nucleoside, such as
an LNA, such as beta-D-oxy-LNA.
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Region F
Region F (5’ flank or 5’ wing) attached to the ‘5 end of region G comprises, contains or consists
of at least one sugar modified nucleoside such as at least 2, at least 3, at least 4, at least 5, at
least 6, at least 7 modified nucleosides. In some embodiments region F comprises or consists
of from 1 to 7 modified nucleosides, such as from 2 to 6 modified nucleosides, such as from 2 to
modified nucleosides, such as from 2 to 4 modified nucleosides, such as from 1 to 3 modified
nucleosides, such as 1, 2, 3 or 4 modified nucleosides.
In an embodiment, one or more or all of the modified nucleosides in region F are 2’ modified
nucleosides.
In a further embodiment one or more of the 2’ modified nucleosides in region F are selected
from 2’-O-alkyl-RNA units, 2’-O-methyl-RNA, 2’-amino-DNA units, 2’-fluoro-DNA units, 2’-
alkoxy-RNA, MOE units, LNA units, arabino nucleic acid (ANA) units and 2’-fluoro-ANA units.
In one embodiment of the invention all the modified nucleosides in region F are LNA
nucleosides. In a further embodiment the LNA nucleosides in region F are independently
selected from the group consisting of oxy-LNA, thio-LNA, amino-LNA, cET, and/or ENA, in
either the beta-D or alpha-L configurations or combinations thereof. In a preferred embodiment
region F has at least 1 beta-D-oxy LNA unit, at the 5’ end of the contiguous sequence.
Region G
Region G (gap region) may comprise, contain or consist of at 5 - 16 consecutive DNA
nucleosides capable of recruiting RNaseH. In a further embodiment region G comprise, contain
or consist of from 5 to 12, or from 6 to 10 or from 7 to 9, such as 8 consecutive nucleotide units
capable of recruiting RNaseH.
In a still further embodiment at least one nucleoside unit in region G is a DNA nucleoside unit,
such as from 4 to 20 or or 6 to 18 DNA units, such as 5 to 16, In some embodiments, all of the
nucleosides of region G are DNA units.
In further embodiments the region G may consist of a mixture of DNA and other nucleosides
capable of mediating RNase H cleavage. In some embodiments, at least 50% of the
nucleosides of region G are DNA, such as at least 60 %, at least 70% or at least 80 %, or at
least 90% DNA.
Region F’
Region F’ (3’ flank or 3’ wing) attached to the ‘3 end of region G comprises, contains or consists
of at least one sugar modified nucleoside such as at least 2, at least 3, at least 4, at least 5, at
least 6, at least 7 modified nucleosides. In some embodiments region F’ comprises or consists
of from 1 to 7 modified nucleosides, such as from 2 to 6 modified nucleosides, such as from 2 to
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modified nucleosides, such as from 2 to 4 modified nucleosides, such as from 1 to 3 modified
nucleosides, such as 1, 2, 3 or 4 modified nucleosides.
In an embodiment, one or more or all of the modified nucleosides in region F’ are 2’ modified
nucleosides.
In a further embodiment one or more of the 2’ modified nucleosides in region F’ are selected
from 2’-O-alkyl-RNA units, 2’-O-methyl-RNA, 2’-amino-DNA units, 2’-fluoro-DNA units, 2’-
alkoxy-RNA, MOE units, LNA units, arabino nucleic acid (ANA) units and 2’-fluoro-ANA units.
In one embodiment of the invention all the modified nucleosides in region F’ are LNA
nucleosides. In a further embodiment the LNA nucleosides in region F’ are independently
selected from the group consisting of oxy-LNA, thio-LNA, amino-LNA, cET, and/or ENA, in
either the beta-D or alpha-L configurations or combinations thereof. In a preferred embodiment
region F’ has at least 1 beta-D-oxy LNA unit, at the 5’ end of the contiguous sequence.
Region D, D’ and D’’
The oligonucleotide of the invention ncomprises a contiguous nucleotide region which is
complementary to the target nucleic acid. In some embodiments, the oligonucleotide may
further comprise additional nucleotides positioned 5’ and/or 3’ to the contiguous nucleotide
region, which are referred to as region D herein. Region D’ and D’’ can be attached to the 5’
end of region F or the 3’ end of region F’, respectively. The D regions (region D’ or D’’) may in
some embodiments form part of the contiguous nucleotide sequence which is complementary to
the target nucleic acid, or in other embodiments the D region(s) may be non-complementary to
the target nucleic acid.
In some embodiments the oligonucleotide of the invention consists or comprises of the
contiguous nucleotide region and optionally 1 – 5 additional 5’ nucleotides (region D’).
In some embodiments the oligonucleotide of the invention consists or comprises of the
contiguous nucleotide region and optionally 1 – 5 additional 3’ nucleotides (region D’’).
Region D’ or D’’ may independently comprise 1, 2, 3, 4 or 5 additional nucleotides, which may
be complementary or non-complementary to the target nucleic acid. In this respect the
oligonucleotide of the invention, may in some embodiments comprise a contiguous nucleotide
sequence capable of modulating the target which is flanked at the 5’ and/or 3’ end by additional
nucleotides. Such additional nucleotides may serve as a nuclease susceptible biocleavable
linker, and may therefore be used to attach a functional group such as a conjugate moiety to the
oligonucleotide of the invention. In some embodiments the additional 5’ and/or 3’ end
nucleotides are linked with phosphodiester linkages, and may be DNA or RNA. In another
embodiment, the additional 5’ and/or 3’ end nucleotides are modified nucleotides which may for
example be included to enhance nuclease stability or for ease of synthesis. In some
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embodiments the oligonucleotide of the invention comprises a region D’ and/or D’’ in addition to
the contiguous nucleotide region.
In some embodiments, the gapmer oligonucleotide of the present invention can be represented
by the following formulae:
F-G-F’; in particular F -G -F’
1-7 4-12 1-7
D’-F-G-F’, in particular D’ -F -G -F’
1-3 1-7 4-12 1-7
F-G-F’-D’’, in particular F -G -F’ -D’’
1-7 4-12 1-7 1-3
D’-F-G-F’-D’’, in particular D’ -F -G -F’ -D’’
1-3 1-7 4-12 1-7 1-3
Method of manufacture
In a further aspect, the invention provides methods for manufacturing the oligonucleotides of the
invention comprising reacting nucleotide units and thereby forming covalently linked contiguous
nucleotide units comprised in the oligonucleotide. Preferably, the method uses phophoramidite
chemistry (see for example Caruthers et al, 1987, Methods in Enzymology vol. 154, pages 287-
313). In a further embodiment the method further comprises reacting the contiguous nucleotide
sequence with a conjugating moiety (ligand). In a further aspect a method is provided for
manufacturing the composition of the invention, comprising mixing the oligonucleotide or
conjugated oligonucleotide of the invention with a pharmaceutically acceptable diluent, solvent,
carrier, salt and/or adjuvant.
Pharmaceutical Salts
For use as a therapeutic, the oligonucleotide of the invention may be provided as a suitable
pharmaceutical salt, such as a sodium or potassium salt. In some embodiments the
oligonucleotide of the invention is a sodium salt.
Pharmaceutical Composition
In a further aspect, the invention provides pharmaceutical compositions comprising any of the
aforementioned oligonucleotides and/or oligonucleotide conjugates and a pharmaceutically
acceptable diluent, carrier, salt and/or adjuvant. A pharmaceutically acceptable diluent includes
phosphate-buffered saline (PBS) and pharmaceutically acceptable salts include, but are not
limited to, sodium and potassium salts. In some embodiments the pharmaceutically acceptable
diluent is sterile phosphate buffered saline. In some embodiments the oligonucleotide is used in
the pharmaceutically acceptable diluent at a concentration of 50 - 300µM solution. In some
embodiments, the oligonucleotide of the invention is administered at a dose of 10 - 1000µg.
provides suitable and preferred examples of pharmaceutically acceptable
diluents, carriers and adjuvants (hereby incorporated by reference). Suitable dosages,
formulations, administration routes, compositions, dosage forms, combinations with other
therapeutic agents, pro-drug formulations are also provided in WO2007/031091.
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Oligonucleotides or oligonucleotide conjugates of the invention may be mixed with
pharmaceutically acceptable active or inert substances for the preparation of pharmaceutical
compositions or formulations. Compositions and methods for the formulation of pharmaceutical
compositions are dependent upon a number of criteria, including, but not limited to, route of
administration, extent of disease, or dose to be administered.
In some embodiments, the oligonucleotide or oligonucleotide conjugate of the invention is a
prodrug. In particular with respect to oligonucleotide conjugates the conjugate moiety is cleaved
of the oligonucleotide once the prodrug is delivered to the site of action, e.g. the target cell.
Applications
The oligonucleotides of the invention may be utilized as research reagents for, for example,
diagnostics, therapeutics and prophylaxis.
In research, such oligonucleotides may be used to specifically modulate the synthesis of
HTRA1 protein in cells (e.g. in vitro cell cultures) and experimental animals thereby facilitating
functional analysis of the target or an appraisal of its usefulness as a target for therapeutic
intervention. Typically the target modulation is achieved by degrading or inhibiting the mRNA
producing the protein, thereby prevent protein formation or by degrading or inhibiting a
modulator of the gene or mRNA producing the protein.
In diagnostics the oligonucleotides may be used to detect and quantitate HTRA1 expression in
cell and tissues by northern blotting, in-situ hybridisation or similar techniques.
For therapeutics, an animal or a human, suspected of having a disease or disorder, which can
be treated by modulating the expression of HTRA1.
The invention provides methods for treating or preventing a disease, comprising administering a
therapeutically or prophylactically effective amount of an oligonucleotide, an oligonucleotide
conjugate or a pharmaceutical composition of the invention to a subject suffering from or
susceptible to the disease.
The invention also relates to an oligonucleotide, a composition or a conjugate as defined herein
for use as a medicament.
The oligonucleotide, oligonucleotide conjugate or a pharmaceutical composition according to
the invention is typically administered in an effective amount.
The invention also provides for the use of the oligonucleotide or oligonucleotide conjugate of the
invention as described for the manufacture of a medicament for the treatment of a disorder as
referred to herein, or for a method of the treatment of as a disorder as referred to herein.
The disease or disorder, as referred to herein, is associated with expression of HTRA1. In some
embodiments disease or disorder may be associated with a mutation in the HTRA1 gene or a
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gene whose protein product is associated with or interacts with HTRA1. Therefore, in some
embodiments, the target nucleic acid is a mutated form of the HTRA1 sequence and in other
embodiments, the target nucleic acid is a regulator of the HTRA1 sequence.
The methods of the invention are preferably employed for treatment or prophylaxis against
diseases caused by abnormal levels and/or activity of HTRA1.
The invention further relates to use of an oligonucleotide, oligonucleotide conjugate or a
pharmaceutical composition as defined herein for the manufacture of a medicament for the
treatment of abnormal levels and/or activity of HTRA1.
In one embodiment, the invention relates to oligonucleotides, oligonucleotide conjugates or
pharmaceutical compositions for use in the treatment of diseases or disorders selected from
eye disorders, such as macular degeneration, including age related macular degeneration
(AMD), such as dry AMD or wet AMD, and diabetic retinopathy. In some embodiments the
oligonucleotide conjugates or pharmaceutical compositions of the invention may be for use in
the treatment of geographic atrophy or intermediate dAMD. HTRA1 has also been indicated in
Alzheimer’s and Parkinson’s disease, and therefore in some embodiments, the oligonucleotide
conjugates or pharmaceutical compositions of the invention may be for use in the treatment of
Alzheimer’s or Parkinson’s. HTRA1 has also been indicated in Duchenne muscular dystrophy,
arthritis, such as osteoarthritis, familial ischemic cerebral small-vessel disease, and therefore in
some embodiments, the oligonucleotide conjugates or pharmaceutical compositions of the
invention may be for use in the treatment of Duchenne muscular dystrophy, arthritis, such as
osteoarthritis, or familial ischemic cerebral small-vessel disease.
Administration
The oligonucleotides or pharmaceutical compositions of the present invention may be
administered topical (such as, to the skin, inhalation, ophthalmic or otic) or enteral (such as,
orally or through the gastrointestinal tract) or parenteral (such as, intravenous, subcutaneous,
intra-muscular, intracerebral, intracerebroventricular or intrathecal).
In some embodiments the oligonucleotide, conjugate or pharmaceutical compositions of the
present invention are administered by a parenteral route including intravenous, intraarterial,
subcutaneous, intraperitoneal or intramuscular injection or infusion, intrathecal or intracranial,
e.g. intracerebral or intraventricular, administration. In some embodiments the active
oligonucleotide or oligonucleotide conjugate is administered intravenously. In another
embodiment the active oligonucleotide or oligonucleotide conjugate is administered
subcutaneously.
For use in treating eye disorders, such as macular degeneration, e.g. AMD (wet or dry),
intraocular injection may be used.
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In some embodiments, the compound of the invention, or pharmaceutically acceptable salt
thereof, is administered via an intraocular injection in a dose from about 10µg to about 200µg
per eye, such as about 50µg to about 150 µg per eye, such as about 100µg per eye. In some
embodiments, the dosage interval, i.e. the period of time between consecutive dosings is at
least monthy, such as at least bi monthly or at least once every three months.
Combination therapies
In some embodiments the oligonucleotide, oligonucleotide conjugate or pharmaceutical
composition of the invention is for use in a combination treatment with another therapeutic
agent. The therapeutic agent can for example be the standard of care for the diseases or
disorders described above
Embodiments of the Invention
1. An antisense oligonucleotide of 10 – 30 nucleotides in length, wherein said antisense
oligonucleotide comprises a contiguous nucleotide region of 10 – 22 nucleotides which are at
least 90% such as 100% complementarity to SEQ ID NO 147:
SEQ ID NO 147: 5’ CCAACAACCAGGTAAATATTTG 3’
2. The antisense oligonucleotide according to embodiment 1, wherein the antisense
oligonucleotide is capable of inhibiting the expression of HTRA1 mRNA.
3. The antisense oligonucleotide according to embodiment 1 or 2, wherein the contiguous
nucleotide region is identical to a sequence present in a sequence selected from the group
consisting of SEQ ID NO 138, 139, 140, 141, 142, 143, 144 and 145:
SEQ ID NO 138: CAAATATTTACCTGGTTG
SEQ ID NO 139: TTTACCTGGTTGTTGG
SEQ ID NO 140: CCAAATATTTACCTGGTT
SEQ ID NO 141: CCAAATATTTACCTGGTTGT
SEQ ID NO 142: ATATTTACCTGGTTGTTG
SEQ ID NO 143: TATTTACCTGGTTGTT
SEQ ID NO 144: ATATTTACCTGGTTGT
SEQ ID NO 145: ATATTTACCTGGTTGTT
4. The antisense oligonucleotide according to any one of embodiments 1 - 3, wherein the
contiguous nucleotide region comprises the sequence SEQ ID NO 146:
SEQ ID NO 146: TTTACCTGGTT
. The antisense oligonucleotide according to any one of embodiments 1 – 4, wherein the
contiguous nucleotide region of the oligonucleotide consists or comprises of a sequence
selected from any one of SEQ ID NO 138, 139, 140, 141, 142, 143, 144 and 145.
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6. The antisense oligonucleotide according to any one of embodiments 1 – 5 wherein the
contiguous nucleotide region of the oligonucleotide comprises one or more 2’ sugar modified
nucleosides.
7. The antisense oligonucleotide according to embodiment 6, wherein the one or more 2’
sugar modified nucleoside is independently selected from the group consisting of 2’-O-alkyl-
RNA, 2’-O-methyl-RNA, 2’-alkoxy-RNA, 2’-O-methoxyethyl-RNA, 2’-amino-DNA, 2’-fluoro-DNA,
arabino nucleic acid (ANA), 2’-fluoro-ANA and LNA nucleosides.
8. The antisense oligonucleotide according to any one of embodiments 5 - 7, wherein the
one or more modified nucleoside is a LNA nucleoside.
9. The antisense oligonucleotide according to any one of embodiments 1 - 8, where the
contiguous nucleotide region of the oligonucleotide comprises at least one modified
internucleoside linkage, such as one or more phosphorothioate internucleoside linkages.
. The antisense oligonucleotide according to embodiment 9, wherein all the
internucleoside linkages within the contiguous nucleotide region are phosphorothioate
internucleoside linkages.
11. The antisense oligonucleotide according to any one of embodiments 1 – 10, wherein the
oligonucleotide is capable of recruiting RNase H.
12. The antisense oligonucleotide according to any one of embodiments 1 - 11, wherein the
oligonucleotide or contiguous nucleotide sequence thereof is or comprises a gapmer.
13. The antisense oligonucleotide of embodiment 11 or 12, wherein the oligonucleotide or
contiguous nucleotide sequence thereof is a gapmer of formula 5’-F-G-F’-3’, where region F and
F’ independently comprise 1 - 7 sugar modified nucleosides and G is a region 6 - 16
nucleosides which is capable of recruiting RNaseH, wherein the nucleosides of regions F and F’
which are adjacent to region G are sugar modified nucleosides.
14. The antisense oligonucleotide according to embodiment 13, wherein region G consists
or comprises 6 – 16 DNA nucleosides.
. The antisense oligonucleotide according to embodiment 13 or 14, wherein region F and
F’ each comprise at least one LNA nucleoside.
16. The antisense oligonucleotide according to any one of embodiments 1 – 15, selected
from the group selected from:
C A A A t a t t t a c c t g G T T G (SEQ ID NO 138, Comp # 138,1)
s s s s s s s s s s s s s s s s s
T T t a c c t g g t t g t T G G (SEQ ID NO 139, Comp # 139,1)
s s s s s s s s s s s s s s s
C C A A a t a t t t a c c t g G T T (SEQ ID NO 140, Comp # 140,1)
s s s s s s s s s s s s s s s s s
C C A a a t a t t t a c c t g g t t G T (SEQ ID NO 141, Comp # 141,1)
s s s s s s s s s s s s s s s s s s s
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A T A t t t a c c t g g t t g T T G (SEQ ID NO 142, Comp # 142,1)
s s s s s s s s s s s s s s s s s
T A T t t a c c t g g t T G T T (SEQ ID NO 143, Comp # 143,1)
s s s s s s s s s s s s s s s
T A t t t a c c t g G t T g T T (SEQ ID NO 143, Comp # 143,2)
s s s s s s s s s s s s s s s
TsAsTststsascscstsgsgsTsTsgsTsT (SEQ ID NO 143, Comp # 143,3)
A T A T t t a c c t g g T T G T (SEQ ID NO 144, Comp # 144,1)
s s s s s s s s s s s s s s s
A t A T T t a c c t g g t T G T (SEQ ID NO 144, Comp # 144,2)
s s s s s s s s s s s s s s s
A t A T t t a c c t g G T T g T T (SEQ ID NO 145, Comp # 145,1)
s s s s s s s s s s s s s s s s
A T A t t t a c c t g G t T g T T (SEQ ID NO 145, Comp # 145,2)
s s s s s s s s s s s s s s s s
A t A T t t a c c t g g t T G T T (SEQ ID NO 145, Comp # 145,3)
s s s s s s s s s s s s s s s s
Wherein a capital letter represents an LNA nucleoside unit, a lowe case letter represents a DNA
nucleoside unit, subscript s represents a phosphorothioate internucleoside linkage, wherein all
LNA cytosines are 5-methyl cytosine.
17. The antisense oligonucleotide according to embodiment 16, wherein the LNA
nucleosides are all beta-D-oxy LNA nucleosides.
18. A conjugate comprising the oligonucleotide according to any one of embodiments 1 –
17, and at least one conjugate moiety covalently attached to said oligonucleotide.
19. A pharmaceutical composition comprising the oligonucleotide of embodiment 1 – 17 or
the conjugate of embodiment 18 and a pharmaceutically acceptable diluent, solvent, carrier, salt
and/or adjuvant.
20. An in vivo or in vitro method for modulating HTRA1 expression in a target cell which is
expressing HTRA1, said method comprising administering an oligonucleotide of any one of
embodiments 1 – 17 or the conjugate according to embodiment 18 or the pharmaceutical
composition of embodiment 19 in an effective amount to said cell.
21. A method for treating or preventing a disease comprising administering a therapeutically
or prophylactically effective amount of an oligonucleotide of any one of embodiments 1 – 17 or
the conjugate according to embodiment 18 or the pharmaceutical composition of embodiment
19 to a subject suffering from or susceptible to the disease.
22. The method of embodiment 21, wherein the disease is selected from the group
consisting of macular degeneration (such as wetAMD, dryAMD, geographic atrophy,
intermediate dAMD, diabetic retinopathy), Parkinson’s disease, Alzhiemer’s disease, Duchenne
muscular dystrophy, arthritis, such as osteoarthritis, and familial ischemic cerebral small-vessel
disease.
23. The oligonucleotide of any one of embodiments 1 – 17 or the conjugate according to
embodiment 18 or the pharmaceutical composition of embodiment 19 for use in medicine.
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24. The oligonucleotide of any one of embodiments 1 – 17 or the conjugate according to
embodiment 18 or the pharmaceutical composition of embodiment 19 for use in the treatment or
prevention of a disease is selected from the group consisting of macular degeneration (such as
wetAMD, dryAMD, geographic atrophy, intermediate dAMD, diabetic retinopathy), Parkinson’s
disease, Alzhiemer’s disease, Duchenne muscular dystrophy, arthritis, such as osteoarthritis,
and familial ischemic cerebral small-vessel disease.
. Use of the oligonucleotide of embodiment 1 – 17 or the conjugate according to
embodiment 18 or the pharmaceutical composition of embodiment 19, for the preparation of a
medicament for treatment or prevention of a disease is selected from the group consisting of
macular degeneration (such as wetAMD, dryAMD, geographic atrophy, intermediate dAMD,
diabetic retinopathy), Parkinson’s disease, Alzhiemer’s disease, Duchenne muscular dystrophy,
arthritis, such as osteoarthritis, and familial ischemic cerebral small-vessel disease.
EXAMPLES
Materials and methods
Oligonucleotide synthesis
Oligonucleotide synthesis is generally known in the art. Below is a protocol which may be
applied. The oligonucleotides of the present invention may have been produced by slightly
varying methods in terms of apparatus, support and concentrations used.
Oligonucleotides are synthesized on uridine universal supports using the phosphoramidite
approach on an Oligomaker 48 at 1 μmol scale. At the end of the synthesis, the oligonucleotides
are cleaved from the solid support using aqueous ammonia for 5-16hours at 60C. The
oligonucleotides are purified by reverse phase HPLC (RP-HPLC) or by solid phase extractions
and characterized by UPLC, and the molecular mass is further confirmed by ESI-MS.
Elongation of the oligonucleotide:
The coupling of β-cyanoethyl- phosphoramidites (DNA-A(Bz), DNA- G(ibu), DNA- C(Bz), DNA-
T, LNAmethyl-C(Bz), LNA-A(Bz), LNA- G(dmf), LNA-T) is performed by using a solution of
0.1 M of the 5’-O-DMT-protected amidite in acetonitrile and DCI (4,5–dicyanoimidazole) in
acetonitrile (0.25 M) as activator. For the final cycle a phosphoramidite with desired
modifications can be used, e.g. a C6 linker for attaching a conjugate group or a conjugate group
as such. Thiolation for introduction of phosphorthioate linkages is carried out by using xanthane
hydride (0.01 M in acetonitrile/pyridine 9:1). Phosphordiester linkages can be introduced using
0.02 M iodine in THF/Pyridine/water 7:2:1. The rest of the reagents are the ones typically used
for oligonucleotide synthesis.
For post solid phase synthesis conjugation a commercially available C6 aminolinker
phorphoramidite can be used in the last cycle of the solid phase synthesis and after
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deprotection and cleavage from the solid support the aminolinked deprotected oligonucleotide is
isolated. The conjugates are introduced via activation of the functional group using standard
synthesis methods.
Purification by RP-HPLC:
The crude compounds are purified by preparative RP-HPLC on a Phenomenex Jupiter C18 10µ
150x10 mm column. 0.1 M ammonium acetate pH 8 and acetonitrile is used as buffers at a flow
rate of 5 mL/min. The collected fractions are lyophilized to give the purified compound typically
as a white solid.
Abbreviations:
DCI: 4,5-Dicyanoimidazole
DCM: Dichloromethane
DMF: Dimethylformamide
DMT: 4,4’-Dimethoxytrityl
THF: Tetrahydrofurane
Bz: Benzoyl
Ibu: Isobutyryl
RP-HPLC: Reverse phase high performance liquid chromatography
T Assay:
Oligonucleotide and RNA target (phosphate linked, PO) duplexes are diluted to 3 mM in 500 ml
RNase-free water and mixed with 500 ml 2x T -buffer (200mM NaCl, 0.2mM EDTA, 20mM
Naphosphate, pH 7.0). The solution is heated to 95ºC for 3 min and then allowed to anneal in
room temperature for 30 min. The duplex melting temperatures (T ) is measured on a Lambda
40 UV/VIS Spectrophotometer equipped with a Peltier temperature programmer PTP6 using PE
Templab software (Perkin Elmer). The temperature is ramped up from 20ºC to 95ºC and then
down to 25ºC, recording absorption at 260 nm. First derivative and the local maximums of both
the melting and annealing are used to assess the duplex T .
Example 1: Testing in vitro efficacy of antisense oligonucleotides targeting rat Htra1 in
C6 cell lines at single dose concentration.
Rat C6 cell line was purchased from ATCC and maintained as recommended by the supplier in
a humidified incubator at 37°C with 5% CO . For assays, 1500 C6 cells/well were seeded in a
96 multi well plate in culture media. Cells were incubated for 2 hours before addition of
oligonucleotides dissolved in PBS. Concentration of oligonucleotides: 25 µM. 4 days after
addition of oligonucleotides, the cells were harvested. RNA was extracted using the PureLink
Pro 96 RNA Purification kit (Ambion, according to the manufacturer’s instructions). cDNA was
then synthesized using M-MLT Reverse Transcriptase, random decamers RETROscript, RNase
inhibitor (Ambion, according the manufacturer’s instruction) with 100mM dNTP set PCR Grade
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(Invitrogen) and DNase/RNase free Water (Gibco). For gene expressions analysis, qPCR was
performed using TagMan Fast Advanced Master Mix (2X) (Ambion) in a doublex set up.
Following TaqMan primer assays were used for qPCR: Htra1, Rn00581870_m1 (FAM-MGB)
and house keeping gene, Tbp, Rn01455646_m1 (VIC-MGB). All primer sets were purchase
from Life Technologies. The relative Htra1 mRNA expression level in the table is shown as % of
control (PBS-treated cells).
Oligonucleotides used:
gaaagggaaatatggg GAAagggaaatatGGG 51
6 gatgaggtataaagtg GATgaggtataaaGTG 54
7 ggtgtgttaataatca GGTgtgttaataaTCA 60
8 cttatgacgcaaactg CTTatgacgcaaaCTG 26
9 tttgtctcctttcctc TTtgtctcctttccTC 70
,1
gaatggaaagatgtaa GAATggaaagatGTAA 27
11 gttctttggctttgct 11,1 GTtctttggctttgCT 63
12,1
12 ttcaatgatatatgct TTCaatgatatatGCT 15
13,1
13 agtatgaagaagtatt AGTatgaagaagtATT 27
14,1
14 cccaatcacctcgcca CCCaatcacct cgCCA 72
,1
gcagtagcaaagacagg GCagtagcaaagacAGG 28
16 aagttgaaatcagtggt 16,1 AAGttgaaatcagTGGT 12
17,1
17 tctggtagtaagaatata TCTGgtagtaagaaTATA 73
18 aacagtaagagctacttt 18,1 AACAgtaagagctaCTTT 62
19,1
19 tcagacacgatacagag TCAgaca cgatacAGAG 39
tggtcagtgataagtaa 20,1 TGGtcagtgataaGTAA 34
21,1
21 gcactgtagatgagaaac GCACtgtagatgagAAAC 37
22,1
22 ataaagtaaacttaatgcc ATAAagtaaacttaaTGCC 32
23,1
23 attggttcttaggagtgggc AttggttcttaggagtggGC 56
24,1
24 attattgttttactcgtga ATTattgttttact cgTGA 32
atgctggggtaatgattg 25,1 ATGctggggtaatgaTTG 58
26,1
26 agtctaaattattgcacaa AGTCtaaattattgcACAA 72
27 ccaattagaacagtagtgg 27,1 CCAAttagaacagtagtGG 58
28,1
28 agtgtctagttaaacagcac AGtgtctagttaaacagCAC 84
29,1
29 taccagagtcaagcatatg TACcagagtcaagcataTG 33
,1
atctaaacttcatgtcagaa ATCtaaacttcatgtcAGAA 86
31,1
31 ttcatacgactgagcatc TTCAta cgactgagcATC 26
32 gtacagttttagatcatc 32,1 GTAcagttttagatCATC 18
33,1
33 atcctaaaagagttcaaca ATCCtaaaagagttcaACA 77
34 cattctttgtcatatact 34,1 CATtctttgtcataTACT 49
SEQ ID NO
Motif
CMP ID NO
Compound
mRNA level
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,1
ttcaaagtgactttcaag TTCAaagtgactttCAAG 11
36,1
36 tcctttctataattacaaa TCCTttctataattaCAAA 35
37,1
37 ctaattctgtagttttgg CTaattctgtagttTTGG 31
38,1
38 actgagtgtgtaatgttga ACtgagtgtgtaatgtTGA 59
39 agagaaatctgtagggc 39,1 AGAgaaatctgtaggGC 56
40,1
40 ttatcaaatcaactagcac TTAtcaaatcaactaGCAC 84
41,1
41 ttatatttgatagtgtgatc TTATatttgatagtgtgATC 55
42,1
42 aagagaagctgttatctaaa AAGAgaagctgttatcTAAA 42
43,1
43 aagtcatgctagagttcc AAgtcatgctagagtTCC 37
44 acacagtgtattcgaggg 44,1 ACAcagtgtatt cgagGG 38
45,1
45 gacacagtgtattcgaggg GAcacagtgtatt cgagGG 52
46 gacacagtgtattcgagg 46,1 GACacagtgtatt cgaGG 26
47,1
47 aggacacagtgtattcgagg AGgacacagtgtatt cgaGG 38
48 aggacacagtgtattcgag 48,1 AGgacacagtgtatt cgAG 32
49,1
49 caggacacagtgtattcgag CAggacacagtgtatt cgAG 53
50,1
50 aggacacagtgtattcg AGgacacagtgtaTTCG 11
51 aacaggacacagtgtattcg 51,1 AAcaggacacagtgtaTTCG 28
52,1
52 tgaatctatacagcaggaa TGAAtctatacagcagGAA 46
53 cttaagttattcatatcca 53,1 CTTaagttattcatatCCA 39
54,1
54 taggtggtagcagatag TAGgtggtagcagatAG 48
55 gtagtaataattctggga 55,1 GTAgtaataattctgGGA 7
56,1
56 agtggtaaggtgaagtgaa AGtggtaaggtgaagTGAA 45
57,1
57 ttttgctgtgataaatagc TTttgctgtgataaaTAGC 65
58,1
58 tttcttatcgttttatga TTTCttat cgttttATGA 24
59,1
59 ggaaaacattaacaaggttg GGAAaacattaacaagGTTG 38
60 tgggtagagtctaggag 60,1 TGggtagagtctaggAG 58
61,1
61 agggagtgactattagag AGggagtgactattaGAG 45
62 cagagtagggaaagtggttc 62,1 CAgagtagggaaagtggtTC 76
63,1
63 accatgttatatttggg ACCAtgttatatttgGG 54
64,1
64 tttattactgaggggaaagg TTTAttactgaggggaaaGG 67
65,1
65 acttgagtgtagtacag ACTtgagtgtagtACAG 21
66,1
66 catactagttttgcagaga CAtactagttttgcagAGA 54
67 ggactagaagtagttac 67,1 GGActagaagtagTTAC 58
68,1
68 agggagtcaaaggttcaa AGggagtcaaaggtTCAA 13
69 tctgtgtattagagaacg 69,1 TCTGtgtattagagAACG 44
70,1
70 tcaaaagctacatcagtc TCAaaagctacatcAGTC 7
71,1
71 accgttgaattagtcac ACCGttgaattagtCAC 39
72,1
72 tttccattaaaatgtttaca TTTCcattaaaatgttTACA 28
73,1
73 gagatggtaaggagtaggag GAgatggtaaggagtaggAG 60
74 agttttagactattctg 74,1 AGTTttagactattCTG 37
75,1
75 gtcaggacataaactcac GTCaggacataaacTCAC 18
76 ttgttggtgtcagggaaaag 76,1 TTGttggtgtcagggaaaAG 20
77,1
77 tcctgaaatattgatgc TCCtgaaatattgaTGC 51
78,1
78 tgccaaaatgactacagt TGCcaaaatgactacAGT 54
79,1
79 ctcaaagttggatcgtaac CTCaaagttggat cgTAAC 37
80,1
80 ttgcattttagaagttat TTGCattttagaagTTAT 49
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81,1
81 tgtcaattagtgtgtttag TGTCaattagtgtgtttAG 20
82,1
82 cataatatttagtctcct CATaatatttagtctCCT 40
83,1
83 tatagttacaatcacca TATAgttacaatcaCCA 30
84,1
84 ttttgtacatactcttcc TTttgtacatactcTTCC 11
85 tagcagtacttaaatggg 85,1 TAGcagtacttaaatGGG 28
86,1
86 tatgttacatatttggatga TATgttacatatttggaTGA 41
87,1
87 catggtatcttttggagag CATggtatcttttggagAG 36
88,1
88 caacatatccagtccag CAAcatatccagtcCAG 22
89,1
89 taattgtgaagtagggtg TAattgtgaagtagGGTG 33
90 actttagaggtttagtcc 90,1 ACTttagaggtttagtCC 55
91,1
91 gagcttttaattctatcc GAgcttttaattctATCC 56
92 ctccttaaatacatgttac 92,1 CTCcttaaatacatgTTAC 49
93,1
93 gagataaatgtttgagaga GAGAtaaatgtttgagAGA 41
94 atgatggtgatttaggat 94,1 ATGAtggtgatttagGAT 22
95,1
95 agtcattcaatttgagaaa AGTCattcaatttgaGAAA 35
96,1
96 cagtggtggtaaggcac CAGtggtggtaaggcAC 53
97 tgaaatggtttagttctg 97,1 TGAAatggtttagttCTG 41
98,1
98 tgccatagtgaaatggttt TGCcatagtgaaatggtTT 57
99 caggaggacatactatt 99,1 CAGgaggacatacTATT 77
100,1
100 atatatacaggcacatgg ATAtatacaggcacaTGG 71
101 gacaggagtctttaaaatg 101,1 GACAggagtctttaaAATG 80
102,1
102 tatttatatagtaatgtgtc TATTtatatagtaatgTGTC 57
103,1
103 ggataaaacagtaccat GGAtaaaacagtaCCAT 77
104,1
104 ggagtttagaagacacat GGAgtttagaagacaCAT 33
105,1
105 gtacaactacagaggtt GTACaactacagagGTT 65
106 aggaaatggtgatggaatg 106,1 AGGaaatggtgatggAATG 58
107,1
107 tcggagtaaaagtgtaaaca TCGGagtaaaagtgtaaACA 81
For Compounds: Capital letters represent LNA nucleosides (beta-D-oxy LNA nucleosides were used), all
LNA cytosines are 5-methyl cytosine, lower case letters represent DNA nucleosides, DNA cytosines
preceded with a superscript represents a 5-methyl C-DNA nucleoside. All internucleoside linkages are
phosphorothioate internucleoside linkages.
Example 2. Testing in vitro potency and efficacy of selected oligonucleotides targeting
rat Htra1 in C6 cell line in a dose response curve.
Rat C6 cell line was described in Example 1. The assay was performed as described in
Example 1. Concentration of oligonucleotides: from 50 µM, half-log dilution, 8 points. 4 days
after addition of oligonucleotides, the cells were harvested. RNA extraction, cDNA synthesis
and qPCR were performed as described in Example 1. n=2 biological replicates. EC
determinations were performed in GraphPad Prism6. The relative Htra1 mRNA level at
treatment with 50 µM oligonucleotide is shown in the table as % of control (PBS). Additional
primer sets (Htra1, Rn00668987_m1 [FAM-MGB] vs. Ppia, Rn006900933_m1 [VIC-MGB] and
Hprt, Rn01527840_m1 [VIC-MGB]) were also tested and the same trends were observed using
those primers (data not shown).
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12 12,1 3,3 14
16 16,1 3,2 11
32 32,1 4,3 27
35,1 2,6 8
50 50,1 1,9 9
55 55,1 2,0 6
58 58,1 4,4 25
65 65,1 3,1 14
68 68,1 4,1 8
70 70,1 1,5 2
75 75,1 3,7 16
76 76,1 4,9 21
81 81,1 3,0 18
84 84,1 2,2 9
88 88,1 6,8 20
94 94,1 2,9 15
Example 3 Testing in vitro efficacy of oligonucleotides targeting human HTRA1, in U251
cell line at single dose concentration.
Human glioblastoma U251 cell line was purchased from ECACC and maintained as
recommended by the supplier in a humidified incubator at 37°C with 5% CO . For assays,
15000 U251 cells/well were seeded in a 96 multi well plate in starvation media (media
recommended by the supplier with the exception of 1% FBS instead of 10%). Cells were
incubated for 24 hours before addition of oligonucleotides dissolved in PBS. Concentration of
oligonucleotides: 5 µM. 3-4 days after addition of compounds, media was removed and new
media (without oligonucleotide) was added. 6 days after addition of oligonucleotides, the cells
were harvested. RNA was extracted using the PureLink Pro 96 RNA Purification kit (Ambion,
according to the manufacturer’s instructions). cDNA was then synthesized using M-MLT
Reverse Transcriptase, random decamers RETROscript, RNase inhibitor (Ambion, according
the manufacturer’s instruction) with 100mM dNTP set PCR Grade (Invitrogen) and
DNase/RNase free Water (Gibco). For gene expressions analysis, qPCR was performed using
TagMan Fast Advanced Master Mix (2X) (Ambion) in a doublex set up. Following TaqMan
primer assays were used for qPCR: HTRA1, Hs01016151_ m1 (FAM-MGB) and house keeping
gene, TBP, Hs4326322E (VIC-MGB) from Life Technologies. The relative HTRA1 mRNA
expression level in the table is shown as % of control (PBS-treated cells).
SEQ ID NO
CMP ID NO
mRNA level
at Max KD
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108,1
108 agatgggtgtgaaagg AGAtgggtgtgaaAGG 35
109,1
109 atgttgtctatgttta ATGttgtctatgtTTA 5
110,1
110 tatgttgtctatgttt TATgttgtctatgTTT 5
111,1
111 gatgtttgcagtattt GATgtttgcagtaTTT 17
112,1
112 tatatagtcgaatagg TATatagtcgaatAGG 18
113,1
113 tttggcttcgtaagtg TTTggcttcgtaaGTG 1
114,1
114 tgaggcagtggagttg TGaggcagtggagtTG 32
115,1
115 tggacaggagggcagc TGgacaggagggcaGC 92
116,1
116 tagagaaggtagaatg TAGagaaggtagaATG 78
117 atttagattagagaag 117,1
ATTTagattagaGAAG 50
118,1
118 gttcttaaatgtcgtt GTTcttaaatgtcGTT 10
119,1
119 aagggcttaccatctt AAGggcttaccatCTT 62
120,1
120 tacttcaattatatac TACttcaattataTAC 25
121,1
121 gcaatgtgtaagaagt GCAatgtgtaagaAGT 15
122,1
122 aaactgttgggatctt AAACtgttgggaTCTT 11
123,1
123 caaactgttgggatct CAAActgttgggATCT 50
124 gcaaactgttgggatc 124,1 GCAaactgttgggATC 11
125,1
125 gatgtttgcagtattt GAtgtttgcagtaTTT 22
126,1
126 attgggtttgatcggt ATTgggtttgat cgGT 15
127,1
127 ctattgggtttgatcg CTAttgggtttgatCG 16
128 tattgggtttgatcgg 128,1
TATtgggtttgatCGG 10
129,1
129 cgaatatgtgctttaa CGAatatgtgcttTAA 8
130,1
130 gctgattatgacgtcg GCTgattatga cgTCG 13
131,1
131 tgctgattatgacgtc TGCtgattatga cGTC 10
132,1
132 attgggtttgatcggt ATTgggtttgatCGGT 18
133,1
133 ctattgggtttgatcg CTAttgggtttgATCG 49
134,1
134 tgctgattatgacgtc TGCtgattatgaCGTC 46
135 tattgggtttgatcgg 135,1 TATTgggtttgaTCGG 58
136,1
136 cgaatatgtgctttaa CGAAtatgtgctTTAA 13
137,1
137 gctgattatgacgtcg GCTGattatga cGTCG 39
For Compounds: Capital letters represent LNA nucleosides (beta-D-oxy LNA nucleosides were used), all
LNA cytosines are 5-methyl cytosine, lower case letters represent DNA nucleosides, DNA cytosines
preceded with a superscript represents a 5-methyl C-DNA nucleoside. All internucleoside linkages are
phosphorothioate internucleoside linkages.
Example 4 Testing in vitro efficacy of a library of oligonucleotides targeting human
HTRA1 mRNA in ARPE19 and U251 cell lines at 2 concentrations.
SEQ ID NO
Motif
CMP ID NO
Compound
mRNA level
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Identification of promising “hot spot” region for HTRA1. A library of n=129 human/cyno/rat
HTRA1 LNA oligonucleotides were screened in U251 and ARPE19 cell lines. From this library
we identified a series of active oligonucleotides targeting human HTRA1 pre-mRNA (SEQ ID
NO 2) between position 33042 - 33064 as shown in figure 1.
Human retinal pigmented epithelium ARPE19 cell line was purchased by from ATCC and
maintained in DMEM-F12 (Sigma, D8437), 10% FBS, 1% pen/strep in a humidified incubator at
37°C with 5% CO . The U251 cell line was described in example 3. For assays, 5000 ARPE19
cells/well were seeded in a 96 multi well plate in culture media (with the exception of 5% FBS
instead of 10%). Cells were incubated for 1 hour before addition of oligonucleotides dissolved in
PBS. 4 days after addition of oligonucleotides, the cells were harvested. The assay with the
U251 cell line was performed as described in example 3. Concentration of oligonucleotides: 25
and 2.5 µM. RNA was extracted using the RNeasy 96 Biorobot 8000 kit (Qiagen, according to
the manufacturer’s instructions). cDNA was then synthesized using Retroscript cDNA synthesis
kit (ThermoFisher, according the manufacturer’s instruction). For gene expressions analysis,
qPCR was performed using the Fluidigm Biomark system. Following TaqMan primer assays
were used for qPCR: HTRA1, Hs01016151_m1 and house-keeping genes, TBP,
Hs99999910_m1 and PPIA, Hs99999904_m1, from Life Technologies. n=2 biologial replicates.
The relative HTRA1 mRNA expression level is shown in the table as % of control (PBS).
Additional HTRA1 primer set (Hs00170197_m1) was also tested and the same trends were
observed (data not shown).
SEQ Comp Compound ARPE19 U251 mRNA
ID NO # mRNA level level
25µ 2.5 25µM 2.5 µM
M µM
138 138,1
CAAAtatttacctgGTTG 79 97 11 60
139 139,1 39 73
TTtacctggttgtTGG 5 37
140 140,1 68 100
C CAAatatttacctgGTT 16 70
141 141,1 78 87
C CAaatatttacctggttGT 16 78
142 142,1 56 78
ATAtttacctggttgTTG 4 23
143 143,1 22 77
TATttacctggtTGTT 3 23
For Compounds: Capital letters represent LNA nucleosides (beta-D-oxy LNA nucleosides were used), all
LNA cytosines are 5-methyl cytosine, lower case letters represent DNA nucleosides. All internucleoside
linkages are phosphorothioate internucleoside linkages.
Example 5, Testing in vitro efficacy of selected human/rat HTRA1 targeting LNA
oligonucleotidesin rat C6 cell lines at single dose concentration.
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Rat C6 cell line was described in Example 1. The assay was performed as described in
Example 1. Concentration of oligonucleotides: 25µM. n=2 biologial replicates. The relative Htra1
mRNA expression level in the table is shown as % of control (PBS-treated cells).
139 139,1 24
140 140,1 6
142 142,1
143 143,1
Example 6, Testing in vitro potency and efficacy of of selected human/cyno/rat LNA
oligonucleotides in ARPE19, U251 and C6 cell lines in a dose response.
ARPE19, U251 and C6 cell lines were described in example 4, 3 and 1, respectively. For
assays, 2000 U251 or ARPE19 cells/well were seeded in a 96 multi well plate in culture media
recommended by the supplier. Cells were incubated for 2 hours before addition of
oligonucleotides dissolved in PBS. The C6 cell line assay was performed as described in
example 1-2. Concentration of oligonucleotides: from 50 µM, half-log dilution, 8 points. 4 days
after addition of oligonucleotides, the cells were harvested. RNA extraction, cDNA synthesis
and qPCR were performed for all cell lines as described in Example 1. Following TaqMan
primer assays were used for U251 and ARPE19 cells: HTRA1, Hs01016151_m1 (FAM-MGB)
and house-keeping gene, TBP, Hs4326322E (VIC-MGB). All primer sets were purchased from
Life Technologies. n=2 biologial replicates. EC50 determinations were performed in Graph Pad
Prism6. The relative HTRA1 mRNA level at treatment with 50 µM oligonucleotide is shown in
the table as % of control (PBS).
mRNA mRNA mRNA
EC50 level at EC50 level at EC50 level at
(µM) max KD (µM) max KD (µM) max KD
138 138,1 10 63 6,2 36 ND ND
139 139,1 10 38 3,2 18 ND ND
140 140,1 4,5 29
7,9 57 1,3 2
141 141,1 4,5 44
9,3 64 ND ND
142 142,1 5,8 40 3,9 25 ND ND
SEQ ID NO
SEQ ID NO
CMP ID NO
CMP ID NO
mRNA level
ARPE19
U251
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143 143,1 3,3 25 1,7 6,0 3,5 5
Example 7, Testing in vitro efficacy of selected human HTRA1 targeting oligonucleotides
in ARPE19 and U251 cell lines at single dose concentration.
ARPE19 and U251 cell lines and assays were described in example 6. RNA extraction was
performed as described in example 1, cDNA synthesis and qPCR were performed using qScript
XLT one-step RT-qPCR ToughMix Low ROX, 95134-100 (Quanta Biosciences). Following
TaqMan primer assays were used for U251 and ARPE19 cells in a douplex set up: HTRA1,
Hs01016151_m1 (FAM-MGB) and house-keeping gene, GAPDH, Hs4310884E (VIC-MGB). All
primer sets were purchased from Life Technologies. n=1 biological replicate. The relative
HTRA1 mRNA expression level in the table is shown as % of control (PBS-treated cells).
Additional primer sets (HTRA1, Hs00170197_m1 [FAM-MGB] vs. TBP Hs4326322E [VIC-MGB])
were also tested for U251 and the same trends were observed using those primers (data not
shown). See figure 2.
143 143,1 46 7
143 143,2 10
143 143,3 50
144 144,1 44
144 144,2 9
145 145,1 51 24
145 145,2 40
145 145,3 42 4
Example 8, Testing in vitro efficacy and potency in human primary RPE cells.
Human primary Retinal Pigmented Epithelium (hpRPE) cells are purchased from Sciencell
(Cat# 6540). For assays, 5000 hpRPE cells/well are seeded in a Laminin (Laminin 521,
BioLamina Cat# LN521-03) coated 96 multi well plate in culture media (EpiCM, Sciencell Cat#
4101). They are expanded with this media for one week and differentiated using the following
media for 2 weeks : MEM Alpha media (Sigma Cat# M-4526) supplemented with N1
supplement (Sigma Cat# N-6530), Glutamine-Penicillin-Streptomycin (Sigma Cat# G-1146),
Non-Essential Amino Acid (NEAA, Sigma Cat# M-7145), Taurine (Sigma Cat# T-0625),
Hydrocortisone (Sigma Cat# H-03966), Triiodo-thyronin (Sigma Cat# T-5516) and Bovine
SEQ ID NO
CMP ID NO
ARPE19 mRNA level
U251 mRNA level
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Serum Albumin (BSA, Sigma Cat# A-9647). Cells are cultured in a humidified incubator at 37°C
with 5% CO .
On the day of the experiment, cells are incubated for 1 hour with fresh differentiation media
before addition of oligonucleotides. These are dissolved in PBS and applied on cells at day 0
and day 4. On day 7, cells are harvested with 50µl of RLT buffer with β-mercapto-ethanol
(Qiagen Cat# 79216). The extraction of the RNA is performed according to the user’s manual of
the Qiagen RNeasy Mini Kit (Cat# 74104; Lot 151048073) including DNase I treatment (Cat#
79254; Lot 151042674). RNA quality control is performed with the Agilent Bioanalyzer Nano Kit
(Agilent; Cat# 5067-1511; Lot 1446). Reverse transcription of total RNA into cDNA (cDNA
synthesis) is performed using the High Capacity cDNA Reverse Transcription Kit which is based
on random hexamer oligonucleotides, according to the manufacturer’s instructions (Thermo
Fisher Scientific, Cat# 4368814; Lot 00314158). The measurement of the cDNA samples is
carried out in triplicates, in a 384-well plate format on the 7900HT real-time PCR instrument
(Thermo Fisher Scientific). The following TaqMan primer assays are used for qPCR: HTRA1,
Hs01016151_m1 and Hs00170197_m1, housekeeping genes, GAPDH, Hs99999905_m1 and
PPIA, Hs99999904_m1, from Life Technologies. n=3 biological replicates. The relative HTRA1
mRNA expression level is shown in the table as % of control (PBS). See figure 3.
Example 9. Rat in vivo efficacy study, 7 days of treatment, intravitreal (IVT) injection,
30µg/eye.
Animals
Experiment was performed on pigmented male Brown Norway rats. Five animals were included
in each group of the study, 15 in total.
Compounds and dosing procedures
To start the experiment, the animals were anesthetized with isoflurane, eyes were desinfected
and dilated before an intravitreal injection of 30µg (in 3µl) per eye.
Euthanasia
At the end of the in-life phase (Day 7) all rats were euthanized with CO before eyes were
harvested for dissection. Retina, sclera and vitreous fluid were taken for further analysis.
Quantification of HTRA1 RNA expression
Retina samples were dissected. Rat retina snap frozen tissue was kept frozen and was lysed in
the testing facility in RLT lysis buffer (Qiagen RNeasy Mini Kit) and RNA extraction was
continued according to the user’s manual of the Qiagen RNeasy Mini Kit (Cat# 74104; Lot
151039852) including DNase I treatment (Cat#79254; Lot 151048613). RNA quality control was
performed with the Agilent Bioanalyzer Nano Kit (Agilent; Cat# 5067-1511; Lot 1446). Reverse
transcription of total RNA into cDNA (cDNA synthesis) was performed using the High Capacity
cDNA Reverse Transcription Kit which is based on random hexamer oligonucleotides,
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according to the manufacturer’s instructions (Thermo Fisher Scientific, Cat# 4368814, Lot
00314158). The measurement of the cDNA samples was carried out in triplicates, in a 384-well
plate format on the 7900HT real-time PCR instrument (Thermo Fisher Scientific). Following
TaqMan primer assays were used for qPCR: Htra1, Rn00581870_m1 and housekeeping genes,
Gapdh, Rn01775763_g1 and Tbp, Rn01455646_m1, from Life Technologies. Rats/group: 5,
n=10 eyes. Each eye was treated as an individual sample. The relative Htra1 mRNA expression
level is shown as % of control (PBS). See figure 4.
Example 10 Rat in vivo efficacy study, 7 days of treatment, intravitreal (IVT) injection,
dose response.
Animals
All experiments were performed on pigmented Brown Norway rats. 17 animals were included in
each group of the study, 34 in total.
Compounds and dosing procedures
The animals were anesthetized with an intramuscular injection of a mix of xylazine and
ketamine. The test item and negative control (PBS) were administered intravitreally in both eyes
of anesthetized animals (3 µL per administration) on study day 1.
Euthanasia
At the end of the in-life phase (Day 8) were euthanized by intraperitoneal an overdose injection
of pentobarbital.
Oligo content measurement and quantification of Htra1 RNA expression
Both eyeballs of all animals in low-dose and mid-dose group as well as from 5 first animals from
high-dose and PBS groups were used for bioanalysis. Immediately after euthanasia, Vitreous
(V), Retina (R) and Choroid (CH) were quickly and carefully dissected out on ice and stored at -
80°C until shipment. Retina sample was lysed in 700 µL MagNa Pure 96 LC RNA Isolation
Tissue buffer and homogenized by adding 1 stainless steel bead per 2 ml tube 2 x 1,5 min
using a precellys evolution homogenizer followed by 30 min incubation at RT. The samples
were centrifuges, 13000 rpm, 5 min. half was set aside for bioanalysis and for the other half,
RNA extraction was continued directly
For bioanalysis, the samples were diluted 10-50 fold for oligo content measurements with a
hybridization ELISA method. A biotinylated LNA-capture probe and a digoxigenin-conjugated
LNA-detection probe (both 35nM in 5xSSCT, each complementary to one end of the LNA
oligonucleotide to be detected) was mixed with the diluted homogenates or relevant standards,
incubated for 30 minutes at RT and then added to a streptavidine-coated ELISA plates (Nunc
cat. no. 436014).
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The plates were incubated for 1 hour at RT, washed in 2xSSCT (300mM sodium chloride,
30mM sodium citrate and 0,05% v/v Tween-20, pH 7.0) The captured LNA duplexes were
detected using an anti-DIG antibodies conjugated with alkaline phosphatase (Roche Applied
Science cat. No. 11093274910) and an alkaline phosphatase substrate system (Blue Phos
substrate, KPL product code 5000). The amount of oligo complexes was measured as
absorbance at 615 nm on a Biotek reader.
For RNA extraction, cellular RNA large volume kit (05467535001, Roche) was used in the
MagNA Pure 96 system with the program: Tissue FF standard LV3.1 according to the
instructions of the manufacturer, including DNAse treatment. RNA quality control and
concentration were measured with an Eon reader (Biotek). The RNA concentration was
normalized across samples, and subsequent cDNA synthesis and qPCR was performed in a
one-step reaction using qScript XLT one-step RT-qPCR ToughMix Low ROX, 95134-100
(Quanta Biosciences). The following TaqMan primer assays were used in a duplex reaction:
Htra1, Rn00581870_m1 and Rn00668987_m1 and housekeeping genes, HPRT,
Rn01527840_m1 and Tbp, Rn01455646_m1, from Life Technologies. The qPCR analyses were
run on a ViiA7 machine (Life Technologies). Rats/group: 5, n=10 eyes. Each eye was treated as
an individual sample. The relative Htra1 mRNA expression level is shown as % of control (PBS).
Histology
Both eyeballs of the 2 remaining animals of high dose and PBS animals were removed and
fixed in 10% neutral buffered formalin for 24 hours, trimmed and embedded in paraffin.
For ISH analysis, sections of formalin-fixed, paraffin-embedded rat retina tissue 4um thick were
processed using the fully automated Ventana Dicovery ULTRA Staining Module (Procedure:
mRNA Discovery Ultra Red 4.0 – v0.00.0152) using the RNAscope 2.5 VS Probe-Rn-HTRA1
(Cat No. 440959, Advanced Cell Diagnostic). Chromogen used is Fastred, Hematoxylin II
counterstain.
Example 11
PoC study, Blue Light-induced retinal degeneration in albino rats
Animals
All experiments were performed on albino Sprague-Dawley rats. Sixteen animals were included
in each group of the study, 42 in total.
Compounds and dosing procedures
The animals were anesthetized with an intramuscular injection of a mix of xylazine and
ketamine. The test item and negative control (PBS) were administered intravitreally in both eyes
of anesthetized animals (3 µL per administration) on study day -3.
The positive control item (PBN) was injected intraperitoneally on Day 0, 4 times (0.5 h before
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starting light exposure, 2 h and 4 h after starting light exposure and just after the end of light
exposure), at a dose volume of 2.5 mL/kg, using a 25-gauge needle mounted on a
1 mL- plastic syringe, protected from light.
Light exposure
The rats were dark adapted for 36 hours and then exposed to a continuous blue fluorescent
light (400 - 540 nm) in clear plastic cages for 6 hours. After exposure, the rats were placed in
dark room for 24 hours before returning to standard cyclic light conditions.
Electroretinogram (ERG)
Electroretinograms (ERGs) were be recorded at baseline and on Day 14 on both eyes after
overnight darkadaption. A-wave and b-wave amplitudes were measured for each ERG
recording
Euthanasia
At the end of the in-life phase (Day 14), the animals were anesthetized and euthanized by
intraperitoneal an overdose injection of pentobarbital.
Outer Nuclear layer (ONL) thickness measurements
From the 10 main animals of each group, both eyeballs were enucleated, fixed in Bouin
Hollande solution and embedded in paraffin. Thin sections (5 to 7 µm thick) were cut along the
vertical meridian and stained with Trichrome-Masson. ONL thickness was measured at seven
points (every 250 µm) from the optic nerve to the peripheral retina in each part (superior and
inferior) of the retina. The thickness of the outer nuclear layer was measured at each point and
the area under the curve (AUC) calculated.
Oligo content measurement and quantification of Htra1 RNA expression
Both eyeballs of 4 satellite animals from test article and PBS groups were used for bioanalysis..
Immediately after euthanasia, Vitreous (V), Retina (R) and Choroid (CH) were quickly and
carefully dissected out on ice and stored at -80°C until shipment. Retina sample was lysed in
700 µL MagNa Pure 96 LC RNA Isolation Tissue buffer and homogenized by adding 1 stainless
steel bead per 2 ml tube 2 x 1,5 min using a precellys evolution homogenizer followed by 30
min incubation at RT. The samples were centrifuges, 13000 rpm, 5 min. half was set aside for
bioanalysis and for the other half, RNA extraction was continued directly.
For bioanalysis, the samples were diluted 10-50 fold for oligo content measurements with a
hybridization ELISA method. A biotinylated LNA-capture probe and a digoxigenin-conjugated
LNA-detection probe (both 35nM in 5xSSCT, each complementary to one end of the LNA
oligonucleotide to be detected) was mixed with the diluted homogenates or relevant standards,
incubated for 30 minutes at RT and then added to a streptavidine-coated ELISA plates (Nunc
cat. no. 436014).
The plates were incubated for 1 hour at RT, washed in 2xSSCT (300mM sodium chloride,
30mM sodium citrate and 0,05% v/v Tween-20, pH 7.0) The captured LNA duplexes were
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detected using an anti-DIG antibodies conjugated with alkaline phosphatase (Roche Applied
Science cat. No. 11093274910) and an alkaline phosphatase substrate system (Blue Phos
substrate, KPL product code 5000). The amount of oligo complexes was measured as
absorbance at 615 nm on a Biotek reader.
For RNA extraction, cellular RNA large volume kit (05467535001, Roche) was used in the
MagNA Pure 96 system with the program: Tissue FF standard LV3.1 according to the
instructions of the manufacturer, including DNAse treatment. RNA quality control and
concentration were measured with an Eon reader (Biotek). The RNA concentration was
normalized across samples, and subsequent cDNA synthesis and qPCR was performed in a
one-step reaction using qScript XLT one-step RT-qPCR ToughMix Low ROX, 95134-100
(Quanta Biosciences). The following TaqMan primer assays were used in a duplex reaction:
Htra1, Rn00581870_m1 and Rn00668987_m1 and housekeeping genes, HPRT,
Rn01527840_m1 and Tbp, Rn01455646_m1, from Life Technologies. The qPCR analyses were
run on a ViiA7 machine (Life Technologies). Rats/group: 5, n=10 eyes. Each eye was treated as
an individual sample. The relative Htra1 mRNA expression level is shown as % of control (PBS).
Histology
Both eyeballs of the remaining 2 satellite animals from test article and PBS groups were
removed and fixed in 10% neutral buffered formalin for 24 hours, trimmed and embedded in
paraffin. ISH RNAscope was performed as described in example 10.
Example 12, Rat in vivo efficacy kinetic study, 3, 7 and 14 days of treatment, intravitreal
(IVT) injection, single dose.
Knockdown (KD) at mRNA level was observed in the retina for 2 selected HTRA1 LNA
oligonucleotides targeting the “hotspot” in human HTRA1 pre-mRNA between position 33042 –
33064 (SEQ ID NO 147). This was observed both with qPCR and ISH readouts (see figure 7A
and /B and the following table).
Residual mRNA Residual mRNA
level Stdev n level Stdev N
3 59 31 12 11 14 4
143.1 7 34 28 12 12 8 4
14 39 35 12 3 5 4
Compound ID
Days of treatment
qPCR
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3 30 29 12 7 5 4
145.3 7 35 32 12 4 3 4
14 30 21 12 10 9 4
The variation of the knockdown is relatively large, see the standard deviations listed in the table.
The variation seems to be at the administration level which can be seen when plotting a dose
response curve for oligo content vs. residual HTRA1 mRNA level (see figure 7C).
Animals
All experiments were performed on albino Sprague-Dawley rats.
Compounds and dosing procedures
The animals were anesthetized in isofluran.. The test item and negative control (PBS) were
administered intravitreally in both eyes of anesthetized animals (3 µL per administration) on
study day 1.
Euthanasia
At the end of the in-life phase (study day 4, 8 or 15) the rats were anesthetized and euthanized by decapitation.
Oligo content measurement and quantification of Htra1 RNA expression
Oligo content measurement and quantification of Htra1 mRNA expression was performed as
described in Example 10.
The relative residual Htra1 mRNA expression level is shown as % of control (PBS).
Histology
Histology was performed as described in Example 10.
Example 13. Cynomolgus monkey (non-human primate, NHP) in vivo pharmacokinetics
and pharmacodynamics (PK/PD) study, 21 days of treatment, intravitreal (IVT) injection,
single dose.
Knockdown was observed for 1 selected HTRA1 LNA oligonucleotide, 145.3, targeting the
“hotspot” in human HTRA1 pre-mRNA between position 33042 - 33064 both at mRNA in the
retina and at protein level in the retina and in the vitreous (see figure 8).
Animals
All experiments were performed on Cynomolgus monkeys (Macaca fascicularis).
Compounds and dosing procedures
Buprenorphine analgesia was administered prior to, and two days after test compound injection.
The animals were anesthetized with an intramuscular injection of ketamine and xylazine. The
test item and negative control (PBS) were administered intravitreally in both eyes of
anesthetized animals (50 µL per administration) on study day 1 after local application of
tetracaine anesthetic.
Euthanasia
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At the end of the in-life phase (Day 22) all monkeys were euthanized by intraperitoneal an
overdose injection of pentobarbital.
Oligo content measurement and quantification of Htra1 RNA expression by qPCR
Immediately after euthanasia, eye tissues were quickly and carefully dissected out on ice and
stored at -80°C until shipment. Retina sample was lysed in 700 µL MagNa Pure 96 LC RNA
Isolation Tissue buffer and homogenized by adding 1 stainless steel bead per 2 ml tube 2 x 1,5
min using a precellys evolution homogenizer followed by 30 min incubation at RT. The samples
were centrifuged, 13000 rpm, 5 min. Half was set aside for bioanalysis and for the other half,
RNA extraction was continued directly.
For bioanalysis, the samples were diluted 10-50 fold for oligo content measurements with a
hybridization ELISA method. A biotinylated LNA-capture probe and a digoxigenin-conjugated
LNA-detection probe (both 35nM in 5xSSCT, each complementary to one end of the LNA
oligonucleotide to be detected) was mixed with the diluted homogenates or relevant standards,
incubated for 30 minutes at RT and then added to a streptavidine-coated ELISA plates (Nunc
cat. no. 436014).
The plates were incubated for 1 hour at RT, washed in 2xSSCT (300mM sodium chloride,
30mM sodium citrate and 0,05% v/v Tween-20, pH 7.0) The captured LNA duplexes were
detected using an anti-DIG antibodies conjugated with alkaline phosphatase (Roche Applied
Science cat. No. 11093274910) and an alkaline phosphatase substrate system (Blue Phos
substrate, KPL product code 5000). The amount of oligo complexes was measured as
absorbance at 615 nm on a Biotek reader.
For RNA extraction, cellular RNA large volume kit (05467535001, Roche) was used in the
MagNA Pure 96 system with the program: Tissue FF standard LV3.1 according to the
instructions of the manufacturer, including DNAse treatment. RNA quality control and
concentration were measured with an Eon reader (Biotek). The RNA concentration was
normalized across samples, and subsequent cDNA synthesis and qPCR was performed in a
one-step reaction using qScript XLT one-step RT-qPCR ToughMix Low ROX, 95134-100
(Quanta Biosciences). The following TaqMan primer assays were used in singplex reactions:
Htra1, Mf01016150_, Mf01016152_m1 and Rh02799527_m1 and housekeeping genes,
ARFGAP2, Mf01058488_g1 and Rh01058485_m1, and ARL1, Mf02795431_m1, from Life
Technologies. The qPCR analyses were run on a ViiA7 machine (Life Technologies).
Eyes/group: n=3 eyes. Each eye was treated as an individual sample. The relative Htra1 mRNA
expression level is shown as % of control (PBS).
Histology
Eyeballs were removed and fixed in 10% neutral buffered formalin for 24 hours, trimmed and
embedded in paraffin.
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For ISH analysis, sections of formalin-fixed, paraffin-embedded retina tissue 4µm thick were
processed using the fully automated Ventana Dicovery ULTRA Staining Module (Procedure:
mRNA Discovery Ultra Red 4.0 – v0.00.0152) using the RNAscope 2.5 VS Probe- Mmu-
HTRA1, REF 486979, Advanced Cell Diagnostics, Inc.. Chromogen used is Fastred,
Hematoxylin II counterstain.
HTRA1 protein quantification using a plate-based immunoprecipitation mass
spectrometry (IP-MS) approach
Sample preparation, Retina
Retinas were homogenized in 4 volumes (w/v) of RIPA buffer (50 mM Tris-HCl, pH 7.4, 150 mM
NaCl, 0.25% deoxycholic acid, 1% NP-40, 1mM EDTA, Millipore) with protease inhibitors
(Complete EDTA-free, Roche) using a Precellys 24 (5500, 15 s, 2 cycles). Homogenates were
centrifuged (13,000 rpm, 3 min) and the protein contents of the supernatants determined
(Pierce BCA protein assay)
Sample preparation, Vitreous
Vitreous humors (300 μl) were diluted with 5x RIPA buffer (final concentration: 50 mM Tris-HCl,
pH 7.4, 150 mM NaCl, 0.25% deoxycholic acid, 1% NP-40, 1mM EDTA) with protease inhibitors
(Complete EDTA-free, Roche) and homogenized using a Precellys 24 (5500, 15 s, 2 cycles).
Homogenates were centrifuged (13,000 rpm, 3 min) and the protein contents of the
supernatants determined (Pierce BCA protein assay)
Plate-based HTRA1 immunoprecipitation and tryptic digest
A 96 well plate (Nunc MaxiSorp) was coated with anti-HTRA1 mouse monoclonal antibody
(R&D MAB2916, 500 ng/well in 50 μl PBS) and incubated overnight at 4ºC. The plate was
washed twice with PBS (200 μl) and blocked with 3% (w/v) BSA in PBS for 30 min at 20 ºC
followed by two PBS washes. Samples (75 μg retina, 100 μg vitreous in 50 μl PBS) were
randomized and added to the plate followed by overnight incubation at 4 ºC on a shaker (150
rpm). The plate was then washed twice with PBS and once with water. 10 mM DTT in 50 mM
TEAB (30 μl) were then added to each well followed by incubation for 1 h at 20 ºC to reduce
cysteine sulfhydryls. 150 mM iodoacetamide in 50 mM TEAB (5 μl) were then added to each
well followed by incubation for 30 min at 20 ºC in the dark in order to block cysteine sulfhydryls.
μl Digestion solution were added to each well (final concentrations: 1.24 ng/ μl trypsin, 20
fmol/ μl BSA peptides, 26 fmol/ μl isotope-labeled HTRA1 peptides, 1 fmol/ μl iRT peptides,
Biognosys) followed by incubation overnight at 20 ºC.
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HTRA1 peptide quantification by targeted mass spectrometry (selected reaction monitoring,
SRM)
Mass spectrometry analysis was performed on an Ultimate RSLCnano LC coupled to a TSQ
Quantiva triple quadrupole mass spectrometer (Thermo Scientific). Samples (20 μL) were
injected directly from the 96 well plate used for IP and loaded at 5 μL/min for 6 min onto a
Acclaim Pepmap 100 trap column (100 μm x 2 cm, C18, 5 μm, 100 Å, Thermo Scientific) in
loading buffer (0.5% v/v formic acid, 2% v/v ACN). Peptides were then resolved on a PepMap
Easy-SPRAY analytical column (75 μm x 15 cm, 3 μm, 100 Å, Thermo Scientific) with integrated
electrospray emitter heated to 40ºC using the following gradient at a flow rate of 250 nL/min: 6
min, 98% buffer A (2% ACN, 0.1% formic acid), 2% buffer B (ACN + 0.1% formic acid); 36 min,
% buffer B; 41 min, 60% buffer B; 43 min, 80% buffer B; 49 min, 80% buffer B; 50 min, 2%
buffer B. The TSQ Quantiva was operated in SRM mode with the following parameters: cycle
time, 1.5 s; spray voltage, 1800 V; collision gas pressure, 2 mTorr; Q1 and Q3 resolution, 0.7
FWHM; ion transfer tube temperature 300 ºC. SRM transitions were acquired for the HTRA1
peptide “LHRPPVIVLQR” and an isotope labelled (L-[U-13C, U-15N]R) synthetic version, which
was used an internal standard. Data analysis was performed using Skyline version 3.6.
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Claims (17)
1. An antisense oligonucleotide of formula: T A T t t a c c t g g t T G T T (SEQ ID NO s s s s s s s s s s s s s s s 143), wherein a capital letter represents an LNA nucleoside unit, a lower case letter represents a DNA nucleoside unit, subscript s represents a phosphorothioate internucleoside linkage.
2. The antisense oligonucleotide according to claim 1, wherein the LNA nucleosides are all beta-D-oxy LNA nucleosides.
3. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide is of formula
4. The pharmaceutically acceptable salt of the antisense oligonucleotide according to any one of claims 1 - 3.
5. The pharmaceutically acceptable salt according to claim 4, wherein the salt is a sodium salt.
6. The pharmaceutically acceptable salt according to claim 4, wherein the salt is a potassium salt.
7. The pharmaceutical composition comprising the antisense oligonucleotide according to any one of claims 1 – 3; and a pharmaceutically acceptable diluent, carrier, salt and/or adjuvant. P33710-WO
8. The pharmaceutical composition according to claim 7, wherein the pharmaceutical composition comprises a pharmaceutically acceptable diluent.
9. The pharmaceutical composition according to claim 8, wherein the pharmaceutically acceptable diluent is phosphate buffered saline.
10. The pharmaceutical composition according to any one of claims 7 – 9, wherein the oligonucleotide is in the form of a pharmaceutically acceptable salt.
11. A pharmaceutical composition comprising the pharmaceutically acceptable salt according to any one of claims 4 – 6; and a pharmaceutically acceptable diluent, carrier, salt and/or adjuvant.
12. The pharmaceutical composition according to any one of claims 7 - 11, wherein the pharmaceutically acceptable salt is a sodium salt or a potassium salt.
13. The antisense oligonucleotide according to any one of claims 1 – 3, or the pharmaceutically acceptable salt according to any one of claims 4 – 6, or the pharmaceutical composition according to any one of claims 7 – 12, for use in medicine.
14. The antisense oligonucleotide according to any one of claims 1 – 3, or the pharmaceutically acceptable salt according to any one of claims 4 – 6, or the pharmaceutical composition according to any one of claims 7 – 12, for use in the treatment of macular degeneration.
15. The use of the antisense oligonucleotide according to any one of claims 1 – 3, or the pharmaceutically acceptable salt according to any one of claims 4 – 6, or the pharmaceutical composition according to any one of claims 7 – 12, for the preparation of a medicament for treatment or prevention of macular degeneration.
16. The antisense oligonucleotide, pharmaceutically acceptable salt, pharmaceutical composition, use or method according to any one of claims 13 – 15, wherein the disease is selected from wetAMD, dryAMD, geographic atrophy, and intermediate dAMD.
17. An in vitro method for modulating HTRA1 expression in a target cell which is expressing HTRA1, said method comprising administering an antisense oligonucleotide according to any one of claims 1 – 3, or the pharmaceutically acceptable salt according to any one of claims 4 – 6, or the pharmaceutical composition according to any one of claims 7 – 12 in an effective amount to said cell. P33710-WO
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
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EP16177508.5 | 2016-07-01 | ||
EP17170129.5 | 2017-05-09 |
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NZ749395A true NZ749395A (en) |
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