Title of Invention

POTENT LNA OLIGONUCLEOTIDES FOR THE INHIBITION OF HIF-1A EXPRESSION

Abstract The present disclosure relates to an LNA oligonucleotide consisting of a sequence selected from the group consisting of 5'-(Tx GxGxcsasasasgscsastscscsTxGx T-3' and 5'-(Gx )TxTxascstsgscscststscsTxTx A-3', wherein capital letters designate a beta-D-oxy-LNA nucleotide analogue, small letters designate a 2-deoxynucleotide, underline designates either a beta-D-oxy-LNA nucleotide analogue or a 2-deoxynucleotide, subscript "s" designates a phosphorothioate link between neighbouring nucleotides/LNA nucleotide analogues, and subscript "x" designates either a phosphorothioate link or a phosphorodiester link between neighbouring nucleotides/LNA nucleotide analogues, and wherein the sequence is optionally extended by up to five 2-deoxynucleotide units. The LNA oligonucleotides are useful for modulating the expression of hypoxia-inducible factor-1a (HIF-1a), e.g. in the treatment of cancer diseases, inhibiting angiogenesis, inducing apoptosis, preventing cellular proliferation, or treating an angiogenic disease, e.g. diabetic retinopathy, macular degeneration (ARMD), psoriasis, rheumatoid arthritis and other inflammatory diseases.
Full Text WO 2006/050734 PCT/DK2005/000721
POTENT LNA OLIGONUCLEOTIDES FOR THE INHIBITION OF HIF-1A EXPRESSION
FIELD OF THE INVENTION
The present invention provides compositions and methods for modulating the expression of
HIF-1a. In particular, this invention relates to LNA oligonucleotides, which are specifically
hybridisable with nucleic acids encoding HIF-la. The LNA oligonucleotides have been shown
to modulate the expression of HIF-1a and pharmaceutical preparations thereof and their use
as treatment of cancer diseases, inflammatory diseases and eye diseases are disclosed.
BACKGROUND OF THE INVENTION
Solid tumors must establish a blood supply and have enhanced glucose metabolism to grow
beyond a few millimeters. How they sense hypoxia, and respond by activating hypoxia-
inducible genes and secreting angiogenrc factors to establish a blood system is central to
cancer biology. Many tumors contain hypoxic microenvlronments, which have been
associated with malignant progression, metastasis and resistance to radiotherapy and
chemotherapy.
The discovery of hypoxia-inducible factor-1 (HIF-1) gave some insight into the regulation of
hypoxia-mducible genes (US 5,882,914 and WO 96/39426; WO 99/48916). HIF-1 is
composed of two subunits HIF-la (HIF-lalpha; referred to herein as "HIF-la") and HIF-ip
and it binds - 1 hypoxia-response elements (HREs) in enhancers of genes encoding
angiogenic factors such as VEGF and glycolysis-related proteins such as glycolytic enzymes
and glucose transporter 1 and 3 (GLU-1 and 3).
It has been demonstrated that engineered down-regulation of HIF-la by intratumoral gene
transfer of an antisense HIF-la plasmid leads to the down-regulation of VEGA and decreased
tumor microvessel density (WO 00/76497, Sun X et al. Gene Therapy (2001) 8, 638-645).
The plasmid contained a 320-bp cDNA fragment encoding 5'-end of HIF-la (nudeotldes 152-
454; Genebank AF003698).
WO 2003/085110 shows LNA antisense oligonucleotides which down-regulates human HIF-la
expression. One compound Is named CUR813 (SEQ ID NO. 11).
The present invention disclosed LNA oligonucleotides, which are more potent than CUR813
(SEQ ID NO. 11). Also the specific LNA oligonucleotides, according to the Invention, induce

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apoptosis and inhibit proliferation. Also, the LNA oligonucleotides which have a 100%
sequence identity to the mouse HIF-la down-regulate the HIF-la expression in the liver,
colon and kidney in mice.
SUMMARY OF THE INVENTION
The present invention provides compositions and methoos for modulating the expression of
HIF-la. In particular, this invention relates to LNA oligonucleotides over 2 specific motifs
targeting HIF-la. These motifs are disclosed as SEQ ID NOS. 3.and 4. Specifically preferred
LNA oligonucleotides are SEQ ID NO. 1 and SEQ ID NO. 2. The LNA oligonucleotides of the
invention are potent inhibitors of HIF-la mRNA expression and protein levels.
More particularly, the present invention provides an LNA oligonucleotide consisting, of a
sequence selected from the group consisting of

wherein capital letters designate a beta-D-oxy-LNA nucleotide analogue, small letters
designate a 2-deoxynucleotide, underline designates either a beta-D-oxy-LNA nucleotide
analogue or a 2-deoxynucleotide, subscript "s" designates a phosphorothioate link between
neighbouring nucleotides/LNA nucleotide analogues, and subscript "x" designates either a
phosphorothioate link or a phosphorodiester link between neighbouring nucleotldes/LNA
nucleotide analogues, and where the nucleotide units in the bracket, (Ix), (T) or (Gx), (A),
respectively, represent optional units, and
wherein the sequence is optionally extended by up to five 2-deoxynucleotide units.
Pharmaceutical compositions comprising the LNA oligonucleotide of the invention are also
provided. Further provided are methods of modulating the expression of HIF-la in cells or
tissues comprising contacting said cells or tissues with one or more of the LNA
oligonucleotides or compositions of the invention. Also disclosed are methods of treating an
animal or a human, suspected of having or being prone to a disease or condition, associated
with expression of HIF-la by administering a therapeutlcally or prophylactically effective
amount of one or more of the LNA oligonucleotides or compositions of the invention. Further,

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methods of using LNA oltgonucleatides for the Inhibition of expression of HIF-la and for .
treatment of diseases associated with HIF-la activity are provided.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1A shows an increased stability of SEQ ID NO. 1 and SEQ ID NO. 5 in rat plasma
(NtacSD male, Li-Heparine (Taconlc, M&B)) compared to SEQ ID NO. 6. The ohgonucteotides
were incubated at 20 uM concentrations-at370C for Q-f 4-, .or 24-hours. No degradation
fragments of SEQ ID NO. 1 can be detected even after 24 hours digestion.
Figure 1B shows Stability of Full length SEQ ID NO- 1 and.SEQ ID NO. 13, a phosphorothioate
and (so-sequential .to SEQ ID NO- 1,. in Rat and Human serum. Oltgonucleotides were added
to human or rat serum at a final concentration of 20 uM. The figure shows LNA oligonucletide
stability up to 1-96 hours in respectively human and rat serum at 37 °C. For rat serum, the
second last panel in Figure IB demonstrates sustained enzyme activity even after 48 hours
and 96 hours. The latter panel function as a negative control demonstrating no degradation
of SEQ ID NO. 1 and SEQ ID NO. 13 when incubated at 37°.C without plasma added.
Figure 1C shows extremely long stability of SEQ ID NO. 1 in human and rat plasma. The ■
oligonucleotide was incubated in human or rat plasma for 1-96 hours and run on a
denaturing gel. Following staining with SyBr gold the amount of full length product was
measured by using a phosphonmager and plotted against time.
Figure 2A shows HIF-la protein down-regulation in LNA oligonucleotides transfected U373
cells. U373 cell were transfected with 2 or 10 nM compound or mock transfected, incubated
at hypoxia and analysed for HIF-1a protein down-regulation by Western blotting. Tubuiin
expression was analysed as control of equal loading.
Figure 2B shows HIF-lalfa protein down-regulation following treatment with SEQ ID NO. 1 in
U373 glioblastoma cancer cell lines. Pan-actin expression was analysed as control of equal
loading. Cells were transfected with 0.2, 1 and 10 nM SEQ ID NO. 1 or SEQ ID NO. 10, which
is a 2bp mm to SEQ ID NO. 1. The lower panel is a quantification of the gel.
Figure 2C shows down-regulation of HIF-a expression 24 hours following treatment with the
HIF-la targeting LNA oligonucleotide, SEQ ID NO. 1, and a LNA containing scrambled control
oligonucleotide SEQ ID NO. 8 in U373 cells. The HIF expression is correlated to either GAPDH
or Beta-actin and related to an untransfected control (mock). Following RNA purification,
mRNA expression is quantified by QPCR.

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Figure 3A and 3B shows induction of apoptosis measured as a kinetic profile of induced
Caspase 3/7 activity following 24-72 hours treatment with LNA oligonudeotides in
gliobtastoma cell line U373 at normoxia or hypoxia. SEQ ID NO. 1 is shown to be a potent
inducer of early apoptosis.
Figure 4A: Induction of early-apoptotic cell stage measured by Annexin V-FITC and PI flow
cytometry analysis after 48 hours. The U373 cells treated with the LNA oligonucleotide SEQ
ID NO. 1 were classified as more "early apoptotic" compareo to mock and SEQ ID NO. 12
treated cells.
Figure 4B: Quantification of induction of early apoptosis in U373 cells following treatment
with SEQ ID NO. 1. Percentage of cells forced into earty apoptosis 48 hours following
treatment of SEQ ID NO. 1 in different dosages. U373 cells were.transfected with SEQ ID NO.
1 or two different scrambled control oligonucleotides SEQ ID NO. 8 and SEQ ID NO. 12.
Following harvest and incubation with Annexin V ab and PI, the number of cells in early
apoptosis was measured by Flow cytometry.
Figure 5A and 5B shows compounds transfected gliobiasrama cell line U373 cells 24-72 hours
after transfection and incubation at either hypoxia or normoxia. SEQ ID NO. 1 Is shown to be
a potent inhibitor of proliferation as measured by MTS assay.
Figure 6A and Figure 6B show In vivo endogenous liver target down-regulation of two
administration regimens using SEQ ID NO. 1. Measuring mRNA levels of HIF-la as well as the
downstream target VEGF shows that SEQ ID NO. 1 is also an effective Inhibitor of said target
Figure 6A: Ip injections daily in hairy mice for 14 days. Hgure 6B: ip injections twice weekly
in hairy mice for 14 days.
Figure 6C shows in vivo endogenous kidney HIF-la after down-regulation administered ip
injections daily in hairy mice for 14 days regimens of SEQ ID NO. 1.
Figure 7A shows that SEQ ID NO. 1 is a potent inhibitor measured by down-regulation of in
vivo expression of HIF-la in liver following administration of SEQ ID NO. 1. Different
thiolated versions of SEQ ID NO. 1 (SEQ ID NO. 5 and SEQ ID NO. 6) and SEQ ID NO. 1
respectively were dosed to hairy mice at 18 or 3.6 mg/kg dally for 14 days and sacrificed.
Expression of HIF-la was measured at mRNA level by QPCR and normalised to beta-actin as
described in M&M.
Figure 7B shows that SEQ ID NO. 1 is also a potent inhibitor measured by down-regulation of
in vivo expression of HIF-la in liver following administration of SEQ ID NO. 1. Different

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thiolated versions of SEQ ID NO. 1 (SEQ ID NO. 5 and SEQ ID NO. 6} and SEQ ID NO. 1
respectively were dosed to hairy mice at 50, 10 or 2 mg/kg twice a week for 14 days and
sacrificed. Expression of HIF-la was measured at mRNA level by QPCR and normalised to
beta-actin.
Figure 7C shows down-regulation of in-vivo expression of HIF-la in kidney following
administration of SEQ ID NO. 1. Different thiolated versions of SEQ ID NO. 1 (SEQ ID NO. 5
and SEQ ID NO. 6) were dosed to hairy mice at 18 or 3.6 mg/kg daily for 14 days and.
sacrificed. Expression of HIF-1a was measured at mRNA level by QPCR and normalised to
beta-actin.
Figure 8A shows superior in vivo efficacy using SEQ ID NO. 1 compared to SEQ ID NO. 11
and SEQ ID NO. 12 (a scrambled control) measured by tumor-weight of U373 tumors from
xenograft. SEQ ID NO. 1, SEQ ID NO. 11 and SEQ ID NO. 12 were dosed at 50 mg/kg twice a
week for one week in U373 xenograft mice implanted at the ovaries. 2 days following the last
dose animals was sacrificed. At sacrifice tumors were weighed and the individual tumor
weight plus the mean tumor weight (red) was calculated and plotted. A statistical significant
difference (P=0.005) was found between the Control group (a scrambled contra! SEQ ID NO.
12) and the mice treated with a SEQ ID NO. 1.
Figure 8B shows vessel density in U373 tumors from xenograft treated with SEQ ID NO. 1.
SEQ ID NO. 1 was dosed at 50 mg/kg twice a week for one week in U373 xenograft mice
implanted at the ovaries. 2 days following the last dose, animals was sacrificed. Vessel-
density was calculated following CD31 staining and related to the total area. A statistical
significant difference (P=0.005) was found between the saline group and the mice treated
with a scrambled control (SEQ ID NO. 12).
Figure 8C shows staining of CD 31 in sections from U373 tumors implanted at the ovaries
and treated with SEQ ID NO. 1 as described for Figure 8B.
Figure 8D shows HIF-la expression quantified by real-time PCR and normalised to GAPDH in
U373 tumors implanted at the ovaries and treated with SEQ ID NO. 1, SEQ ID NO. 11, SEQ
ID NO. 12 and PBS as described for Figure 8B.
Figure 9A shows in vivo uptake (in ug per gram tissue) plus target down-regulation (%
inhibition of HIF-la mRNA expression correlated to B-actin expression) of hairy mice following
one i.v. dose of SEQ ID NO. 1 of 25mg/kg. SEQ ID NO. 1 has a half-life of approximately 46
hours in kidney and 66 hours in the liver. Figure 9B upper panel shows SEQ ID NO. 1 dosed
at 50 mg/kg once i.p. in hairy mice. Five animals treated with SEQ ID NO. 1 at 50 mg/kg

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were sacrificed following 1, 3, 4, 5 and 8 days after treatment and HIF-la expression was
analysed and normalised to Beta-actin. Expression of HIF-la was measured at mRNA level dy
QPCR and normalised to beta-actin as described in example 8. In the lower panel 5EQ ID NO.
1 was dosed at 25 or 50 mg/kg once i.v. in hairy mice. Five animals treated with SEQ ID NO.
1 at 25 or 50 mg/kg were sacrificed following 1, 2, 3, 4, 5 and 8 days after treatment and
were analysed for full length SEQ ID NO. 1 by HPLC methods as described in exampiel3.
Data are presented as μg SEQ ID NO. 1/gram tissue..
Figure 9C shows HIF-lo expression quantified by real-time PCR and normalised to GAPDH in
mouse liver in mice receiving one dose of 50 mg/kg i.p.of SEQ ID NO. 1 and SEQ ID NO. 16
and sacrificed at day 1 and 10.
Figure 10A shows duration of action of SEQ ID NO. 1 inhibiting HIF-la expression in
xenograft mice dosed 25 mg/kg for 7 days and sacrificed 1 or 5 days after the last dose.
Figure 10B shows in vivo liver, skin tumor and kidney uptake of fam-labeted version of SEQ
ID NO. 1 (SEQ ID NO. 7) at 25 mg/kg/day for seven days and sacrificed 5 days following the
last treatment.
Figure 10C shows target down-regulation (% inhibition of HIF-la mRNA expression correlated
to GAPDH expression) plus in vivo uptake (in ug per gram tissue) of SEQ ID NO. 7 in the liver
of xenograft mice treated with 5 mg/kg/day SEQ ID NO.7, scrambled control SEQ ID NO. 20
or saline t.p. on days 7, 10, 13 and 17 after transplantation as described.in example 17.
Figure 10D shows target down-regulation (% inhibition of HIF-la mRNA expression
correlated to p-actin expression) after treatment with SEQ ID NO. 7 or scrambled control SEQ
ID NO. 20 plus in vivo uptake (in ug per gram tissue) of SEQ ID NO. 7 in mouse colon treated
as described in example 17.
Figure 10E shows in vivo uptake (in ug per gram tissue) of SEQ ID NO. 7 in xenograft tumors
HT29 and PC3 treated as described in example 17.
Figure 11 shows in vivo endogenous liver target down-regulation of HIF-la and VEGF mRNA
after 5 doses of 30 mg/kg every 3rd day of SEQ ID NO. 1 compared to the one mismatch
control SEQ ID NO. 9.
Figure 12A, Figure 12B, Figure 12C and Figure 12D shows expression of VEGFA and MMP-2
following treatment with the HIF-la targeting LNA oligonucleotide, SEQ ID NO. 1, and a
scrambled control SEQ ID NO. 8 in U373 cells. A dose -dependent down-regulation in VEGFA

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and MMP-2 expression (secretion) is observed 48 hours following treatment with SEQ ID NO.
1 or a scrambled control (SEQ ID NO. 8) in U373 cells. The VEGFA (Figures 12A, 12B.and
12C) and MMP-2 (Figures 12D and 12E) expression is related to cell number and normalized
to mock. In Figures 12A, 12C and 12D VEGFA and-MMP-2 expression is-measured 48 hours
following treatment, whereas in Figures 12 B and 12E secretion of VEGFA and MMP-2 is
quantified 24-120 hours following tranfection.
Figure 13 shows down-regulation of HIF-1a protein msasjred by western blot and disruption
of tube formation of HUVEC cells treated with SEQ ID NO. 1 at 1 and 5 nM compared to SEQ
ID NO. 8 and untreated control.
Frgure 14A Whole body radioluminograms showing the distribution of radroactivity at 5
minutes a), 4 hours b). 24 hours c) and 18 days d) after a single intravenous administration
of 3H- labelled SEQ ID NO. 1 in female pigmented mice.
Figure 14B shows the distribution of radioactivity at 5 minutes and 7 days and that a very
strong retention of the JH- labelled SEQ ID NO. 1 compound is observed in bone marrow,
kidney, liver, lung, skin, spleen, unne, gastric mucosa, lymph node, uvea of the eye and.
uterus after 7 days.
Figure 15 shows uptake of a FAM-labelled version of SEQ ID NO. 1 (SEQ ID NO, 7) in
different cell types within bone marrow, spleen and peripheral blood-1 hour following
administration of SEQ ID NO. 7 compared to untreated ceils measured by FACS analysis.
Figure 16A shows HIF-la expression measured by real-time PCR and normalised to 18S RNA
in the liver and kidney of cynomolgus monkeys treated with 40, 10 and 6mg/kg SEQ ID NO.
1 twice a week for 4 weeks. Figure 16B shows uptake of SEQ ID NO. 1 in liver and kidney of
cynomolgus monkeys one day following the last dose or 4 weeks following the last dose
(recovery animals) treated as described above together with data on recovery animals (R),
which were left untreated for 4 weeks after end of treatment.
DESCRIPTION OF THE INVENTION
The present invention employs particular LNA oligonucleotides, namely LNA oligonucleotides
comprising the sequence SEQ ID NO. 3 and SEQ ID NO. 4, for use in modulating the function
of nucleic acid molecules encoding HIF-la. The modulation is ultimately a change in the
amount of HIF-la produced. In one embodiment, this is accomplished by providing antisense
LNA oligonucleotides, which specifically hybridise with nucleic acids encoding HIF-la. The

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modulation is preferably an inhibition of the expression of BIF-1a, which leads to a decrease
in the number of functional HIF-1a proteins produced.
The LNA oligonucleotides
More particular, the present invention provides an LNA oligonucleotide consisting of a
sequence selected from the group consisting of

wherein capital letters designate a beta-D-oxy-LNA nucleotide analogue, small letters
designate a 2-deoxynudeotide, underline designates either a beta-D-oxy-LNA nucleotide
analogue or a 2-deoxynucleotide, subscript "s" designates a phosphorothioate link between
neighbouring nucteotides/LNA nucteotidc analogues, and subscript "x" designates either a
phosphorothioate link or a phosphorodiester link between neighbouring nucleottdes/LNA
nucleotide analogues, and where the nucleotide units in the bracket, (Ix), (T), or (£x),(A),
respectively, represent optional units, and
wherein the sequence is optionally extended by up to five 2-deoxynucleotide units.
The terms "LNA oligonucleotide defined herein", "LNA oligonucleotide according to the
invention", and the like, refer to the "LNA oligonucleotide" defined above as well as the
embodiments, variants, salts, prodrugs, etc. provided in the following.
The above-defined LNA oligonucleotides based on SEQ ID NO. 3 and SEQ ID NO. 4 have a
length of 13-20 nucleotide units. The minimal sequence length of 13 is obtained if the
nucleotide units in the bracket, (Tx), (T) or (Gx), (A), respectively, are absent, and the
maximum sequence length of 20 is obtained if the nucleotide units in the bracket, (Tx), (T) or
(Gx), (A), respectively, are present and if the sequence SEQ ID NO. 3 or SEQ ID NO. 4 is
extended by five 2-deoxynucleotide units.
In one embodiment, the nucleotide units In the bracket, (Tx), (T) or (Gx), (A), respectively,
are absent, and in another currently more preferred embodiment, the nucleotide unit in the
bracket, (Tx), (T) or (Gx), (A), respectively, are present. Also interesting are the

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embodiments, where the 5'-terminal optional unit, (Tx) or (Gx), respectively, is present and
where the 3'-terminal optional unit, (T) or (A), respectively, is absent, and the embodiments
where the 5'-terminal optional unit, (Tx) or (Gx), respectively, is absent and where the S'-
terminal optional unit, (T) or (A), respectively, is present.
The selection of a beta-D-oxy7LNA.nucleotide analogue or a 2-deoxynucleotfde for the
underlined nucleotide units in the above SEQ ID NO. 3 and SEQ ID NO. 4 appears to be less
critical. However, in one embodiment, both-of the underlined- nudeotide units designate a 2-
deoxynucleotide. In another currently more preferred embodiment, one or both of the
underlined nucteotide units designate a beta-D-oxy-LNA nucleatide analogue.
In one variant, the S'-terminal nucleotide unit tn the bracket, (Tx) or (Gx), respectively, is
absent, and the 3'-terminal other underlined nucleotide unit, (I) or (A), respectively,
designates a 2-deoxynucleotide, or more preferable, a beta-D-oxy-LNA nucleotide analogue.
In another variant, the 5'-terminal nucleotide unit in the bracket, (Tx) or (Gx), respectively,
designate a 2-deoxynucleotide, or, more preferable, a beta-D-oxy-LNA nucleotide analogue,
and the 3'-terminal other underlined nucleotide unit, (T) or (A), respectively, is absent.
In another variant, the nucleotide units in the bracket are present, and one or both of the
underlined nucteotide units designate a beta-D-oxy-LNA nucleotide analogue, i.e. (i) the S'-
terminal underlined nucleotide designates a beta-D-oxy-LNA nudeotide analogue and the S'-
terminal underlined nucleotide units designates a 2-deoxynucleotide, or (ii) the 3'-terminal
underlined nucleotide designates a beta-D-oxy-LNA nucleotide analogue and the 5'-termmal
underlined nucleotide units designates a 2-deoxynucleotide, or (iii) the 3'-termlnal as well as
the 5'-terminal underlined nucleotides designate a beta-D-oxy-LNA nucleotide analogue.
In a further variant, the nucleotide units in the bracket, (Tx) or (Gx), respectively, is present,
and both of the underlined nucleotide units designate a 2-deoxynucleotide.
Although the sequences referred to as SEQ ID NO. 3 and SEQ ID NO. 4 (and more particular
the sequences referred to as SEQ ID NO. 1 and SEQ ID NO. 2 (see further below)) are
believed to substantially represent the full functionality of the defined LNA oligonucleotides,
extension of SEQ ID NO. 3 and SEQ ID NO. 4 with up to five 2-deoxynucleotide units, e.g. 1
unit, 2 units, 3 units, 4 units, or even 5 units, is believed to be possible without detrimental
effects on the beneficial properties of the base sequences, SEQ ID NO. 3 and SEQ ID NO. 4.
This being said, the sequence may be extended at the 3'-terminal end, the 5'-terminal end or
at the 3'-terminal end as well as at the 5'-terminal end, provided that the total number of 2-
deoxynucleotide units does not exceed 5.

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Hence, in one embodiment (which may be combined with the foregoing)the LNA
otigonucleotide consists of 15, 16, 17, 18, 19 or 20 nucleotide units selected from 2-
deoxynudeotides and beta-D-oxy-LNA nucleotide analogues, in particular the LNA
oligonucleotide consists of 16 nucleotide units selected from 2-deoxynucleotides and beta-D- ■
oxy-LNA nucleotide analogues. In other embodiments (which may be combined with the
foregoing) the LNA oligonucleotide consists of 13,14, 15, or 16 nucleotide units selected
from 2-deoxynudeotides and-beta-D-oxy-LNA nucleotide-analogues, in particular the LNA
oligonucleotide consists of 14 or 15 nucleotide units selected from 2-deoxynucleotides and
beta-D-oxy-LNA nucleotide analogues. -
At least for the sake of convenience in the preparation of the LNA oligonucleorides, it is often
preferred that the sequence is extended by one 2-deoxynucleotide unit at the 3'-end, cf.,
e.g., SEQ ID NO. 1 and SEQ ID NO. 2 below. Most preferable, SEQ ID NO. 3 is extended by
an adenosine 2-deoxynucleot)de unit at the 3'-cnd, and SEQ ID NO. 4 is extended by a
cytosine 2-deoxynuc!eotide at the 3'-end.
As mentioned above, subscript "s" designates a phosphorothioate (-O-P(O,S)-O-) link -
between neighbouring nudeotides/LNA nucleotide analogues, and subscript "x" designates
either a phosphorothioate (-O-P(O,S)-O-) link or a phosphorodiester (-O-P(O)2-O-) link
between neighbouring nudeotides/LNA nucleotide analogues. It follows that any 2-
deoxynudetides by which the sequence ts extended may be linked by either either a
phosphorothioate (-O-P(O,S)-O-) link or a phosphorodiester (-O-P(O)2-O-) link.
It is noted that subsequence CsasasgsastsCsCsT of SEQ ID NO. 3 and subsequence
asCstsgsCsCststsCsT of SEQ ID NO. 4 are indicated as fully phosphorothiolated, cf. subscript "s".
Although is it is not currently preferred, it is believed that one, and possibly also two, of the
phosphorothioate links may be replaced by other links, in particular phosphorodiester links,
without severely compromising the stability of the LNA oligonucleotide. Thus, such variants
where one or two of the phosphorothioate links are replaced by, e.g., phosphorodiester links
also fall within the intended scope of the present Invention.
In one currently preferred embodiment, however, all nucteotide units in the sequence are
linked by a phosphorothioate group.
One subgroup of particularly Interesting LNA oligonucleotides are those selected from the
group consisting of


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is currently most preferred.
Another subgroup of particularly interesting LNA oligonucteotides are those selected from the
group consisting of

In the present context, the term "nucleoside" Is used In its normal meaning, i.e. it contains a
2-deoxyribose or ribose unit which is bonded through its number one carbon atom to one of
the nitrogenous bases adenine (A), cytosine (C), thymine (T), uracil (U) or guanine (G).
In a similar way, the term "nudeotide" means a 2-deoxyribose or ribose unit which is bonded
through its number one carbon atom to one of the nitrogenous bases adenine (A), cytosine
(C), thymine (T), uracil (U) or guanine (G), and which is bonded through its number five
carbon atom to an internucleoside phosphate group, or to a terminal group.
The term "nucleic acid" is defined as a molecule formed by covalent linkage of two or more
nucleotides. The terms "nucleic acid" and "polynucleotide" are used Interchangeable herein.
The term "nucleic acid analogue" refers to a non-natural nucleic acid binding compound.

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The term "LNA monomer" typically refers to a bicyclic nucleoside analogue, as described in
International Patent Application: WO 99/14226 and. subsequent applications, WO 00/56746,
WO 00/56748, WO 00/66604, WO 00/125248, WO 02/28875, WO 2002/094250 and WO
03/006475 aii incorporated herein by reference.
Beta-D-oxy-LNA is the LNA nucleotlde analogue use-In the LNA oligonucleotidesof the
present invention, and the monomer structure (nucleoside) is shown in Scheme 1.

Beta-D-oxy-LNA
Scheme 1
In Scheme 1, Z* and Z indicate the position of a internucleotide linkage to a neighbouring
nucleoside or a terminal group (i.e. either a 5'-terminal group or a 3'-terminal group).
One particular example of beta-D-oxy-LNA monomer is the thymidine LNA monomer (LNA
nucleoside analogue) (1S,3R, 4R, 7S)-7-hydroxy-l-hydroxymethyl-5-methyl-3-(thymin-lyl)-
2,5-dioxa-bicyclo[2:2:l]heptane, i.e. T-beta-D-oxy-LNA.
The term "oligonucleotide" refers, in the context of the present invention, to an ollgomer
(also called oligo) or nucleic acid polymer (e.g. ribonucleic acid (RNA) or deoxyribonucleic
acid (DNA)) or nucleic acid analogue of those known in the art, preferably Locked Nucleic
Acid (LNA), or a mixture thereof. This term includes ollgonucleotldes composed of naturally
occurring nucleobases, sugars and internucleoside (backbone) linkages as well as
oligonucleotides having non-naturally-occurring portions which function similarly or with
specific improved functions. Fully or partly modified or substituted oligonucleotides are often
preferred over native forms because of several desirable properties of such oligonucleotides
such as for instance, the ability to penetrate a cell membrane, good resistance to extra- and
intracellular nucleases, high affinity and specificity for the nucleic acid target. The LNA
oligonucleotides of the invention exhibit the above-mentioned properties.

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By the terms "unit" and "nucteotide unit" Is understood a monomer, i.e. a 2-deoxynucleotide
or a beta-D-oxy-LNA nucieotlde analogue.
The term "at least one" comprises the integers larger than or equal to 1, such as 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 and so. forth.
The term "a" as used about a nuclcoside, a nucleoside analogue, a SEQ ID NO, etc. is
intended to mean one ormore. In particular, the expression "a component (such as a
nucteoside, a nucleoside analogue, a SEQ ID NO or the like) selected from the group
consisting of ..." is intended to mean that one or more of the cited components-may be
selected. Thus, expressions like "a component selected from the group consisting of A, B and
C" is intended to include all combinations of A, B and C, i.e. A, B, C, A+B, A+C, B+C and
A+B+C.
Throughout this specification, the word "comprise", or.variations such as "comprises" or
"comprising", will be understood to imply the inclusion of a stated element, integer or step,
or group of elements, integers or steps, but not the exclusion of any other element, integer
or step, or group of elements, integers or steps.
Preparation of the LNA oligonudeotides
The LNA nucleotide analogue building blocks (8-D-oxy-LNA) can be prepared following
published procedures and references cited therein, see, e.g., WO 03/095467 Al; D. S.
Pedersen, C. Rosenbohm, T. Koch (2002) Preparation of LNA Phosphoramidites, Synthesis 6,
802-808; and WO 2004/069991 A2.
The LNA oligonudeotides can be prepared HS described In the Examples and in WO 99/14226,
WO 00/56746, WO 00/56748, WO 00/66604, WO 00/125248, WO 02/28875, WO
2002/094250 and WO 03/006475. Thus, the LNA oligonudeotides may be produced using the
oligomerisation techniques of nucleic acid chemistry well-known to a person of ordinary skill
in the art of organic chemistry. Generally, standard oligomerisation cycles of the
phosphoramidite approach (S. L. Beaucage and R. P. Iyer, Tetrahedron, 1993, 49, 6123; S.
L. Beaucage and R. P. Iyer, Tetrahedron, 1992, 48, 2223) are used, but e.g. H-phosphonate
chemistry, phosphotriester chemistry can also be used.
For some monomers, longer coupling time, and/or repeated couplings and/or use of more
concentrated coupling reagents may be necessary or beneficial.

WO 2006/050734 PCT/DK2005/000721
14
The phosphoramidites employed couple typically with satisfactory >95% step-wise yields.
Oxidation of the phosphorous(lll) to phosphorous(V) is normally done with e.g.
iodine/pyridme/HzO. This yields after deprotection the native phosphorodiester
mtemucteoside linkage. In the case that a phosphorothioate internucleoside linkage is
prepared a thtoiation step is performed by exchanging the normal, e.g. iodine/pyridine/H2O,
oxidation used for synthesis of phosphorodiester internucleoside linkages with an oxidation
using the ADTT reagent (xanthane hydride (0.01 M in acetonitrile:pyridine 9:1; v/v)). Other
thiolation reagents are also possible to use, such as Beaucage and PADS. The
phosphorothioate LNA otiganucleotides were efficiently synthesized with stepwise coupling
yields >= 98%.
Purification of LNA oligonucleotides can be accomplished using disposable reversed phase
purification cartridges and/or reversed phase HPLC and/or precipitation from ethanol or
butanol. Capillary gel electrophoresis, reversed phase HPLC, MALDI-MS, and ESI-MS were
used to verify the purity of the synthesized LNA oligonucleotides.
Salts
The LNA oligonucleotide can be employed in a variety of pharmaceutically acceptable sails.
As used herein, the term refers to salts that retain the desired biological activity of the LNA
oligonucleotide and exhibit minimal undesired toxicological effects. Non-limiting examples of
such salts can be formed with organic amfno acid and base addition salts formed with metal
cations such as zinc, calcium, bismuth, barium, magnesium, aluminum, copper, cobalt,
nickel, cadmium, sodium, potassium, and the like, or with a cation formed from ammonia,
/V,/V-dlbenzylethylene-diamine, D-glucosaminer tetraethylammonium, or ethylenediamine; or
combinations, e.g., a zinc tannate salt or the like.
Such salts are formed, from the LNA oligonucleotide which possess phosphorodiester group
and/or phosphorothioate groups, and are, for example, salts with suitable bases. These salts
include, for example, nontoxic metal salts which are derived from metals of groups la, Ib, Ha
and lib of the Periodic System of the elements, in particular suitable alkali metal salts, for
example lithium, sodium or potassium salts, or alkaline earth metal salts, for example
magnesium or calcium salts. They furthermore include zinc and ammonium salts and also
salts which are formed with suitable organic amines, such as unsubstituted or hydroxyl-
substituted mono-, di- or tri-alkylamines, in particular mono-, di- or trl-alkylamines, or with
quaternary ammonium compounds, for example with N-methyl-N-ethylamine, diethylamlne,
triethylamine, mono-, bis- or tns-(2-hydroxy-lower alkyl)amines, such as mono-, bis- or tris-
(2-hydroxyethyl)amine, 2-hydroxy-tert-butyiamine or tris(hydroxymethyl)methylamine, N,N-

WO 2006/050734 PCT/DK2005/000721
15
di-lower alkyl-N-(hydroxy-lower alkyt)amlnes, such as N,N-dimethyl-N-(2-hydroxyethyl)-
amine or tri-(2-hydroxyethyl)amine, or N-metnyl-D-glucamine, or quaternary ammonium
compounds such as tetrabutytammonium salts. Lithium salts, sodium salts, magnesium salts,
zinc salts or potassium salts are preferred, with sodium salts being particularly preferred.
Prodrugs
In one embodiment, the LNA oligonucleotide may be in the form of a pro-drug.
Oligonucleotides are by virtue negatively charged ions. Due to the lipophilic nature of cell
membranes, the cellular uptake of oligonucleotides is reduced compared to neutral or
lipophilic equivalents. This polarity "hindrance" can be avoided by using the pro-drug
approach (see e.g. Crooke, R. M. (1998) in Crooke, S. T. Antisense research and Application.
Springer-Vertag, Benin, Germany, vol. 131, pp. 103-140). In this approach, the LNA
oligonucleotides are prepared in a'protected mannerso that the LNA oltgonucleotldcs are
neutral when it is administered. These protection groups are designed in such a way that
they can be removed then the LNA oligonucleotide is taken up be the cells. Examples of such
protection groups are S-acetylthioethyl (SATE) or S-pivaloylthioethyl (r-butyl-SATE). These
protection groups are nuclease resistant and are selectively removed intracellulary.
Conjugates
A further aspect of the invention relates to a conjugate comprising an LNA oligonucleotide as
defined herein at least one non-nucleotide or non-polynucleotide moiety covalently attached
to said LNA oligonucleotide.
In a related aspect of the Invention, the LNA oligonucleotide of the invention is linked to
ligands so as to form a conjugate, said ligands intended to increase the cellular uptake of the
conjugate relative to the antisense oligonucleotides.
In the present context, the term "conjugate" is intended to indicate a heterogenous molecule
formed by the covalent attachment of an LNA oligonucleotide as described herein (i.e. an LNA
oligonucleotide comprising a sequence of nucleosldes and LNA nucleoside analogues) to one
or more non-nucleotide or non-polynucleotide moieties.
Thus, the LNA oligonucleotides may, e.g., be conjugated or form chimera with non-nucleotide
or non-polynucleotide moieties including Peptide Nucleic Acids (PNA), proteins (e.g.
antibodies for a target protein), macromolecules, low molecular weight drug substances, fatty
acid chains, sugar residues, glycoproteins, polymers (e.g. polyethylene glycol), micelle-

WO 2006/050734 PCT/DK2005/000721
16
forming groups, antibodies, carbohydrates, receptor-binding groups, steroids such as
cholesterol, polypeptides, intercalating agents such as an acridine derivative, a long-chain
alcohol, a dendrimer, a phosphoiipid and other llpophilic groups or combinations thereof, etc.,
just as the LNA oligonucteotides may be arranged in dimenc or dendritic structures. The LNA
oligonucleotides or conjugates of the invention may aiso be conjugated or further conjugated
to active drug substances/ for example; aspirin, ibuprofen, a-sutfa drug,-an antidiabetic, an
antibacterial agent, a chemotherapeutic agent or an antibiotic.
Conjugating in this way may confer advantageous properties with regard to the
pharmacokinetic characteristics of the LNA oligonucleotides. In particular, conjugating in this
way achieves increased cellular uptake.
In one embodiment, an LNA oligonucleotide is linked to ligands so as to form a conjugate,
said ligands intended to increase the cellular uptake of the conjugate relative to the antisense
LNA oligonucleotides. This conjugation can take place at the terminal positions 5'/3'-OH but
the ligands may also take place at the sugars and/or the bases. In particular, the growth
factor to which the antisense LNA oligonucleotide may be conjugated, may comprise
transfernn or folate. Transferrin-polylysine-oligonucleotide complexes or folate-polylysine-
oligonucleotide complexes may be prepared for uptake by cells expressing high levels of
transferrin or folate receptor. Other examples of conjugates/ligands are cholesterol moieties,
duplex intercalators such as acridine, poly-L-lysine, "end-capping" with one or more
nuclease-resistant linkage groups such as phosphoromonothioate, and the like.
The preparation of transferrin complexes as carriers of oligonucleotide uptake into cells is
described by Wagner et al., Proc. Natl. Acad. Sci. USA 87, 3410-3414 (1990). Cellular
delivery of folate-macromolecule conjugates via folate receptor endocytosis, including
delivery of an antisense oligonucleotide, is described by Low et al., U.S. Patent 5,108,921.
Also see, Leamon et al., Proc. Natl. Acad. Sci. 88, 5572 (1991).
Pharmaceutical composition
A particularly interesting aspect of the invention is directed to a pharmaceutical composition
comprising an LNA oligonucleotide as defined herein or a conjugate as defined herein, and a
pharmaceutically acceptable diluent, carrier or adjuvant.The pharmaceutical composition Is .
preferably suitable for injection, for topical administration, or for intraocular administration
(see further below).

WO 2006/050734 PCT/DK2005/000721
17
Directions for the preparation of pharmaceutical compositions can be found in "Remington:
The Science and Practice of Pharmacy" by Alfonso R. Gennaro, and in the following.
Pharmaceuticslly acceptable diluents, carriers or adjuvants are part of the pharmaceutical
composition. Capsules, tablets and pilis etc. may contain for example the following
compounds: microcrystalline cellulose, gum or gelatin as binders; starch or lactose as
excipients; stearates as lubricants; various sweetening or flavouring agents. For capsules the
dosage unit may contain a liquid carrier like fatty oils. Likewise coatings of sugar or enteric
agents may be part of the dosage unit. The pharmaceutical composition may also be
emulsions of the active pharmaceutical Ingredients (including the LNA oligonucleotide) and a
lipid forming a micellular emulsion.
An LNA otigonudeotide may be mixed with any material that do not impair the desired action,
or with material that supplement the desired action. These could include other drugs
including other oligonucieoside compounds.
For parenteral, subcutaneous, intradermal or topical administration, the formulation may
include a sterile diluent {e.g. water), buffer(s), regulators of tonicity and ionic strength and
antlbacterials. The active LNA oligonucleotide may be prepared with carriers that facilitate
uptake, protect against degradation or protect against immediate elimination from the body,
including implants or microcapsules with controlled release properties. For intravenous
administration the preferred carriers are physiological saline (0.9%) or buffered saline (e.g.
phosphate buffered saline).
In a preferred embodiment, injections or infusions of the LNA oligonudeotides are given at or
near the site of neovascularization. For example, the LNA oligonudeotides of the invention
can be delivered to retinal pigment epithelial cells in the eye. Preferably, the LNA
oligonudeotides is administered topically to the eye, e.g. in liquid or gel form to the lower
eye lid or conjunctival cul-de-sac, as is within the skill in the art (see, e.g., Acheampong AA
et al, 2002, Drug Metabol. and Disposition 30: 421- 429, the entire disclosure of which is
herein incorporated by reference).
The pharmaceutical compositions of the present invention may be administered in a number
of ways depending upon whether local or systemic treatment is desired and upon" the area to '
be treated. Administration may be (a) oral, (b) pulmonary, e.g., by inhalation or insufflation
of powders or aerosols, including by nebulizer; intratracheal, intranasal, (c) topical including
epidermal, transdermal, ophthalmic and to mucous-membranes including vaginal and rectal
delivery; or (d) parenteral including intravenous, Intraarterial, subcutaneous, mtraperttoneat .
or intramuscular injection or infusion; or intracranial, e.g., Intrathecal or intraventricular,

WO 2006/050734 PCT/DK2005/000721
18
administration. In one embodiment, the active LNA oligonudeotide is administered
intravenous, intraperitonal, orally, topically or as a boius injection or administered directly in
to the target organ.
It is currently believed that the most appropriate administration form is by intravenous
infusions or oral.
Pharmaceutical compositions and formulations for topical administration may include
transdermal patches, ointments, lotions, creams, gels, drops, sprays, suppositories, liquids
and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases,
thickeners and the like may be necessary or desirable. Coated condoms, gloves and the like
may also be useful. Preferred topical formulations include those in which the oligonucleotides
of the invention are in admixture with a topical delivery agent such as liplds, liposomes, fatty
acids, fatty acid esters, steroids, chelating agents and surfactants. Compositions and
formulations for oral administration include but are not restricted to powders or granules,
microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media,
capsules, gel capsules, sachets, tablets or minitablets. Compositions and formulations for
parenteral, intrathecal or intraventricular administration may include sterile aqueous
solutions which may also contain buffers, diluents and other suitable additives such as, but
not limited to, penetration enhancers, carrier compounds and other pharmaceutically
acceptable carriers or excipients.
Pharmaceutical compositions of the present invention include, but are not limited to,
solutions, emulsions, and liposome-containing formulations. These compositions may be
generated from a variety of components that include, but are not limited to, preformed
liquids, self- emulsifying solids and self-emulsifying semisolids. Delivery of drug to tumour
tissue may be enhanced by carrier-mediated delivery including, but not limited to, cationic
liposomes, cydodextrins, porphyrin derivatives, branched chain dendrimers, polyethylenimine
polymers, nanoparticles and microspheres (Dass CR. J Pharm Pharmacol 2002; 54(l):3-27).
A particularly preferred parenteral administration route is Intraocular administration. It is
understood that intraocular administration of the present LNA oligonucleotides can be
accomplished by injection or direct (e.g., topical) administration to the eye, as long as the
administration route allows the LNA oligonucleotides to enter the eye. In addition to the
topical routes of administration to the eye described above, suitable intraocular routes of
administration include inlravitreat, intraretinal, subretinal, subtenon, pen- and retro-orbital,
trans-corneal and trans-scleral administration.

WO 2006/050734 PCT/DK2005/000721
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For intraocular administration, the pharmaceutical composition may be administered
topically, for example, by patch or by direct application to the eye, or by tontophoresis
Ointments, sprays, or droppable liquids can be delivered by ocular delivery systems known in
the art such.as applicatora or eyedroppers. The compositions can be administered directlyto
the surface of the eye or to the interior af the eyelid. Such compositions can include
mucomimetics such as hyaluronic add, chondrottin sulfate, hydroxypropyl methylcellulose or
poly(vinyl alcohol), preservatives such as sorbic acid, EDTA or benzyichronium chloride, and
the usual quantities of diluents and/or carriers.
The LIMA oligonucleotide of the invention may be provided in sustained release compositions,
such as those described in, for example, U.S. Patent Nos. 5, 672,659 and 5,595,760. The use
of immediate or sustained release compositions depends on the nature of the condition being
treated. If the condition consists of an acute or over-acute disorder, treatment with an
immediate release form will be preferred over a prolonged release composition. Alternatively,
for certain preventative or long-term treatments, a sustained release composition may be
appropriate.
An LNA oligonucleotide can be injected into the interior of the eye, such as with a needle or
other delivery device.
In one embodiment, the pharmaceutical compositions comprise an LNA oiigonucleotide of the
invention (e.g., 0.1 to 90% by weight), or a physiologically acceptable salt thereof, mixed
with a physiologically acceptable carrier medium. Preferred physiologically acceptable carrier
media are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid
and the like.
Pharmaceutical compositions of the invention can also comprise conventional pharmaceutical
excipients and/or additives. Suitable pharmaceutical excipicnts include stabilizers,
antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents. Suitable
additives include physiologically biocompatible buffers (e.g., tromethamine hydrochloride),
additions of chelants (such as, for example,-DTPA or DTPA- btsamlde) or calcium chelate
complexes (as for example calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of
calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate
or calcium lactate). Pharmaceutical compositions of the Invention can be packaged for use in
liquid form, or can be lyophilized.
For solid compositions, conventional non-toxic solid earners can be used; for example,
pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin,
talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.

WO 2006/050734 PCT/DK2005/000721
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Preferably, an LNA oligonucleotide is included in a unit formulation such as in a
pharmaceuticatly acceptable carrier or diluent in an amount sufficient to deliver to a patient a
therapeutically effective amount without causing serious side effects in the treated patient.
The pharmaceutical formulations of the present invention, which may conveniently be.
presented in unit dosage form, may be prepared according to conventional techniques well-
known in the pharmaceutical industry. Such techniques include the step of bringing into
association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In
general the formulations are prepared by uniformly and Intimately bringing into association
the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if
necessary, shaping the product.
The compositions of the present invention may be formulated Into any of many possible
dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft
gels and suppositories. The compositions of the present invention may also be formulated as
suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further
contain substances which Increase the viscosity of the suspension including, for example,
sodium carboxymethylcellulose, sorbitol and/or dcxtran. The suspension may also contain
stabilizers.
In preferred embodiments of the pharmaceutical compositions, the LNA oligonucleotide is
formulated in an aqueous carrier, in particular an aqueous carrier comprising a buffer for
keeping the pH in the range of 4.0-8.5, and having an ionic strength of 20-2000 mM.
The term "aqueous carrier" means that the pharmaceutical composition in question is in
liquid form, and that the liquid carrier predominantly Is composed of water, I.e. that at least
80% (w/w), or at least 90% (w/w), or even at least 95% (w/w), of the carrier consists of
water. Other liquid ingredients may also be used, e.g. ethanol, DMSO, ethylene glycol, etc.
The aqueous carrier preferably comprises saline or a buffer for keeping the pH In the range of
4.0-8.5. Preferably, the buffer wilt keep the pH inthe range of 5:0-8.0, such as in the range
of 6.0-7.5, such as buffered saline, e.g. phosphate buffered saline (PBS).
The ionic strength/tonicity of the pharmaceutical composition is also of importance. Thus,
typically, the liquid pharmaceutical composition has an tonic strength of in the range of 20-
2000 mM, such as in the range of 50-1500 mM, or in the range of 100*1000 mM.

WO 2006/050734 PCT/DK2005/000721
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Combination drugs
It should be understood that .the pharmaceutical composition according to the invention
optionally comprises further antisense compounds, chemotherapeutic agents, anti-
inflammatory compounds, antiviral compounds, cytostatic compounds, anti-angiogenetic
compounds, anti-proliferative compounds, pro-apoptotic compounds, signal transduction
modulators, kinase inhibitors and/or Immuno-modulating compounds. It- is currently believed
that it is particularly Interesting to combine the LNA ollgonucleotlde with at least one
chemotherapeutic agents.
As stated, the pharmaceutical composition of the invention may further comprise at least one
chemotherapeutic agent. The chemotherapeutic compound is typically selected from the
group consisting of adrenocorticosterolds, such as prednisone, dexamethasone or decadron;
altretamine (hexaien, hexamethylmelamine (HMM)); amifostine (ethyol); aminoglutethimide
(cytadren); amsacrine (M-AMSA); anastrozole (arimldex); androgens, such as testosterone;
asparaginase (elspar); Avastin; bacillus calmette-gurin; bicalutamide (casodex);
biphosphanate; bleomycin (blenoxane); bortezomib; busulfan (myleran); carboplatin
(paraplatin); carmustine (BCNU, BiCNU); chlorambucil (leukeran); chlorodeoxyadenosine (2-
CDA, cladriblne, leustatin); cisplatin (platinol); cyclophosphamid; cytosine arabinoside
(cytarabine); dacarbazine (DTIC); dactinomycin (actinomycin-D, cosmegen); daunorubicin
(cerubidme); docetaxel (taxotere); doxorubicin (adriomycin); epirubicin; estramustine
(emcyt); estrogens, such as diethylstilbestrol (DES); ctoposide (VP-16, VePesid, etopophos);
fludarabine (fludara); fiutamide (eulexin); 5-FUDR (floxuridine); 5-fluorouracil (5-FU);
gemcitabine (gemzar); gosereiin (zodaiex); herceptin (trastuzumab); hydroxyurea (hydrea);
idarubicin (idamycin); ifosfamide; IL-2 (proieukin, aldesleukin); interferon alpha (intron A,
roferon A); irlnotecan (camptosar); leuprolide (lupron); levamisole (ergamisole); lomustine
(CCNU); mechlorathamine (mustargen, nitrogen mustard); melphalan (alkeran);
mercaptopurine (purlnethol, 6-MP); methotrexate (mexate); 2-methoxyestradiol (2ME2,
Panzem); mitomycin-C (mutamucin); mitoxantrone (novantrone); octreotide (sandostatin);
pentostatin (2-deoxycoformycin, nipent); plicamycin {mithramycin, mithracm);
prorocarbazine (matulane); streptozocin; tamoxifln (nofvadex); taxol (paclttaxel); teniposide
(vumon, VM-26); Thatidomide; thiotepa; topolecan (hycamtin); tretinoin (vesanoid, all-trans
retinoic acid); vinblastine (valban); vincristine (oncovin) and vtnorelbine (navelbine).
For the treatment of multiple myeloma, chemotherapeutic agents like melphalan,
cyclophosphamid, prednisane, vincristine, doxorubicin, carmustine, dexamethasone,
thalldomide, bortezomib, and biphosphanate are preferred.

WO 2006/050734 PCT/DK2005/000721
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For the treatment of renal carcinoma, chemotherapeutic agents like gemcitabine, 5-
fluorouracil (5-FU), 5-fluorodeoxyuridme, paditaxel, carboplatin, ifosfamide, doxorublcln,
vinblastine, IFN-alpha, and IL-2 are preferred.
In one variant, the present invention provides pharmaceutical compositions containing (a)
one or more LNA oligontideotides and (b) one or more other chemotherapeutic compounds
which function by a non-antisense mechanism. When used with the LNA oligonudeotides,
such chemotherapeutic compounds may be used individually (e.g. mithramycin and
oligonucleotide), sequentially (e.g. mithramycin and oligonucleotide for a period of time
followed by another agent and oligonucleotide), or in combination with one or more other
such chemotherapeutic compounds or in combination with radiotherapy. All
chemotherapeutic compounds known to a person skilled in the art including those explicitly
mentioned above are here incorporated as combination treatments with an LNA
oligonucleotide according to the invention.
In one embodiment, the pharmaceutical composition is administered in combination with a
taxane compound.
The term "taxane compound" is intended to encompass paclitaxel (Taxol®), paclitaxel
derivatives, docetaxel, taxotere, modified taxanes, and taxoid analogues. Paclitaxel (Taxol®)
is a diterpene isolated from the bark of the Western (Pacific) yew, Taxus brevifolia and is
representative of a class of therapeutic agents having a taxane ring system. Paclitaxel and its
analogs have been produced by partial synthesis from 10-deacetylbaccatln III, a precursor
obtained from yew needles and twigs, and by total synthesis. See Holton, et al., J. Am.
Chem. Soc. 116:1597-1601 (1994) and Nlcolaou, et al., Nature 367:630 (1994). Paclitaxel
has demonstrated efficacy in several human tumours in clinical trials. See McGuire, et al.,
Ann. Int. Med. 111:237-279 (1989); Holmes, etal., J. Natl. Cancer Inst. 83:1797-1805
(1991); Kohn et at., J. Natt. Cancer Inst. 86:18-24 (1994); and Kohn, et al., American
Society for Clinical Oncology 12 (1993). The modified taxane or taxoid analogs are those
compounds having a taxane ring bearing modified side cnains. A number of these analogs
have improved properties, such as greater water solubility and stability than that of naturally
occurring paclitaxel. These analogs are known to those skilled in the art and are disclosed, for"
example, in U.S. Pat. Nos. 5,278,324; 5,272,171; 5,254,530; 5,250,683; 5,248,796; and
5,227,400, the disclosures of which are incorporated herein by reference. Paclitaxel and
taxotere can be preparedby the methods in WO 93/18210, EP 0 253 739; EP 0 253 739, and
WO 92/09589, the disclosures of which are incorporated herein by reference. In particular
embodiments, the taxane compound is paclitaxel or taxotere.

WO 2006/050734 PCT/DK2005/000721
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The weight ratio between the taxane compound(s) and the LNA oligonudentide in said
composition is typically in the range of 50:1 to l:25,.such.as In the range of 25:1 to 1:25,.or.
in the range of 10:1 to 1:25, or in the range of 1:1 to 1:25, or in the range of 50:1 to 1:10,
or in the range of 1:1 to 1:50, or in the range of 25:1 to 1:10.
In a further embodiment, pharmaceutical compositions of the Invention may contain one or
more LNA aligonudeotides and one or more additional antisense compounds targeted to a
second nucleic acid target. Two or more combined compounds may be used together or
sequentially.
Anti-inflammatory drugs, including but not limited to nonsteroidal anti-inflammatory drugs
and corticosteroids, antiviral drugs, and immuno-modulating drugs may also be combined in
compositions of the invention. Two or more combined compounds may be used together or
sequentially.
Furthermore, the pharmaceutical compositions comprising the LNA oligonucleotides may be
used in combination with radiotherapyr etc.
Medical treatment
LNA oligonucleotides of the invention are useful for a number of therapeutic applications as
indicated herein. In general, therapeutic methods of the invention include administration of a
therapeutically effective amount of an LNA-modified oligonucleotide to a mammal,
particularly a human.
Hence, the present invention also relates to an LNA oligonucleotide as defined herein or a
conjugate as defined herein for use as a medicament.
Dosing is dependent on seventy and responsiveness of the disease state to be treated, and
the course of treatment lasting from several days to several months, or until a cure is
effected or a diminution of the disease state is achieved. Optimal dosing schedules can also
be assessed by measurements of drug in the body of the patient or by surrogate markers.
Optimum dosages may vary depending on the relative potency of individual oligonucleotides.
Generally, it can be estimated based on EC50s found to be effective in in vitro and in vivo ■
animal models. In general, dosage is from 0.01 pg to 1 g per kg of body weight, and may be
given once or more daily, weekly, monthly or yearly, or even once every. 2 to 10 years or by
continuous infusion for hours up to several months. The repetition rates for dosing can be

WO 2006/050734 PCT/DK2005/000721
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estimated based on measured residence times and concentrations of the drug in bodily fluids
or tissues. Following successful treatment, it may be desirable to have the patient undergo .
maintenance therapy to prevent the recurrence of the disease state. It is currently believed
that the most relevant doses are 0.01 mg to 100 mg, such as 0.1 mg to 40 mg, or 0.5 mg to
10 mg, per kg of body weight. Such doses may be given once daily, but more preferably less
frequent, e.g; 1-3 timesper week, for a period of 1-4 weeks. Maintenance therapy may be
continued, e.g. 1-4 times per month or even less frequent such 1-10 times per year.
A person skilled In the art will appreciate that LNA oligonucleotides can be used to combat
HIF-1a linked diseases by many different principles, which thus falls within the spirit of the
present invention.
As used herein, the terms "target nucleic acid" encompass DNA encoding the HIF-la, RNA
(including pre-mRNA and mRNA) transcribed from such DNA, and also cDNA derived from
such RNA.
As used herein, the term "gene" means the gene including exons, introns, non-coding 5'and
3 'regions and regulatory elements and all currently known variants thereof and any further
variants, which may be elucidated.
As used herein, the term "LNA oligonucleotide" refers to an oligonucleotide which can induce
a desired therapeutic effect in humans through for example binding by hydrogen bonding to
either a target gene "Chimeraplast" and TFO", to the RNA transcript(s) of the target gene
"antisense inhibitors", "siRNA", "miRNA", "rlbozymes" and oligozymes" or to the proteln(s)
encoding by the target gene "aptamer", splegelmer" or "decoy".
As used herein, the term "mRNA" means the presently known mRNA transcript(s) of a
targeted gene, and any further transcripts, which.may be identified.
As used herein, the term "modulation" means either an increase (stimulation) or a decrease
(inhibition) in the expression of a gene. In the present invention, inhibition is the preferred
form of modulation of gene expression and mRNA is a preferred target.
As used herein, the term "targeting" an antisense compound to a particular target nucleic
acid means providing the antisense oligonucleotide to the cell, animal or human in such a
way that the antisense compound are able to bind to and modulate the function of its
intended target.

WO 2006/050734 PCT/DK2005/000721
25
The LNA ofigonucleotides may be designed as siRNA' s which are small double stranded RNA
molecules that are used by celts to silence specific endogenous or exogenous genes by an as
yet poorly understood "antisense-lfke" mechanism.
The clinical effectiveness of antisense oligonucieotides depends to a significant extent on
their pharmacokinetics e.g. absorption, distribution, cellular uptake, metabolism and
excretion. In turn, these parameters are guided significantly by the underlying chemistry and
the size and three-dimensional structure of the oligonucleotide.
Modulating the pharmacokinetic properties of an LNA oligonucleotide according to the
invention may further be achieved through attachment of a variety of different moieties. For
instance, the ability of oligonucieotides to pass the cell membrane may be enhanced by
attaching for instance llpid moieties such as a cholesterol moiety, a thioether, an aliphatic
chain, a phosphotipid or a polyamine to the oliganucieotide. Likewise, uptake of LNA
oligonucieotides into cells may be enhanced by conjugating moieties to the oligonucleotide
that interacts with molecules in the membrane, which mediates transport into the cytoplasm.
The pharmacodynamic properties can according to the invention be enhanced with groups
that improve LNA oligonucleotide uptake, enhance biostability such as enhance LNA
oligonucleotide resistance to degradation, and/or increase the specificity and affinity of
oligonucieotides hybridisation characteristics with target sequence e.g. a mRNA sequence.
The pharmaceutical composition according to the invention can be used for the treatment of
many different diseases. Like cancer ceils proliferating vascular endothelial cells are sensitive
to down-regulation of HIF-la expression. The pharmaceutical composition according to the
invention can therefore be used in the treatment of diseases characterized by abnormal
disease causing angiogenesis. Examples of such diseases are cancers in general and
artherosclerosis, psoriasis, diabetic retinopathy, macular degeneration, rheumatoid arthritrs,
asthma, inflammatory bowel disease, warts, allergic dermatitis and Karposis sarcoma.
Generally stated, one aspect of the invention :s directed to a metnod of treating a mammal
suffering from or susceptible to a disease caused by abnormal angiogenesis, comprising . -
administering to the mammal a therapeutically effective amount of an LNA oligonucleotide or
a conjugate as defined herein.
Furthermore, the invention also relates to a method of .inhibiting angiogenesis comprising the
administration of an LNA oligonucleotide as defined herein or a conjugate as defined herein or
a pharmaceutical composition asr defined herein.

WO 2006/050734 PCT/DK2005/000721
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An Interesting aspect of the invention is directed to the use of an LNA oligonucleotide as
defined herein or as conjugate as defined herein for the preparation of a medicament for the
treatment of a disease selected from artherosclerosis, psoriasis, diabetic retinopathy, macular
degeneration, rheumatoid arthritis, asthma, inflammatory bowel disease, warts, allergic
dermatitis, inflammation, and skin inflammation, or other skin related diseases.
The pharmaceutical composition according to the invention can also be used In the treatment
of inflammatory disease, inflammations such as skin inflammations or other skin diseases or
disorders, e.g. psoriasis and rheumatoid arthritis.
Similarly, another interesting aspect of the invention is directed to a method for treating a
disease selected from the group consisting of artherosclerosis, psoriasis, diabetic retinopathy,
rheumatoid arthritis, asthma, inflammatory bowel disease, warts, allergic dermatitis,
inflammation, and skin inflammation, said method comprising administering an LNA
oligonucleotide as defined herein or a conjugate as defined herein or a pharmaceutical
composition as defined herein to a patient in need thereof.
Particularly interesting are angiogenic diseases include diabetic retinopathy, macular
degeneration, psoriasis, rheumatoid arthritis inflammatory bowel disease, and other
inflammatory diseases. These diseases are characterized by the destruction of normal tissue
by newly formed blood vessels in the area of neovasculanzation. For example, in macular
degeneration, the choroid is invaded and destroyed by capillaries. The angiogenesis-dnven
destruction of the choroid in macular degeneration eventually, leads to partial or full
blindness.
The methods of the Invention is preferably employed for treatment or prophylaxis against
diseases caused by cancer, particularly for treatment of cancer as may occur ir> tissue such
as lung, breast, colon, prostate, pancreas, liver, thyroid, kidney, brain, tastes, stomach,
intestine, bowel, spinal cord, sinuses, bladder, urinary tract or ovaries cancer.
Furthermore, the invention described herein encompasses a method of preventing or treating
cancer comprising a therapeutically effective.amount of a HIF-1a modulating LNA -
oligonucleotide, including but not limited to high doses of the LNA oligonucleotide, to a
human in need of such therapy. The Invention further encompasses the use of a short period
of administration of a HIF-la modulating LNA oligonucleotide. Normal, non-cancerous ceils
divide at a frequency characteristic for the particular cell type. When a cell has been
transformed into a cancerous state, uncontrolled cell proliferation and reduced cell death
results, and therefore, promiscuous cell division or cell growth is a hallmark of a cancerous
cell type.

WO 2006/050734 PCT/DK2005/000721
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Examples of types of cancer, include, but are not limited to, non-Hodgkin's lymphoma,
Hodgkin's lymphoma, leukemia (e.g., acute leukemia such as acute lymphocytic leukemia,
acute myelocytic leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, multiple
myeloma), colon carcinoma, rectal carcinoma, pancreatic cancer, breast cancer, ovarian
cancer, prostate cancer, renal cell carcinoma, hepatoma, bile duct carcinoma,
choriocarcinoma, cervical cancer, testicular cancer, lung carcinoma, bladder carcinoma,
melanoma, head and neck cancer, brain cancer, cancers of unknown primary site,
neoplasms, cancers of the peripheral nervous system, cancers of the central nervous system,
tumors (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic
sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma,
lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma,
rhabdomyosarcoma, squamous cell carcinoma, basal cell carcinoma, adcnocarcinoma, sweat
gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary
adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma,
seminoma, embryonal carcinoma, Wilms' tumor, small cell lung carcinoma, epithelial
carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma,
pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma,
neuroblastoma, and retinoblastoma), heavy chain disease, metastases, or any disease or
disorder characterized by uncontrolled or abnormal cell growth.
The term "carcinoma" is intended to indicate a malignant tumor of epithelial origin. Epithelial
tissue covers or lines the body surfaces Inside and outside the body. Examples of epithelial
tissue are the skin and the mucosa and serosa that line the body cavities and internal organs,
such as intestines, urinary bladder,.uterus, etc. Epithelial tissue may also extend into deeper
tissue layers to from glands, such as mucus-secreting glands.
The term "sarcoma" is intended to indicate a malignant tumor growing from connective
tissue, such as cartilage, fat, muscles, tendons and bones.
The term "glioma", when used herein, Is Intended to cover a malignant tumor originating
from glial cells.
In the use of an LNA oligonudeotide of the invention or as conjugate of the invention for the
manufacture of a medlcament-for the treatment of cancer, said-cancer may suitably be in the
form of a solid tumor. Furthermore, said cancer is also suitably a carcinoma. The carcinoma
is typically selected from the group consisting of malignant melanoma, basal cell carcinoma,
ovarian carcinoma, breast carcinoma, non-small cell lung cancer, renal cell carcinoma,
bladder carcinoma, recurrent superficial bladder cancer, stomach carcinoma; prostatic
carcinoma, pancreatic carcinoma, lung carcinoma, cervical carcinoma, cervical dysplasia,

WO 2006/050734 PCT/DK2005/000721
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laryngeal papillomatosis, colon carcinoma, colorectal carcinoma and carcinoid tumors. More
typically, said carcinoma is selected from the group consisting of malignant melanoma, non-
small cell lung cancer, breast carcinoma, colon carcinoma and renal cell carcinoma. The
malignant melanoma is typically selected from the group consisting of superficial spreading
melanoma, nodular melanoma, lentigo maligna melanoma, acral melagnoma, amelanotic
melanoma and desmoplastic melanoma.
Alternatively, the cancer may suitably be a sarcoma. The sarcoma is typically in the form
selected from the group consisting of osteosarcoma, Ewlng's sarcoma, chondrosarcoma,
malignant fibrous histiocytoma, fibrosarcoma and Kaposi's sarcoma.
Alternatively, the cancer may be a glioma.
The LNA oligonucleotides and conjugates defined herein are also believed to be particularly
useful for the treatment of a cancer disease selected from the group consisting of multiple
myeloma, renal cancer, cervical cancer, brain cancer, and breast cancer.
The invention also provides a method for treating cancer, said method comprising
administering an LNA oligonucleotide as defined herein or a conjugate as defined herein or a
pharmaceutical composition as defined herein to a patient in need thereof. In one variant, the
cancer is in the form of a solid tumor. The solid cancer may suitably be a carcinoma or a
sarcoma or a glioma, as discussed above.
Accordingly, a further aspect of the invention is directed to the use of an LNA oligonucleotide
as defined herein or as conjugate as defined herein for the manufacture of a medicament for
the treatment of cancer, wherein said medicament further comprises a chemotherapeutic
agent selected from those defined above under "Combination drugs" Suitably, the further
chemotherapeutic agent is selected from taxanes such as Taxol, Padltaxel or Docetaxel.
Alternatively stated, the invention is furthermore directed to a method for treating cancer,
said method comprising administering an LNA oligonucleotide as defined herein, or a
conjugate as defined herein or a pharmaceutical composition as defined herein to a patient in
need thereof and further comprising the administration of a a further chemotherapeutic
agent. Said further administration may be such that the further chemotherapeutic agent is
conjugated to the LNA oligonucleotide of the invention, is present in the pharmaceutical
composition, or is administered in a separate formulation.
In a preferred embodiment, the present invention provides pharmaceutical compositions
containing (a) one or more antisense compounds and (b) one or more other -

WO 2006/050734 PCT/DK2005/000721
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chemotherapeutic agents which prevent mlcrotubule depolymerization and tension forming at
the kinetochores of sister chromatids, but not the attachment of microtubules to the
kinetochores. Such chemotherapeutic agents include taxanes as defined above, in particular
Taxol, Paclitaxel and Docetaxel. When used with the LNA oligonucleotides of the invention,
such chemotherapeutic agents should be used sequentially initiating with oligonucleotide
treatment for a period of time which sensitises the target cells to subsequent co-treatment
with the chemotherapeutic agent by reducing the level of HIF-la protein in tumor cells and
proliferating endothelial cells of the tumor vasculature.
In another preferred embodiment, the medical treatment using an LNA oligonucleotide
according to the present invention is combined with radiation therapy. When used with the
LNA oligonucleotides of the invention, radiation therapy should be used sequentially initiating
with oligonucleotide treatment for a period of time which sensitises the target cells to
subsequent additional radiotherapy by reducing the level of HIF-la protein in tumor cells and
proliferating endothelial cells of the tumor vasculature.
The LNA oligonucleotides of the present Invention can also be utilized for as research
reagents for diagnostics, therapeutics and prophylaxis. In research, the antlsense
oligonucleotides may be used to specifically inhibit the synthesis of HIF-la genes in celts and
experimental animals thereby facilitating functional analysis of the target or an appraisal of
its usefulness as a target for therapeutic intervention. In diagnostics the antlsense
oligonucleotides may be used to detect and quanbtate HIF-la 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 HIF-la is treated by administering antisense LNA oligonucleotides in
accordance with this invention. Further provided are methods of treating an animal particular
mouse and rat and treating a human, suspected of having or being prone to a disease or
condition, associated with expression of HIF-la by administering a therapeutically or
prophylactically effectlve:amount of one or more of the antisense LNA oligonucleotides or
conjugates or pharmaceutical compositions of the invention.
A further aspect of the invention is directed to.a method of inducing apoptosis comprising the
administration of an LNA oligonucleotide as herein, a conjugate as defined herein or a
pharmaceutical composition as defined herein. The induction of apoptosis may be in vitro or
in vivo. The induction may be done on a cellular assay or within a tissue sample or within the
living mammal.
A related aspect of the invention is directed method of preventing cellular proliferation
comprising the administration of an LNA oligonucleotide as defined herein or a conjugate as

WO 2006/050734 PCT/DK2005/000721
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defined herein or a pharmaceutical composition as defined herein. The prevention of
proliferation may be in vitro or in vivo. The prevention may be done on a cellular assay or
within a tissue sample or within the living mammal.
Still further, the invention also relates to a method of treating an angiogenic disease
comprising the administration of an LNA oligonucleotide as defined herein or a conjugate as
defined herein or a pharmaceutical composition as defined herein, such that angiogenesis
associated with the angiogenic disease is inhibited.
In one embodiment, the angiogenic disease comprises a tumor associated with a cancer; see
also above. The cancer is preferably selected from the group consisting of breast cancer, lung
cancer, head and neck cancer, brain cancer, abdominal cancer, colon cancer, colorectal
cancer, esophagus cancer, gastrointestinal cancer, glioma, liver cancer, tongue cancer,
neuroblastoma, osteosarcoma, ovarian cancer, pancreatic cancer, prostate cancer,
retinoblastoma, Wilm's tumor, multiple myeloma, skin cancer, lymphoma, and blood cancer.
Alternatively, the cancer Is selected from the group consisting of multiple myeloma, renal
cancer, cervical cancer, colon cancer, brain cancer, and breast cancer.
The angiogenic disease may also be selected from the group consisting of diabetic
retinopathy, macular degeneration, and inflammatory diseases. Particularly, the angiogenic
disease is an inflammatory disease selected from inflammatory bowel disease, psoriasis and
rheumatoid arthritis.
Treatment of macular degeneration is believed to be particularly relevant with the LNA
oligonudeotides of the invention?.
Kits
If the pharmaceutical composition in liquid form is under risk of being subjected to conditions
which will compromise the stability of the LNA oligonucleotide, it may be preferred to produce
the finished product containing the LNA oligonucleotide in a solid form, e.g. as a freeze dried
material, and store the product is such solid form. The product may then be reconstituted
(e.g. dissolved or suspended) in a saline or in a buffered saline ready for use prior to
administration.
Hence, the present invention also provides a kit comprising

WO 2006/050734 PCT/DK2005/000721
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(a) a first component containing an LNA oltgonudeotide or a conjugate as defined
hereinabove in solid form, and
(b) a second component containing saline or a buffer solution (e.g. buffered saline) adapted
for reconstitution (e.g. dissolution or suspension) of said-LNA otigonucieotide.
Preferably said saline or buffered saline has a pH in the range of 4.D-8.5, and a molartty of
20-2000 mM, In a preferred embodiment the saline or buffered saline has a pH of 6.0- 8.0
and a motarity of 100-50.0 mM. In a most preferred embodiment the saiine or buffered saline
has a pH of 7.0-8.0 and a molarity of 120-250mM .
For such a kit, the LNA oligonucleotide is preferably selected from.the group consisting of
SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, and SEQ ID
NO. 18. More particular,the LNA oiigonucleotide is selectedfrom the group consisting of SEQ
ID NO. 1 and SEQ ID NO. 2.
The invention is further illustrated in a non-limiting manner by the following examples.
EXPERIMENTALS
Example 1: Monomer synthesis
The LNA monomer building blocks and derivatives thereof were prepared following published
procedures and references cited therein, see, e.g. WO 03/095467 Al and D. S. Pedersen, C.
Rosenbohm, T. Koch (2002) Preparation of LNA Phosphoramidites, Synthesis 6, 802-808.
Example 2: Oiigonucleotide synthesis
Oligonucleotides were synthesized using the phosphoramldite approach on an Expedite
8900/MOSS synthesizer (Multiple Oligonucleotide Synthesis System) at 1 |jmol or 15 umol
scale. For larger scale synthesis an Akta Oligo Pilot was used. At the end of the synthesis
(DMT-on), the oligonucleotides were cleaved from the solid support using aqueous ammonia
for 1-2 hours at room temperature, and further deprotected for 4 hours at 65°C. The
oligonucleotides were purified by reverse phase HPLC (RP-HPLC). After the removal of the
DMT-group, the oligonucleotides were characterized by AE-HPLC, RP-HPLC, and CGE and the
molecular mass was further confirmed by ESI-MS. See below for more details.

WO 2006/050734 PCT/DK2005/000721
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Preparation of the LNA-solid support:
Preparation of the LNA succinyl hemiester
5'-O-Dmt-3'-hydroxy-LNA monomer (500 mg), succinic anhydride (1.2 eq.) and DMAP (1.2
eq.) were dissolved in DCM (35 mL). The reaction was stirred at room temperature overnight.
After extractions with NaH2PO4 0.1 M pH 5.5 (2x) and brine (1x), the organic layer was
further dried with anhydrous Na2SO4 filtered and evaporated. The hemiester derivative was
obtained in 95% yield and was used without any further purification.
Preparation of the LNA-support
The above prepared hemiester derivative (90 μmol) was dissolved in a minimum amount of
DMF, DIEA and pyBOP (90 umol) were added and mixed together for 1 mm. This pre-
activated mixture was combined with LCAA-CPG (500 A, 80-120 mesh size, 300 mg) in a
manual synthesizer and stirred. After 1.5 hours at room temperature, the support was
filtered off and washed with DMF, DCM and MeOH. After drying, the loading was determined
to be 57 μmol/g (see Tom Brown, Dorcas J.S.Brown. Modern machine-aided methods of
oligodeoxynbonucleotide synthesis. In: F.Eckstein, editor. Oligonucleotides and Analogues A
Practical Approach. Oxford: IRL Press, 1991: 13-14).
Elongation of the oliqonucleotide
The coupling of phosphoramidites (A(bz), G(ibu), 5-methyl-C(bz)) or T-p-cyanoethyl-
phosphoramldite) 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.
The thiolatlon is carried out by using xanthane chloride (0.01 M in acetonitrile:pyndine 10%).
The rest of the reagents are the ones typically used for oligonucleotide synthesis. The
protocol provided by the supplier was conveniently optimised.
Purification by RP-HPLC:
Column: Xterra RP18
Flow rate: 3 mL/min
Buffers: 0.1 M ammonium acetate pH 8 and acetonitrile
Abbreviations

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DMT: Dimethoxytrityl
DCI: 4,5-Dlcyanoimtdazole
DMAP: 4-Dimethylaminopyridirve
DCM: Dichloromethane
DMF: Dimethylformamide
TKF: Tetrahydrofurane
DIEA: N,N-dlisopropylethylamine
PyBOP: Benzotriazole-1-yl-oxy-tris-pyrrolidino-phosphonium hexafluorophosphate
Bz: Benzoyl
Ibu: Isobutyryl

WO 2006/050734 PCT/DK2005/000721
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Example 3: Design of the LNA oligonucfeotide

In Table 1, capital letters designate an p-D-oxy-LNA nucleotide analogue (p-D-oxy-LNA),
small letters designate a 2-deoxynucleotide, underline designates either a beta-D-oxy-LNA
nucleotide analogue or a 2-deoxynucleotide subscript "s" designates a phosphorothioate link
between neighbouring nucleotides/LNA nucleotide analogues, and no subscript between
neighbouring nucleotides/LNA nucleotide analogues designates a phosphorodiester link, and
subscript "x" designates either a phosphorothioate link or a phosphorodiester link between

WO 2006/050734 PCT/DK2005/000721
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neighbouring nudeotides/LNA nudeotide analogues, and nucleotide units tn a bracket, e.g.
(Tx) or (Gx), respectively, represent an optional unit.-All LNA-C monomers are 5-methyl-C
(HeC).
Measurement of melting temperature (Tm) of the compounds:
A 3 pM solution of SEQ ID NO. 1 in 10 mM sodium phosphate/100 mM NaCI/ 0.1 nM EDTA,
pH 7.0 was mixed with its complement DNA/RNA 3 uM ir. 10 mM sodium phosphate/100 mM
NaCt/ 0.1 nM EDTA, pH 7.0 at 90 "C for a minute and allowed to cool to room temperature.
The Tm of the duplex was then determined by increasing the temperature l°C/mirv. from 25 to -
95*C. The Tm of SEQ ID NO. 1 is shown in Table 2 below: ■
Table 2

LIMA oligonucleotide stability was tested in plasma from human or rats (it could also be
mouse, monkey or dog plasma). In 45 nl plasma, 5 nl LNA oligonucleotide is added (a final
concentration of 20 pM). The LNA oligonucieotides are Incubated in plasma for times ranging
from 0 to 96 hours at 37 °C (the plasma is tested for nuclease activity up to 96 hours and
shows no difference in nuclease cleavage-pattern). At the indicated time the sample were
snap frozen in liquid nitrogen. 2 uL (equals 40 pmol) LNA oligonucleotide in plasma was
diluted by adding 15 pL of water and 3 uL 6x loading dye (Invitrogen). As marker a 10 bp
ladder (In vitrogen 10821-015) is used. To 1 nl ladder 1 μl 6x loading and 4 μl water is
added. The samples are mixed, heated to 65 °C for 10 min and loaded to a prerun gel (16%
acrylamide, 7 M UREA, 1x TBE, prerun at 50 Watt for 1 h) and run at 50-60 Watt for 2½
hours. Subsequently the gel is stained with lx SyBR gold (molecular probes) in lx TBE for 15
mln. The bands were visualised using a phospholmager from Biorad. (See Figure 1A in rat
plasma & Figure IB human and rat plasma.)
LNA oligonucleotide stability was tested in plasma from human (it could also be rat, mouse,
monkey or dog plasma). A final concentration of 20 pM (between 1 or 5 uL) of LNA
oligonucleotide was add to a total volume of 20 pL plasma and incubated for the
times ranging from 0 to 24 hours (it could be up to 72 hours r.trte plasma has been tested for

WO 2006/050734 PCT/DK2005/000721
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nuclease activity up to 72 hours and there is no difference in cleavage-pattern). At the "
indicated time the sample were stored at -80°C..l uL (equal s 20 pmol) LNA oligonucleotides
in plasma was diluted 10 x in water and run on a 16% acrylamide, 7 M UREA gel with a 10 bp
ladder (from In vitrogen (cat no. 10821-015)). The gel was run at approximately 40 Watt for
2-3 hours before It was stained with lx SyBR gold (molecular probes) in lx TBE for 15 min.
The bands were visualised using a phosphoimager from Biorad. (See Figure 1)
Example 5: In vitro model: Cell culture
The effect of LNA oligonucleotides on target nucleic acid expression can be tested- in any of a
variety of cell types provided that the target nucleic acid is present at measurable levels.
Target can be expressed endogenously or by transient or stable transfection of a nucleic acid
encoding said nucleic acid.
The expression level of target nucleic acid can be routinely determined using, for example,
Northern blot analysis, Quantitative PCR, Ribonuclease protection assays. The following cell
types are provided for illustrative purposes, but other cell types can be routinely used,
provided that the target is expressed in the cell type chosen.
Cells were cultured in the appropriate medium as described below and maintained at 37°C at
95-98% humidity and 5% CO2. When cultured under hypoxia or anoxia, O2 levels were kept
at 1-2% or 0-0.5%, respectively. Cells were routinely passaged 2-3 times weekly.
15PC3: The human prostate cancer cell line 15PC3 was kindly donated by Dr. F. Baas,
Neurozintuigen Laboratory, AMC, The Netherlands and was cultured in DMEM (Sigma) + 10%
fetal bovine serum (FBS) + Glutamax I + gentamicin.
PC3: The human prostate cancer cell line PC3 was purchased from ATCC and was cultured in
F12 Coon's with glutamine (Gibco) + 10% FBS + gentamicin.
518A2: The human melanoma cancer cell line 518A2 was kindly donated by Dr. B. Jansen,
Section of experimental Oncology, Molecular Pharmacology, Department of Clinical
Pharmacology, University of Vienna and was cultured in DMEM (Sigma) + 10% fetal bovine
serum (FBS) + Glutamax I + gentamicin.
U373: The U373 glioblastoma cells were cultured in EMEM (Sigma) containing 10% fetal
bovine serum plus Glutamax I, WEAA, Sodium Pyruvate and-gentamicin at 37°C, 95%
humidity and 5% CO?.

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HeLa: The cervical carcinoma cell line HeLa was cultured in MEM (Sigma) containing 10%
fetal bovine serum gentamicin at 37°C, 95% humidity and 5% CO2.
MPC-11: The. murine multiple myeloma cell line MPC-11 was purchased from ATCC and
maintained in DMEM with 4mM Glutamax+ 10%- Horse Serum.
DU-145: The human prostate cancer cell line DU-145 was'purchased from ATCC and
maintained in RPMI with Glutamax + 10% FBS..
RCC-4 +/- VHL: The human renal cancer cell line RCC4 stably transfected with plasmid
expressing VHL or empty plasmid was purchased from ECACC and maintained according to
manufacturers instructions.
786-0: The human renal cell carcinoma cell line 786-0 was purchased from ATCC and
maintained according to manufacturers Instructions
HUVEC: The human umbilical vein endotheiial cell line HUVEC was purchased from Camcrex
and maintained in EGM-2 medium.
K562: The human chronic myelogenous leukaemia cell line K562 was purchased from ECACC
and maintained in RPMI with Glutamax + 10% FBS. U87MG: The human glioblastoma cell
line U87MG was purchased from ATCC and maintained according to the manufacturers
instructions.
B16: The murine melanoma cell line B16 was purchased from ATCC and maintained
according to the manufacturers instructions.
LNCap: The human prostate cancer cell line LNCap was purchased from ATCC and maintained
in RPMI with Glutamax + 10% FBS
Example 6: In vitro model: Treatment with antisense oligonucleotide
Cell culturing and transfections: U373 or HeLa cells were seeded in 12-well plates at 37°C
(5% CO2) in D growth media supplemented with 10% FBS, Glutamax I and Gentamicin.
When the cells were 60-70% confluent, they were transfected in duplicates with different
concentrations of otigonucleotides (0.2 - 100 nM) using Lipofectamine 2000 (2.5 - 5 ug/mt).
Transfections were carried out essentially as described bv Dean et af. (1994, JBC 269:16416-
16424). In short, ceits were incubated for 10 mln. with Lipofectamine in OptiMEM followed by

WO 2006/050734 PCT/DK2005/000721
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addition of oligonucleotide to a total volume of 0.5 mi transfectlon mix per well. After 4
hours, the transfection mix was removed, cells were washed and grown at 37°C.for
approximately 20 hours (mRNA analysis and protein analysis) during either normoxia or
hypoxia in the appropriate growth medium. Ceils were then harvested for protein and RNA
analysis.
Example 7: in vitro model;.Extraction of RNA and cDNA synthesis
Total RNA Isolation
Total RNA was isolated either using RNeasy mini kit (Qiagen cat. no. 74104) or using the
Trizol reagent (Life technologies cat. no. 15596).
For total RNA isolation using RNeasy mini kit (Qiagen), cells were washed with PBS, and Col!
Lysis Buffer (RTL, Qiagen) supplemented with l% mercaptoethanol was added directly to the
wells. After a few minutes, the samples were processed according to manufacturer's
instructions.
Tissue samples were homogenised using a Retsch 300MM homogeniser and total RNA was
isolated using the Trizol reagent or the RNeasy mini kit as described by the manufacturer.
First strand synthesis
First strand synthesis was performed using either OmniScnpt Reverse Transcriptase kit or M-
MLV Reverse transcriptase (essentially described by manufacturer (Ambion)) according to the
manufacturer's instructions (Qiagen). When using OmniScript Reverse Transcriptase 0.5 ug
total RNA each sample, was adjusted to 12 ul and mixed with 0.2 ul poly (dT)12-18 (0.5 ug/μl)
(Life Technologies), 2 ul dNTP mix (5 mM each), 2 pi lOx RT buffer, 0.5 ul RNAguard™ RNase
Inhibitor (33 units/ml, Amersham) and 1 ul OmniScript Reverse Transcriptase followed by
incubation at 37°C for 60 mm. and heat inactivation at 93°C for 5 min.
When first strand synthesis was performed using random decamers and M-MLV-Reverse
Transcriptase (essentially as described by manufacturer (Ambion)) 0.25 ug total RNA of each
sample was adjusted to 10.8 ul in H2O. 2 μl decamers and 2 ul dNTP mix (2.5 mM each) was
added. Samples were heated to 70°C for 3 min. and cooled immediately in ice water and
added 3.25 μl of a mix containing (2 ΜI.10X RT buffer; 1 μl M-MLV Reverse Transcriptase;

WO 2006/050734 PCT/DK2005/000721
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0.25 μl RNAase inhibitor). cDNA is synthesized at 429C for 60 min followed by heating
tnactivation step at 95°°C for 10 min and finally cooled to 4OOC.
Example 8: in vitro and in vivo model: Analysis of Oligonudeotide Inhibition of HIF-1a
Expression by Real-time PCR
Antisense modulation of HIF-la expression can be assayed m a variety of ways known in the
art. For example, HIF-la mRNA levels can be quantitated by,-e.g., Northern blot analysis,
competitive polymerase chain reaction (PCR), RIbonuclease protection assay (RPA) or real-
time PCR. Real-time quantitative PCR is presently preferred. RNA analysis can be performed
on total cellular RNA or mRNA.
Methods of RNA isolation and RNA analysis such as Northern blot analysis are routine in the
art and is taught in, for example, Current Protocols in Molecular Biology, John Wiley ond
Sons.
Real-time quantitative (PCR) can be conveniently accomplished using the commercially
available iQ Multi-Color Real Time PCR Detection System available from BioRAD.
Real-time Quantitative PCR Analysis of HIF-la mRNA Levels
Quantitation of mRNA levels was determined by real-time quantitative PCR using the iQ Multi-
Color Real Time PCR Detection System (BioRAD) according to the manufacturers Instructions.
Real-time Quantitative PCR is a technique well-known in the art and is taught in for example
Held et al. Real time quantitative PCR, Genome Research (1996), 6: 986-994.
Platinum Quantitative PCR SuperMix UDG 2x PCR master mix was obtained from Invitrogen
cat# 11730. Primers and TaqMan® probes were obtained from MWG-Biotech AG, Ebersberg,
Germany
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S RNA or p-actin mRNA quantity
was used as an endogenous control for normalizing any variance in sample preparation.
The sample content of human GAPDH mRNA was quantified using the human GAPDH AB1
Prism Pre-Developed TaqMan Assay Reagent (Applied Blosystems cat. no. 4310884E)
according to the manufacturer's instructions.

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For human HIF-la, the PCR primers were: forward primer: 51-
CTCATCCAAGAAGCCCTAACGTGTT -3' (SEQ ID NO. 21} {finalconcentratton in the assay; 0.9
MM) reverse primer: 5' -GCTTCTCTGAGCATTCTGCAAAGC-3' (SEQ ID NO. 22) (final
concentration in the assay; 0.9 uM) and the PCR probe was: 5' FAM -
CCTCAGGAACTGTAGTTCTTTCACTCAAAGCGACA -TAMRA 31 (SEQ ID NO. 23) (final
concentration in the assay; 0.1 μM).
For cynomolgus HIF-la, the PCR primers were: I forward primer: 5'-
GCTTACCATCAGCTATTTGCGTGTG -3' (final concentration in the assay; 0.9 μM) (SEQ ID NO.
24) reverse primer: 5' - GAACCATAACAAAACCATCCAAGGC -31 (SEQ ID NO. 25) (final
concentration in the assay; 0.9 μM) and the PCR probe was: 51 FAM -
TCATCTTCAATATCCAAATCACCAGCATCCAGAAG -TAMRA 31 (SEQ ID NO. 26) (final
concentration in the assay; 0.1 pM).
For quantification of 18S ribosomal RNA, the TaqMan Eukaryotic 18S rRNA Endogenous
Control reagent, (PART# 4310875, Applied Biosystems) was used according to the
manufacturers instructions.
For quantification of mouse GAPDH mRNA the following primers and probes were designed:
Sense primer 5'-AAGGCTGTGGGCAAGGTCATC-3' (SEQ ID NO. 27) (0.3 nM final
concentration),
antisense primer 5'-GTCAGATCCACGACGGACACATT-3'(SEQ ID NO. 28) (0.6 jiM final
concentration),
TaqMan probe 5'-FAM-GAAGCTCACTGGCATGGCATGGCCTTCCGTGTTC-TAMRA-3'(SEQ ID NO.
29) (0.2 μM final concentration).
Real time PCR using Taoman probes
The cDNA from the first strand synthesis performed as described in example 6 was diluted 2-
20 tfmes, and analyzed by real time quantitative PCR. The primers and probe were mixed
with 2 x Platinum Quantitative PCR SuperMix UDG (cat. # 11730, Invitrogen) and added to
3.3 μl cDNA to a final volume of 25 id. Each sample was analysed in triplicates. Assayings
fold dilutions of a cDNA that had been prepared on material purified from a cell line
expressing the RNA of Interest generated standard curves for the assays. Sterile H2O was
used instead of cDNA for the no template control. PCR program: 50°C for 2 minutes, 95°C for
10 minutes followed by 40 cycles of 95°C, 15 seconds, 60°C, 1 minutes.

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Relative quantities of target mRNA sequence were determined from the calculated Threshold
cycle using the iCyder iQ Real-time Detection System software, (See Figure 2).
SvBR Green Real Time PCR
To determine the relative mouse HIF1α mRNA level cDNA was used in quantitative PCR
analysis using an iCycler from BioRad.
To 8 μl of 5-fold diluted cDNA was added 52 ul of a mix containing 29.5 μl Platinum qPCR
Supermix-UDG (in-vitrogen), 1030 nM of each primer, 0.57 X SYBR Green (Molecular probes)
and 11.4 nM Fluorescein (Molecular probes).
Duplicates of 25 μl was used for Q-PCR: 50°C for 120 sec, 95°C for 120 sec. and 40 cycles
[95°C for 30 sec. and 60°C for 60 sec.].
HIF1a mRNA expression was normalized to mouse β-actin mRNA which was similarly
quantified using Q-PCR.
Primers:
mHIFla: 5'-TGGGACTTTCTTTTACCATGC-3'(SEQ ID NO. 30) and 5'-
GGAGTGTTTACGTTTTCCTGAAG-3'(SEQ ID NO. 31)
mβ-actin: 5'- CCTTCCTTCTTGGGTATGGAA-3 '(SEQ ID NO. 32) and 5 '-
GCTCAGGAGGAGCAATGATCT-3' (SEQ ID NO. 33)
mVEGF: 5 "-CACGACAGAAGGAGAGCAGAAGTC-3' (SEQ ID NO. 34) and 5' -
GTCGGGGTACTCCTGGAAGATGT-3 ' (SEQ ID NO. 35)
BCL-2: forward: 5'-gccctgtgg3tgactgagta-3' (SEQ ID NO. 36) and reverse: 5'-
cagccaggagaaatcaaacag-3' (SEQ ID NO. 37)
2-fold dilutions of cDNA synthesised from untreated mouse flbroblasts (Ltk cells) (diluted 5
fold and expressing both HIFla and β-actin) was used to prepare standard curves for the
assays. Relative quantities of HIFla mRNA were determined from the calculated Threshold
cycle using the iCycler iQ Real Time Detection System software.

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Example 9: In vitro analysis: Western blot analysis of HIF-1a protein levels
The in vitro effect of HIF-la LNA otigonudeotides on HIF-la protein levels in transfected cells
was determined by Western Blotting.
Cells were harvested and lysed in 50 mM Tris-HCI pH 6.8, 10% glycerol, 2.5% SDS, 5 mM
DTT and 6 M urea supplemented with protease inhibitor cocktail (Roche). Total protein
concentrations were measured using a BCA protein assay kit (Pierce). 20-100 ug total protein
was run on 10-12% Bis-Tris gels In MOPS buffer or on 3-8% Tris Acetate gels and blotted
onto a PVDF membranes according to manufacture's instructions (Invitrogen). After
overnight incubation in blocking buffer (PBS-T supplemented with 5% low fat milk powder),
the membranes were incubated overnight with of an anti-HIF-la antibody, Bcl-2 antibody
VEGF antibody or antibodies detecting other downstream of HIF-la. As control of loading,
tubulin or actin were detected using monoclonal antibodies from Neomarker. Membranes
were then incubated with secondary antibodies and HIF-la were visualized using a
chromogenic immunodetection kit (Invitrogen) or a chemiluminescens ECL+ detection kit
(Amersham). (See Figure 2A and Figure 2B)
Example 10: In vitro analysis: Antisense Inhibition of Human HIF-la Expression using
antisense oligonucleotides and their effect on the downstream targets VEGFA and MMP-2
The LNA oligonucleotides do also have an effect on the downstream targets VEGFA and MMP-
2 in media from U373 cells. U373 cells are seeded to 0.3 x 106 cells In T25 flasks (time
study) or 0.6 x 106 cells in T80 flasks (48 hours cone, study). U373 cells is placed at 37°C
(5% CO2) in growth media supplemented with 10% FBS, Glutamax I and Gentamicin. The
day after seeding cells were transfected with LNA oligonucleotides in duplicates or triplicates
using different concentrations of oligonucleotides (0.2 - 10 nM) using Lipofectamme 2000
(2.5 pg/ml). Transfections were carried,out essentially as described by Dean.et a/. (1994,. .
JBC 269:16416-16424). In short, cells were Incubated for 10 min. with Lipofectamme in
OptiMEM followed by addition of oiigonudeotide. After 4 hours, the transfection mix was
removed, celts were washed and grown-at 370C for approximately 20 hours (mRNA analysis
and protein analysis) during normoxia or hypoxia in the appropriate growth medium.
Supernatant from cells were harvested at the time indicated. Addition of protease Inhibitors
were added prior to storage at -80°C. Human VEGFA ellsa (Cat #OVE-00) and MMP-2 elisa
(cat # DMP-200) from RD systems was used according to manufacturer. Dependent on the
time of harvest supernatant was diluted 5-50 fold prior to measurement. See Figures 12A-E.

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Example 11: Apoptosis induction by LNA ollgonudeotides
Culturing of cells
The glioblastoma cell line U373 (ATCC) was cultured in MEM (Sigma) supplemented with 10%
fetal bovine serum, Glutamax I, NEAA, Sodium Pyruvate and gentamicin at 37°C, 95%
humidity and 5% CO2. When cell reached 60-70% confluency cells were transfected using
LJpofectamine 2000 (2.5 ng/ml).
The cervical carcinoma cell line Hela was cultured in MEM (Sigma) containing 10% fetal
bovine serum gentamicin at 37°C, 95% humidity and 5% CO2. When cell reached 60-70%
confluency cells were transfected using Lipofectamine 2000 (5 jig/ml).
Measurement of active Caspase 3/7 activity
U373 cells were seeded to a density of 7000 cells per well in white 96 well plate (Nunc
136101) in complete MEM the day prior to transfection. The next day cells were washed once
in prewarmed OptlMEM followed by addition of 72 μl OptiMEM containing 2.5 ng/ml
Lipofectamine2000 (In vitrogen). Cells were incubated for 7 min before adding 18 μl
oligonucleotides diluted in OptiMEM. The final oligonucleotide concentration ranged from 0.2
nM to 100 nM. After 6 hours of treatment, cells were washed in OptiMEM and 100 nl DMEM
containing serum was added. Similar 96 well plates with treated U373 cells were cultured
under normoxia or under Hypoxia/anoxia by placing the 96 well plates in anaerocult bags
(Merck) until the time of harvest. Plateswere equilibrated to room temperature for 15 min at
the time indicated. 100 μl of the highly sensitive Caspase 3/7-GloTM Reagent (Promega) was
added directly to the cells in 96well and plates were incubated for 1 hours min before
recording luminescence (luclferase activity) in Luminoskan Ascent instrument from Thermo
Labsystems after further 1 min tag period. The luciferase activity is measured as Relative -
Light Units per seconds (RLU/s). The data-was .processed in the Ascent software2,4.2..and .
graphs of fold induction In -relative to mock were drawn in excel.
Transfected cells incubated with the caspase 3/7 inhibitor, which block active caspase 3/7
activity were used to demonstrate specificity of the apoptotic response. Moreover,
Staurosporine, camptothecine or taxol Induced-celts served as positive control. (See Figure
3A and Figure 35.)
Annexin V-FITC flow cytorrtetrv analysis

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1 x 106 HeLa cells were seeded in T75 flasks one day prior to transfection. On the day of
transfection, the cells were washed once in 370C OptiMEM followed by addition of 7 ml
OptiMEM containing 2.5 tig/ml Lipofectamine2000 (In vitrogen). Cells were incubated for 7
min before adding 1700 μl oligonucleotides diluted in OptiMEM to a final concentration of 1-
25nM. Mock transfected cells served as control. After 4 hours of treatment, cells were washed
in OptiMEM and 10 ml culture medium was added. Following oligonucleotide treatment cells
were allowed to recover for 24-72 hours before they were harvested by scraping and washed
twice in PBS. 2 x 105 cells were incubated with 5 μl Annexln V-FITC and 10 μl propidium
iodide (PI- 10 mg/ml) and incubated for 15 min at room temperature in the dark. Incubation
of transfected cells with purified recomblnant Annexin V (10 μg) prior to adding Annexin V-
FITC were used to demonstrate specificity and selectivity of the staining. Moreover, TRAIL
(Apo2L) induced HeLa cells (0.5μg/ml) were used as positive control.
0.6 x 106 U373 cells were seeded in T75 flasks one day prior to transfection. On the day of
transfection, the cells were washed once in 37°C OptiMEM followed by addition of 7 ml
OptiMEM containing 2.5 ng/ml Lipofectamine2000 (In vitrogen). Cells were incubated for 7
min before adding 1700 μl oligonucleotides diluted in OptiMEM to a final concentration of 1-
25 nM. Mock transfected cells served as control. After 6 hours of treatment cells were washed
in OptiMEM and 10 ml culture medium was added. Following oligonucleotide treatment cells
were allowed to recover for 24-48 hours before they were harvested by scraping and washed
twice in PBS. 2 x 105 cells were incubated with 5 ^1 Annexin V-FITC and 10 nl propidium
iodide (PI- 10 mg/ml) and incubated for 15 min at room temperature in the dark. Incubation
of transfected celts with purified recombmant Annexin V (10 pg) prior .to adding Annexin V-
FITC were used to demonstrate specificity and selectivity of the staining. Moreover,
Staurosporine (0.2 μM) induced U373 cells were used as positive control. (See Figure 4A and
4B.)
Example 12: Proliferation inhibition by LNA oligonucleotides
Ceils were treated according to exampic 11.
Measurement of proliferating viable cells (MTS assay)
U373 cells were seeded to a density of 7000 cells per well in clear 96 well plate (Scientific
Orange no. 1472030100) in DMEM the day prior to transfection. The next day cells were
washed once in prewarmed OptiMEM followed by addition of 72 μl OptiMEM containing 2.5
jig/ml Lipofectamine2000 (Invitrogen). Cells were incubated for 7 mtn before adding 18 \ioligonucleotides diluted in OptiMEM. The final oligonucleotide concentration ranged from 5 nM

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to 100 nM. After 6 hours of treatment, cells were washed in OptiMEM and 100 μl serum
containing DMEM was added. Similar 96 well plates with treated U373 cells were cultured
under normoxia or under Hypoxia/anoxia by placing the 96 well plates in anaerocult bags
(Merck) until the time of harvest. Viable cells were measured at the times indicated by
adding 20 nl the tetrazollum compound [3-(4,5-dlmethyl-2-yl)-5-(3-carboxymethoxyphenyl)-
2-(4-sulfophenyl)-2H-tetrazolium, Inner salt; MTS] and an electron coupling reagent
(phenazine ethosulfate; PES) (CellTiter 96® AQueous One Solution Cell Proliferation Assay,
Promega). Viable cells were measured at 490 nm and 650 nm in a Powerwave (Biotek
Instruments).
The inhibition of growth rate AOD (490-650 nm)/h were plotted against the LNA
oligonucleotide concentration relative to mock, which were set to 100%. (See Figure 5A and
Figure 5B).
Example 13: In-vivo uptake and target down-regulation of LNA oligonucleotides
Hairy mice were treated either daily or twice a week (5 times) during a 14 days period i.p
injection with saline or SEQ ID NO. 1 and different thiolated versions hereof. SEQ ID NO. 5 is
partly thiolated (in the gap) whereas SEQ ID NO. 6 has a phosphodiester backbone. Mice
were treated with a total dose of 10 mg/kg/14 days, 50 mg/kg/14days, or 250 mg/kg/14
days given either daily or twice weekly.
RNA purification and cDNA synthesis from tissue
Approximately 10 mg tissue was homogenized in 400 μl RTL buffer (Qiagen) supplemented
with 1% mercaptoethanol. Total RNA was isolated using RNeasy mini kit (Qiagen) according
to manufacture's instructions.
First strand synthesis was performed using random.decamers and M-MLV-Reverse
Transcnptasc (essentially as described by manufacturer (Ambion)). For each sample, €.25 ug
total RNA was adjusted to 10.8 pi in H2O. 2 μl decamers and 2 ul dNTP mix (2.5 mM each)
was added. Samples were-heated to 70 °C for 3 min. and coded immediately in ice water and
added 3.25 μl of a mix containing (2 μl 10x RT buffer; 1 ul M-MLV Reverse Transcriptase;
0.25 ul RNAase inhibitor). cDNA is synthesized at 42°C for 60 min followed by heating
inactivation step at 95°C for 10 min and finally cooled to 4°C.
Quantitative Real Time PCR analysis

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To determine the relative mouse HlF 1a mRNA level in treated and untreated samples, the
generated cDNA was used in quantitative PCR analysis using an iCycler from BioRad.
To 8 pi of 5-fold diluted cDNA was added 52 μl of a mix containing 29.5 ul Platinum qPCR
Supermix-UDG (in-vitrogen), 1030 nM of each primer, 0.57 X SYBR Green (Molecular probes)
and 11.4 nM Fluorescein (Molecular probes).
Duplicates of 25 ul was used for Q-PCR: 50°C for 120 sec, 95°C for 120 sec. and 40 cycles
[95°C for 30 sec. and 60°C for 60 sec.].
HIF10 mRNA expression was normalized to mouse β-actln and/or Gapdh mRNA which was
similarly quantified using Q-PCR.
mHIF10: 5'-TGGGAC111C1111ACCATGC-3'(SEQ ID NO. 30) and 5'-
GGAGTGTTTACGI I I ICCTGAAG-3 '{SEQ ID NO. 31)
mβ-actin: 5'- CCTTCCTTCTTGGGTATGGAA-3'(SEQ ID NO. 32) and 5 '-
GCTCAGGAGGAGCAATGATCT-3' (SEQ ID NO. 33)
mVEGF: 5'-CACGACAGAAGGAGAGCAGAAGTC-3' (SEQ ID NO. 34) and 5'-
GTCGGGGTACTCCTGGAAGATGT-3 ' (SEQ ID NO. 35)
mGAPDH: 5'- AGCCTCGTCCCGTAGACAAAAT-3 '-(SEQ ID NO. 38) and 5 '-
GTTGATGGCAACAATCTCCACTTT-3' (SEQ ID NO. 39)
mBcl-2: forward: 5'-gccctgtggatgactgagt3-3' (SEQ ID NO. 36) and reverse: 5'-
cagccaggagaaatcaaacag-3' (SEQ ID NO. 37)
2-fold dilutions of cDNA synthesised from untreated mouse fibroblasts (Ltk cells) (diiuted 5
fold and expressing both HIFla and fl-acttn) was used to prepare standard curves for the
assays. Relative quantities of HIFla mRNA were determined from the calculated Threshold
cycle using the iCycler iQ Real Time- Detection System software.
Extraction of LNA oligonucleotide from tissue
Approximately 100 mg tissue was homogenized mech3nicatly in 5QQ pi Extraction buffer
(0.5% Igepal CA-630, 25 mM Tris pH 8.0, 25 mM EDTA, 100 mM NaCI containing 1 mg/ml

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RNAse A ) and incubated overnight at 37° C. 500 ml was spiked with reference
oligonucleotide and extracted by adding 1 ml phenol-isoamyl-choloroform (25:l:24(v/v/v)).
The aqueous phase was transferred to a new tube and extracted again. If necessary the
extract was lyophilized.
IEX HPLC analysis of extracted LNA oligonucleotldes
A sample volume of 50 μL was separated over a DNAPac PA-100 (2x250 mm, Dionex) column
equipped with a guard column DNAPac PA-100 (2x50 mm, Dionex). The columns were heated
to 40'C. The flow rate was 0.25 mL/mln. and detection wavelength 260 nm. A gradient of the
mobile phases A: TRIS (20 mM), EDTA (1 mM) and sodiumperchlorate (10 mM) pH: 7.6, B:
TRIS (20 mM), EDTA (1 mM) and sodiumperchlorate (1M) pH: 7.6, (0-13 min., A:20%, B:
20%; 14-18 min., A: 40%, B: 60%; 22-28 mln., A 0%, B: 100%; 33-38 min., A: 80%, B:
20%).
Figure 6A and Figure 6B show in vivo uptake (in ug per gram tissue) plus target down-
regulation (% inhibition of HIF-1a mRNA expression correlated to p-actin expression relative
to saline treated mice following i.p. administration of SEQ ID NO. 1 either daily or twice a
week for 14 days (as described above)).
Figure 6C shows in vivo endogenous kidney target down-regulation administered ip injections
daily in hairy mice for 14 days regimens of SEQ ID NO. 1.
Figure 7A shows that SEQ ID NO. l"is a potent inhibitor in the liver measured by Q-PCR on
HIF-la expression upon daily administration.
Figure 7B shows that SEQ ID NO. 1 is also a potent inhibitor in the liver measured by Q-PCR
on HIF-la expression upon administration twice a week..
Figure 7C SEQ ID NO. 1 is a potent inhibitor in the kianey measured by Q-PCR on HIF-la
expression upon daily administration.
Example 14: In vivo efficacy of SEQ ID NO. 1 in mice bearing U373 xenograft tumours
The effect of oligonucleotide treatment on growth of tumour xenografts on nude mice can be
measured using different tumour cell fines. Examples of such cell lines are human tumour cell
lines U87 (glioDlastoma), U373 (gliobiastoma), 15PC3 (prostate cancer) , PC3 (prostate.

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cancer), DU145 (prostate cancer), LNCap (prostate cancer and murine tumour cell line B16
(melanoma).
Treatment of subcutaneous tumour xenografts on nude mice using LNA oligonucleotides.
Tumour cells were implanted subcutaneously and then serially passaged by three consecutive
Transplantations. Tumour fragments of 1 mm were Implanted subcutaneously with a krocar
needle in NMRI nude mice. Alternatively, cancer cells typically 10E6 to 10E7 cells suspended
in 300 uL matrigel (BD Bioscience), were subcutaneously injected Into the flanks of NMRI:
nude mice. Mice were treated by intra-peritoneal injections 5 mg/kg/day. Individual
treatment of the mice started when tumour volume reached 50 mm3. Treatment with PBS
was initiated when mean tumour volume of the control (saline treated) group reached 50
mm3. The experiment was terminated when tumours of any group reached maximum allowed
sizes. The tumour sizes of all mice were measured daily by callper measurements. The effect
of treatment was measured as tumour size and tumour growth rate.
In another study using SEQ ID NO. 1, vital tumor pieces from U373 donor mice are
transplanted onto the fat tissue of the ovaries (day 0) of nude mice. On day four and nine
after transplantation mice are treated with LNA oligonucleotide at 50 mg/kg (i.p). Mice are
sacrificed 2 days after the last dose (day 11) and tumor weight plus staining of tumors with
CD-31 ab is performed (See Figures 8A and 8C).
Figures 8B and 8C show vessel density in U373 tumors from xenograft treated with SEQ ID
NO. 1. Figure 10D shows HIF-1a mRNA expression in U373 tumours measured by QPCR.
SEQ ID NO. 1 was dosedat 50 mg/kg twice a week for one week in-U373 xenograft mice
implanted at the ovaries. 2 days following the last dose animals was sacrificed. Vessel-
density was calculated following CD31 staining and related to the tota! area. A statistical
significant difference (P=0,005) was found between the satine group and the mice treated
with a scrambled control (SEQ ID NO. 12).
Example 15: Tissue half-life and target knockdown in liver and kidney of SEQ ID NO. 1
60 NMRI female mice, (app. 25g) was split In groups of 5 and dosed 30mg/kg SEQ ID NO.l,
i.p. (10 mL/kg 2.5 mg/ml) at day 0, 3, 7, 10 and 14. The groups were taken down at day 14.
The control groups were .dosed with 0.9% saline. Tissue samples was taken and prepared in
RNA-later.

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Figure 11 shows in vivo uptake (in ug per gram tissue) plus target down-regulation (%
inhibition of HIF-1a and VEGF mRNA expression correlated to p-actln expression) of mice
following 5 i.p. doses of SEQ ID NO. 1 30mg/kg.
Example 16: Duration of action and LNA oligonucleotide uptake in vivo
Duration of Action: 20 Balb/cA-nu, female mice, (app. 25g) PC3, prostate cancer cell line
(ECACC#90112714) was split in groups of 5 and dosed 25 mg/kg SEQ ID NO. 7, i.p. (10
mL/kg 2.5 mg/ml) every day from day 7 to day 13. The groups were taken down one and 5
days after dosing. The control groups were dosed with 0.9% saline. Tissue samples were
taken and prepared in RNA-later. Figure 10A shows duration of action of mRNA expression 1
and 5 days post treatment.
LNA oligonucleotide uptake: Following formalin fixation, the tissues were paraffin embeeded.
The tissue were placed in Holt's solution (30 g saccharose, 1 g acacia gum, 15mg thymol,
distillled water at 100 ml).over night and frozen. Cryosectiorts at 4. my's monted on
coated glass and placed in DAPI solution. The fluorochrome was visualised in flourescence
microscopy. Figure 10B shows htstologicaf results from tissue from fiver, kidney and tumor
are from mice treated with a fam- labeled version SEQ ID NO. 1-at 25 mg/kg/day for seven
days and sacrificed the 5 days following the last treatment. The picture of the skin is from
mice treated the same way, however, sacrificed the day after the last treatment and
overexposed in order to see the weak staining of the basaf cells of the skin (the lower blue
line). These data suggests the following:
Liver: the staining in hepatocytes in mainly located in the cytoplasm
Kidney: Very intensive stainingof the proximal tobutr andless staining of the distal tubult.
Tumor: Endothelial cell, macrophages are stained (mouse cells).
Skin: An intense staining af the dermis (endothelial cells and macrophages) and in the . .
cytoplasma of the basal layer of the epidermis.
Example 17: LNA oligonucleotide uptake and efficacy in vivo
At day 0.3xl0'6 cells (PC3 and HT29) were mixed with 300 μl matrixgel and implanted on
Balb/cA-nu, female mice, (app. 25g). On day 7, 10, 13, 17 mice were treated by intra-

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peritoneal injections 5 mg/kg/day with either saline, a fam labeled version of SEQ ID NO. l
(SEQ ID NO. 7) or a fam labeled version of SEQ ID NO. 8 (SEQ ID NO. 20). Three days (day
20) or 10 days (day 27) after the last dose, the animals were sacrificed. The saline control
group was dosed with 0.9% saline. Tissue samples were taken and prepared in RNA-later
until measurement of LNA oligonucleotide content by HPLC analysis or analysis of HIF-la
mRNA down-regulation, (see Figures 10C-E).
Visualisation of LNA oligonucleotide uptake: Following formalin fixation the tissues were
paraffin embedded. The tissue were placed in Holt's solution (30 g saccharose, 1 g acacia
gum, 15 mg thymol, distilled water as 100 ml) over night and frozen. Cryosections at 4 my's
monted on coated glass and placed in DAPI solution. The fluorochrome was visualised in
flourescence microscopy (data demonstrating the same blodistnbution as in Figure 10B - data
not shown).
Example 18: In vivo LNA oligonucleotide specificity study of HIF-1a. and VEGF
Mismatch study: 15 NMR1 female mice, (app. 25g) were split in groups of 5 and dosed 30
mg/kg SEQ ID NO. 1 or SEQ ID NO. 9i.p. (10 mL/kg, 3.0 mg/ml) over 30 sec day 0, 3, 7,
10, 14. The control groups were dosed with 0.9% saline. The groups were taken down 3-4
hours after last injection. Tissue samples were taken and prepared in RNA-later..
Figure 11 shows in vivo endogenous liver target down-regulation of HIF-la and VEGF mRNA
after 5 doses of 30 mg/kg every 3rd day of SEQ ID NO. 1 compared tothe one mismatch
control SEQ ID NO. 9.
Example 19: In vivo potency of a 14 mer-version of SEQ ID NO. 1.
NMRI female mice (0.025 kg) were treated by mtra-perttoneat injections 5 mg/kg/day with
SEQ ID NO. 1. Saline animate served as control animals and were dosed with 0.9% saline.
Five animals were sacrificed 1 day or 10 days after dosing. Tissue samples were taken and
prepared in RNA-later untH measurement HIF-la mRNA expression by QPCR and normalised .
to beta-acttn as described in M&M.
Example 20: Preparation of the three-dimensional aortic ring cultures
Angiogenesis was studied by cuituring rings of mouse aorta in three-dimensional coilagen
gels with some modifications of the method originally reported for the rat aorta (Masson et

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al., 2002 Biol Preoced Online 4(1) p.24-31). Hairy mice were treated once i.v. with LNA
oligonucleotides at a dose ranging from (10 mg/kg to 50 mg/kg). Three days after dosing the
thoracic aortas were removed from the mice, sacrificed by cervical dislocation and
immediately transferred to a culture dish containing ice RPMI Medium (Invitrogen) containing
10% Fetal Calf Serum. The peri-aortic fioroadipose tissue was carefully removed with fine
microdissecting forceps and iridectomy scissors paying special attention not to damage the
aortic wall. One millimeter long aortic rings (approximately 15 per aorta - a max of 1.5 cm of
the aorta) were sectioned and extensively rinsed In 3 consecutive washes of RPMI with FBS.
Ring-shaped explants of mouse aorta were then embedded in 60 uL of matrigel (BD
biosciences - Matrixgel: 356234) in a well of a 96 well plate. Following Insertion of the aorta
another 40 uL of matrigel is added and left at 37°C for 10 min to solidify. 100 uL of EGM2
(Cambrix) with and without growth factors is added to the wells. As a control, aorta rings arc
additionally covered with EGM2 media contaning 10 uM Ciplatin. The medium was changed
every second day.
Example 21: Quantitative whole body autoradlography scud/ In mice after single intravenous
administration of 'JH-iabelled SEQ ID NO. 1
Nine female C57B1/6J (8 weeks Taconic, DK) mice were given 50 mg/kg of each test item
intravenously in a tail vein 1.5 mO/kg 3H-SEQ ID NO. 1. " .
3H-SEQ ID NO. 1 had a specific activity of 155 MCi/mL
The volume given to each animal was 10 mL/kg.of the test formulation.. Individual mice were"
killed at 5 min, 15 mm, 1 hour, 4 hours, 24 hours, 2 days, 4 days, 7 days and 18 days after
administration of each test item.
For whole body autoradlography, the mice were anaesthetized by isofluran, and then
immediately immersed in hexane cooled with dry ice to -80°C, ABR-SOP-0130/04.-The frozen
carcasses were embedded in a gel of aqueous carboxymethyl cellulose (CMC), frozen in
ethanol, cooled with dry ice (-80°C) and sectionedsagittaty for whole body autoradlography,
according to the standard.method, ABR.-SOP-0131/04. From each animal, 20 um sections
were cut at different levels with a-cryomicrotome (Leica CM 3600} at a temperature of about
-20°C. The obtained sections were caught on tape (Minnesota Mining and Manufacturing-Co.,
No. 810) and numbered consecutively with radioactive ink. After being freeze-dried at -20°C
for about 24 hours, selected sections were covered with a thin layer of talcum powder and
put on imaging plates (Fuji, Japan).

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Sections were chosen for phosphor imaging to best represent the tissues and organs of
interest. Together with a set of 3H calibration standards, the sections were covered with a
thin layer of talcum powder and put on Imaging plates. Due to the low energy of 3H, talcum
powder was used instead of plastic foil in order to protect the image plate. The imaging
plates were exposed for 3-7 days at room temperature, enclosed in light tight cassettes in a
lead shielding box to protect from environmental radiation.
Following exposure the imaging plates were scanned at a pixel size of 50 μm using BAS 2500
(Fuji Film Sverige AB, Sweden). The tissues and organs of interest were quantified using
AIDA, version 2.43 (Raytest, Germany).
A water-soluble standard test solution of 3H radioactivity was mixed with whole blood and
used for the production of the calibration scale. The standard series consisted of 10 dilutions
from 65.44 to 0.30 nCi/mg. For the purpose of quantification, it was assumed that all tissues
had similar density and quench characteristics as that of whole blood. The tissue density was
set to 1 g/ml. The limit of quantification was defined as the mean concentration value of
eight measurements for background plus three-times thestandarddeviation value of these
measurements.
The various tissues and organs were identified either on the autoradiograms or on the
corresponding tissue sections. The term uvea used in this study includes the retinal pigment
epithelium representing melanin containing structures, chorowds and sclera "of-the eye. (see
Figures 14A and 14B}.
Example 22: Western clot of HUVEC ceils transfected with SEQ ID NO. 1-
Normal Human Umbilical VelivEndothelial (HUVEC) celis were cultured in Cambnx-EGM2
medie were transfected as described in example using 2 and 5 nM SEQ ID NO. 1 or 5 nM SEQ
ID NO. 8. Following transfectson celts were exposed hypoxia (1% Oxygen) for 16 hours. At
harvest cells were washed in PBS and iysed in a SDS containing lysis buffer (as described in
example). 50 μg was loaded to-Tris-Acetategels and run at 150 V for 1 hour. Western
blotting was performed as described in example and the blot was incubated in anti-human-
HIF-1a (i:500) prior to visualisation by enhanced chemiluminescence. A potent down-
regulation by SEQ ID NO. 1 is seen, whereas the scrambled control SEQ ID NO. 8-does not
down-regulate HIF-1a expression in HUVEC cells.

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Example 23: In vitro Tubeformation/Capillary-Like Structure Formation Assay
Induction of tubulogenesls was performed using Matrigel (Venetsanakos E, Mirza A, Fanton C
et al. Induction of tubulogenesis in telomerase-immortalized human microvascular
endothelial cells by glioblastoma cells. Exp Cell Res 2002;273:21-33). Matrigel was thawed
on ice to prevent premature polymerization; aliquots of 50 ul were plated into individual wells
of 96-well tissue culture plates (Nunc) and allowed to polymerize at 37°C for at least 30
minutes. Transfected HUVEC Cells were removed by treatment with trypsin 0.05%-EDTA. The
cells were washed In serum-containing medium then resuspended to 2-x10E5 cells/ml. Into
each culture well 100-ul transfected or un-transfected HUVEC cell suspension in culture media
with growth factors (VEGF, hFGF-B, R3-IGF-l,hEGF with FBS (2%)) and heparin was added
(n=10). Untreated, mock-transfected as well as HUVEC cells transfected with a scrambled
control oligo (5EQ ID NO. 8) were used as controls. Dose of control or test compound was
assayed in 6-10 individual weils and the experiments were performed at least three times.
For quantification of tube formation the wells was photographed. (See Figure 13)
Example 24: FACS analysis of uptake in cells of the spleen, bone marrow and peripheral
blood.
NMRI female mice (0.025 kg) were treated with a fam labelled version of SEQ ID NO. 1, SEQ
ID NO. 7 (50 mg/kg) or an equivalent number of molecules of the Fam amidite (at 3 rng/kg)
or 0.9% saline. Cells were sacnficedl hour post injection and cells from spleen, Peripheral
Blood (1 ml to which 1 ml PBS containing 0.l% sodium azide + 50 mfheparin sulfate is
added- place on ice) or Bone marrow is harvested
Spleen
Place spleen in a metal mesh, and wet with lml R10 (R10 tissue culture medium containing
10% FCS) containing azide. Push the tissue through the mesh and flush through with a total
of 4m! RIO + A2ide. Remove 0.5 rnl of tissue suspension and discard the remainder. The red
blood cells are lysed in the suspension by adding 50 ml Red Cell Lysis buffer mix and leave at
RT for 10 min. Spin 2000 rpm 10 rnins. If necessary to remove the residual red cells repeat
this process. Count and block cells.
Spin cells down and rcsuspend In L.O ml FACS buffer containing azide. Assume ceil numbers
5x106 cells per spleen for blocking and add 5 μl of murip.e CD16/CD32 per million cells (25 ul
Blocking is added).

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Peripheral Blood
The red cells are lysed by adding 50 ml of Red Cell Lysis Solution. Cells are spun down and
the process is repeated if necessary. Cells are washed once with PBS, resuspend and count.
Non-specific antibody binding is blocked by adding murine CD16/CD32 at the rate 5pE per
million cells. Leave at RT for 10 min, then proceed to lineage stains.
Bone Marrow
Cut the bone as close to each end as possible using sterile scissors. Draw up lml of sterile
PBS- into lml syringe fitted with a 25G needle. Insert the needle into one end of the bone -
usually easiest at the knee - and flush the PBS through the bone. Repeat until the bone is
clear. Draw the bone marrow up into the needle several times to break up the marrow. If
concerned about the number of red cells a lysis step can be used as above.
Count the cells and block as above. Place 150,000 cells in a sterile eppendorf tube on ice for
the Bone Marrow Cultures.
FACS stains
Lineage stains are performed using specific markers. As described:
Stains

1. CD4 APC, CD8 PE FITC, 7AAD T-cells
2. Gr-1 PE, f4/80 APC neutrophils, macrophages
3. Gr-1 PE, Mac-IAPC myelo-monocytic
4. CD34 PE lineage APC stem cells
5. B220 APC, CD19 PE B cells
6. CD11b PE, CD11c APC dendritic cells
Isotypes

7. American hamster IgGl APC CDllc.
8. Rat IgG2a APC CD4, B220
9. Rat IgG2a PE cd8a, CD19, CD34

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10. Rat IgG2b PE Gr-1 CD11b
The stains are performed in 96 wells and a total number of 100 |jl blocked cells are stained
with 100 pi stain mix (either isotype controls or specific lineage markers). The stains are
performed on ice and left for 30 mln. The cells are spun for 2000 rpm for 2 min. The
supernatant is sucked off and the cells are washed with 200 pi FACS buffer and repeat the
centrifugation step. Wash a total of three times. At the end the cells are resuspended in 200
pi of FACS buffer and add to a FACS tube which already contains 200 pi of FACS + 5 pi of
7AAD.
FACS analysis was carried out by using Becton Dickinson FACS Callbur (see Figure 15).
Endothelial cells, granulocytes and CD4+ lymphocytes and macrophages of peripheral blood
and dendritic cells and granulocytes of the bone marrow and granulocytes of the spleen was
shown to stain positive for FAM-labeting five days following administration of SEQ ID NO. 7.
Example 25: Hif-la and oligonudeotide content of SEQ ID NO. 1 in cynomolgus monkey
tissues
In the mam toxicity study in cynomotgus monkeys tissues including liver and kidneysamples
were snap frozen and stored at -70°C for subsequent analysis, (see Figure 16A and 16B) The
monkeys had been treated with intravenous injection of 0, 6, 10 and 40 mg/kg/occasion
twice weekly for four weeks In the groups of animals receiving 0, 10 or 40 mg/kg/occasion
some animals were fcllowed-for a recovery period of 4 weeks without treatment.
RNA was extracted from samples as described in Example 13 and HIF-la mRNA content was
measured as described in Example 8 (see-Figure 16A). Oltgonudeotide content was
measured as described below (see Figure 16B).
Sample preparation: Extraction from liver and kidney tissues
Chemicals/reagents:
Protelnase K(25.1 mg/ml): Sigma P4850.
Phenol-chloroform-isoamyi-aicohol (25:24:l(v/v/v), saturated with 10mM Tris, pH: 8.0, lmM
EDTA: Sigma P2069

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Igepal CA-630: Sigma, 18896
Extraction buffer: 0.5% Igepal CA-630, 25 mM Tris pH 8.0, 25 mM EDTA, 100 mM NaCI, pH
8.0 (adjusted with 1 N NaOH)
1 mg/ml of Proteinase K in extraction buffer: Prepared before each extraction.
Tissues (~100 mg) is weighed off (tissue is kept on dry-ice before and after weighing). 500pl
extraction buffer containing proteinase K (1 mg/ml) is added. The tissue is homogenized
mechanically and the homogenate is incubated over night at 37°C.
Reference samples are prepared by dissolving SEQ ID NO. 2 in extraction buffer at the
relevant concentration range. Exactly 100 mg liver tissue from un-treated animals is weighed
off (kept on dry-ice before and after weighing). Extraction buffer (with proteinase K, 1
mg/ml) containing the reference material is added to the tissue samples to a total volume of
0.5 ml. The tissue is mechanically homogenized and is incubated over night at 37°C. The
detection signal of SEQ ID NO. 2 from these samples is used to prepare a standard curve
covering the lowest and the highest concentrations found-in tne treated animals.
Tissue samples are transferred to 2 ml microtubes with screw caps. 1 ml phenol-chloroform-
soamyl-alcohol (25:24: l(v/v/v)) is added following vigorously shaking for 5mir*. Phase -
separation is achieved by centrifugation at 4000 RPM for 15 min. The aqueous phase (upper- -
phase) is transferred to a new tube (compatible with the evaporator) and 500 ul Milli-Q-H2O
is added to the organic phase (residual from the firstrextraction). The tubes are stirred
vigorously again for 5 min, following centrifugation at 4000 RPM for 15 min (SAN039 in room
115). The aqueous phases (water phases from 1. extraction and wash) are pooled and
evaporated to dryness (80°C, under nitrogen). The residual is reconstituted in 200 ul Milli-Q-
Water following centnfugatlan at 4000 RPM for 15 mm. The samples are transferred to HPLC-
vials for analysis.
HPLC analysis of oligonucleotide in liver and kidney tissues: Subsequent to the extraction
SEQ ID NO. 2 is analysed by Ion exchange HPLC:
Column:Dlonex, DNA pac PA 100: 2 x 50 mm (guard), 2 x 250 mm (analytical).
Column temp: 42°C
Injection vol.: 50 μl

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Wash-solvent: Milli-Q-H2O
Purge-solvent: Milll-Q-H2O
Detection :UV, 260 nm
Solvents:
Buffer A: 1 mM EDTA, 20 mM TRIS-CI, 10 mM NaCIO4,pH: 7.6 (1 N NaOH)
Buffer B: 1 mM EDTA, 20 mM TRIS-CI, 1 M NaCIO4,pH: 7.6 (1 N NaOH)
Example 26: Duration of action of in vivotreatment using SEQ ID NO.l
Hairy mice were treated with one i.p. injection of 50mg/kg SEQ ID NO. 1. 5 animals in each
group were sacrificed at days 1 and 10 after dosing (see Figure 9C) or at days 1, 2, 3, A, 5
and 10 after dosing (see Figure 9B). MF-lo mRNA expression was analysed by real-time
QPCR and normalised to GAPDH.
Example 27: in vivo eye disease comeal model
Mice and anesthesia. BALB/c mice 6-8 weeks of age. Mice were anesthetized using a
mixture of ketamine and xyiazine (120 mg/kg body weight and 20 mg/kg body weight,
respectively).
Mouse model of suture-Induced, inflammatory corneai neovascularization. The
mouse modef of suture-induced inflammatory corneai neovasculanzation (CNV) was used as
previously described by Streilein JW, Bradley D, Sano Y, Sonoda Y. Immunosuppressi-ve.
properties of tissues obtained from eyes with experimentally manipulated corneas, invest.
Ophthalmol. Vis. Sci. 1996;37:413-424. Briefly, a 2-mm-diameter corneai trephine was
placed gently on the central cornea of anesthetized mice solely to mark the central corneai
area. Three 11-0 sutures were then placed intrastromally with two stromal incursions each
extending over 120° of the corneai circumference. The outer point of suture placement
chosen was halfway between, the limbus and the tine outlined by the 2-mm trephine; the
inner suture point was at the same distance from the 2-mm trephine (me to .obtain
standardized angiogenic responses. Sutures were left in place for 7 days. Mice were
euthanized and the cornea with limbus was excised, ana flat-mount double-
immunohistochemistry was performed. The presence of inflammatory cells in normal corneas

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and their recruitment into corneas 1 week after suture placement was quantified in
hematoxylin and eosin-stained serial sections of plastic-embedded corneas fixed in 10%
paraformaldehyde after enucleation. In addition, for further characterization of inflammatory
colls recruited to the cornea, double immunohistochemlstry was-performedon corneal whole
mounts and frozen sections with the macrophage markers CDllb. The sections was
moreover stained for endothelial cells (vessels by CD31), markers for VEGF, and VEGFR's.
Example 28: The corneal miovpocket assay
The corneal micropocket assay was performed as previously described (Cao Y, et at. Vascular
endothelial growth factor C induces angiogenesis in vivo. Proc. Natl. Acad. Sd. U. S. A. .
1998;95:14389-14394 ). Briefly, corneal mrcropockets were created using a modified von .
Graefe knife, and a micropeJIet (0.4 x 0.4 mm) of sucrose aluminum sulfate coated with
hydron polymer containing 200 ng of VEGF-A164 (R&D) or 200 ng of recombinant bfgf (RDI,
Flanders, New Jersey, USA) was implanted Into each pocket. The pellet was positioned 0.6-
0.8 mm from the iimbus and the site was covered with antibiotic ointment (erythromycin)
and was left in place for 10 days (n > 5-10 mice each). Hemangiogenic and lymphangtogenic
responses were quantified as described above using double immunostaming with CD31/LYVE-
1. The maximal extent of blood versus lymph vessel outgrowth between subjacent Iimbus
and pellet was graded semiquarttitatively in four categories for both vessel types: 0, no
outgrowth; 1, outgrowth less than 1/3 of the limbus-pellet distance; 2, outgrowth between
1/3 and 2/3 of the limbus-pellet distance; 3, vessel reaching pellet.
Example 29: in vivo psoriasis model
In vivo Human Skin/SCID Mouse Chimera
Human skin xenografts were orthotopically transplanted onto 7- to 8-week-old SCID mice
(Taconic, DK) following previously described procedures by Wrone-Smith T, Nickoloff BJ:
Dermal injection of immunocytes induces psoriasis. J CHn Invest 1996, 98:1878-1887.
Briefly, human skin xenografts measuring 1.5.x 1.5 x 0.5 cm were sutured to the flank of
SCID mice with absorbable 5-0 Vicryl Rapide suture (Ethicon, Somerville, NJ) and covered
with Xeroform dressings (Kendall Co., Mansfield, MA). Dressings were removed 1- week later
and animals maintained pathogen-free throughout the study. The mice were treated with .
SEW ID NO. 1 and SEQ ID NO. 7 twice a week at 50 rng/kg one-three weeks after
transplantation. Human skin/SCID mouse chimeras were kitted following 2-3 weeks of
treatment and 4-mm punch biopsies (Baker's Biopsy Punch, Cummins Derm, Miami, FL) were
obtained from each xenograft. Biopsies were fixed in neutraf-buffered formalin for paraffin

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embedding and/or mounted on gum tragacanth (Sigma Chemical Co., St. Louis, MO), snap-
frozen in liquid nitrogen-chilled isopentane, and stored at -80°C.
Immunostaining
Cryostat sections of skin were stained for relevant marker including endotheial cells
(CD31/CD34), macnophages (cdllb) VEGF, VEGFR or HIF-la. The sections were counter-
stained with hematoxylin and eosin (as described previously}. All slides were examined and
photographed.

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embedding and/or mounted on gum tragacanth (Sigma Chemical Co., St. Louis, MO), snap-
frozen in liquid nitrogen-chilled Isopentane, and stored at -80°C.
Immunostaining
Cryostat sections of skin were stained for relevant marker including endotheial cells
(CD31/CD34), macrophages (cdllb) VEGF, VEGFR or HIF-la. The sections were counter-
stained with hematoxylln and eosin (as described previously). All slides were examined and
photographed.

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CLAIMS
1. An LNA oligonucleotlde consisting of a sequence selected from the group consisting of

wherein capital letters designate a beta-D-oxy-LNA nucleotide analogue, small letters
designate a 2-deoxynucleotide, underline designates either a beta-D-oxy-LNA nucleotide
analogue or a 2-deoxynucleotide, subscript "s" designates a phosphorothioate link between
neighbouring nucleotides/LNA nucleotide analogues, and subscript "x" designates either a
phosphorothioate link or a phosphorodiester link between neighbouring nucleotides/LNA
nucleotide analogues, and where the nucleotide units in the bracket represent optional units,
and wherein the sequence is optionally extended by up to five 2-deoxynucleotide units.
2. The LNA oligonucleotide according to claim 1, wherein the nucleotide unit in the bracket,
(Ix) or (Gx), respectively, is present.
3. The LNA oligonucleotide according to any one of the claims 1 and 2, where one or both of
the underlined nucleotide units designate a beta-D-oxy-LNA nucleotide analogue.
4. The LNA oligonucleotide according to any one of the preceding claims, wherein the LNA
oligonucleotide consists of 15, 16, 17, 18, 19 or 20 nucleotide units selected from 2-
deoxynucleotides and beta-D-oxy-LNA nucleotide analogues.
5. The LNA oligonucleotide according to claim 4, wherein the LNA oligonucleotide consists of
16 nucleotide units selected from 2-deoxynucleotides and beta-D-oxy-LNA nucleotide
analogues.
6. The LNA oligonucleotide according to any one of the preceding claims, wherein the
sequence is extended by one 2-deoxynucleotide unit at the 3'-end.
7. The LNA oligonucleotide according to any one of the preceding claims, wherein all
nucleotide units in the sequence are linked by a phosphorothioate group.

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8. The LNA oligonucleotide according to claim 1, which is selected from the group consisting
of

10. The LNA oligonucleotide according to claim 1, which is selected from the group consisting
of

12. A conjugate comprising an LNA oligonucleotide according to any one of the claims 1-11
and at least one non-nucleotide or non-polynucleotide moiety covalently attached to said LNA
oligonucleotide.
13. A pharmaceutical composition comprising an LNA oligonucleotide as defined in any one of
the claims 1-11 or a conjugate as defined in claim 12, and a pharmaceutically acceptable
diluent, carrier or adjuvant.
14. The pharmaceutical composition according to claim 13, which comprises an aqueous
carrier, said carrier comprising a buffer for keeping the pH in the range of 4.0-8.5 and having
an Ionic strength of 20-2000 mM.

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15. The pharmaceutical composition according to any one of the claims 13-14, which is
adapted for intraocular administration.
16. The pharmaceutical composition according to any one of the claims 13-15 further
comprising at least one chemotherapeutlc agent.
17. An LNA oligonucleotide as defined in any one of the claims 1-11 or a conjugate as defined
in claim 12 for use as a medicament.
18. Use of an LNA oligonucleotide as defined in any one of the claims 1-11 or a conjugate as
defined in claim 12 for the manufacture of a medicament for the treatment of cancer.
19. The use according to claim 18, wherein said cancer is in the form of a solid tumor.
20. The use according to claim 18, wherein the cancer is selected from the group consisting
of multiple myeloma, renal cancer, cervical cancer, colon cancer, brain cancer, and breast
cancer.
21. A method for treating cancer, said method comprising administering an LNA
oligonucleotide as defined in any one of the claims 1-11 or a conjugate as defined in claim 12
or a pharmaceutical composition as defined in any one of the claims 13-16 to a patient in
need thereof.
22. The method according to claim 21, wherein the cancer is selected from the group
consisting of multiple myeloma, renal cancer, cervical cancer, colon cancer, brain cancer, and
breast cancer.
23. Use of an LNA oligonucleotide as defined in any one of the claims 1-11 or a conjugate as
defined in claim 12 for the preparation of a medicament for the treatment of a disease
selected from the group consisting of artherosclerosis, psoriasis, diabetic retinopathy,
macular degeneration, rheumatoid arthritis, asthma, inflammatory bowel disease, warts,
allergic dermatitis, inflammation, and skin Inflammation.
24. The use according to claim 23, wherein the disease is selected from inflammatory bowel
disease, psoriasis and rheumatoid arthritis.
25. A method for treating a disease selected from the group consisting of artherosclerosis,
psoriasis, diabetic retinopathy, macular degeneration, rheumatoid arthritis, asthma,

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inflammatory bowel disease, warts, allergic dermatitis, inflammation, and skin inflammation,
said method comprising administering an LNA oligonucleotide as defined in any one of the
claims 1-11 or a conjugate as defined in claim 12 or a pharmaceutical composition as defined
in any one of the claims 13-16 to a patient in need thereof.
26. The method according to claim 25, wherein the disease is selected from inflammatory
bowel disease, psoriasis and rheumatoid arthritis.
27. A method of treating a mammal suffering from or susceptible from a disease caused by
abnormal angiogenesis, comprising administering to the mammal a therapeutically effective
amount of an LNA oligonucleotide as defined in any one of the claims 1-11 or a conjugate as
defined in claim 12.
28. A method of inhibiting angiogenesis comprising the administration of an LNA
oligonucleotide as defined in any one of the claims 1-11 or a conjugate as defined in claim 12
or a pharmaceutical composition as defined in any one of the claims 13-16.
29. A method of inducing cellular apoptosis comprising the administration of an LNA
oligonucleotide as defined In any one of the claims 1-11 or a conjugate as defined in claim 12
or a pharmaceutical composition as defined in any one of the claims 13-16.
30. A method of preventing cellular proliferation comprising the administration of an LNA
oligonucleotide as defined in any one of the claims 1-11 or a conjugate as defined in claim 12
or a pharmaceutical composition as defined in any one of the claims 13-16.
31. A method of treating an angiogenic disease comprising the administration of an LNA
oligonucleotide as defined in any one of the claims 1-11 or a conjugate as defined In claim 12
or a pharmaceutical composition as defined in any one of the claims 13-16, such that
angiogenesis associated with the angiogenic disease is inhibited.
32. The method according to claim 31, wherein the angiogenic disease is selected from the
group consisting of diabetic retinopathy, macular degeneration, and inflammatory diseases.
33. The method according to claim 32, wherein the angiogenic disease is an inflammatory
disease selected from inflammatory bowel disease, psoriasis and rheumatoid arthritis.
34. The method according to claim 32, wherein the angiogenic disease is macular
degeneration and diabetic retinopathy.

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35. A kit comprising
(a) a first component containing an LNA oligonudeotide as defined in any one of the claims
1-11 or a conjugate as defined in claim 12 in solid form, and
(b) a second component containing saline or a buffer solution adapted for reconstitution of
said LNA oligonucleotides.

The present disclosure relates to an LNA oligonucleotide consisting of a sequence selected from the group consisting of 5'-(Tx GxGxcsasasasgscsastscscsTxGx T-3' and 5'-(Gx )TxTxascstsgscscststscsTxTx A-3', wherein capital letters designate a beta-D-oxy-LNA nucleotide analogue, small letters designate a 2-deoxynucleotide, underline designates either a beta-D-oxy-LNA nucleotide analogue or a 2-deoxynucleotide, subscript "s" designates a phosphorothioate link between neighbouring nucleotides/LNA nucleotide analogues, and subscript "x" designates either a phosphorothioate link or a phosphorodiester link between neighbouring nucleotides/LNA nucleotide analogues, and wherein the sequence is optionally extended by up to five 2-deoxynucleotide units. The LNA oligonucleotides are useful for modulating the expression of hypoxia-inducible factor-1a (HIF-1a), e.g. in the treatment of cancer diseases, inhibiting angiogenesis, inducing apoptosis, preventing cellular proliferation, or treating an angiogenic disease, e.g. diabetic retinopathy, macular degeneration (ARMD), psoriasis, rheumatoid arthritis and other inflammatory diseases.

Documents:

01791-kolnp-2007-abstract.pdf

01791-kolnp-2007-assignment.pdf

01791-kolnp-2007-claims.pdf

01791-kolnp-2007-correspondence others 1.1.pdf

01791-kolnp-2007-correspondence others.pdf

01791-kolnp-2007-description complete.pdf

01791-kolnp-2007-drawings.pdf

01791-kolnp-2007-form 1.pdf

01791-kolnp-2007-form 3 1.1.pdf

01791-kolnp-2007-form 3.pdf

01791-kolnp-2007-form 5.pdf

01791-kolnp-2007-international publication.pdf

01791-kolnp-2007-international search report.pdf

01791-kolnp-2007-sequence listing.pdf

1791-KOLNP-2007-(08-09-2011)-ABSTRACT.pdf

1791-KOLNP-2007-(08-09-2011)-AMANDED CLAIMS.pdf

1791-KOLNP-2007-(08-09-2011)-DESCRIPTION (COMPLETE).pdf

1791-KOLNP-2007-(08-09-2011)-DRAWINGS.pdf

1791-KOLNP-2007-(08-09-2011)-FORM 1.pdf

1791-KOLNP-2007-(08-09-2011)-FORM 13.pdf

1791-KOLNP-2007-(08-09-2011)-FORM 2.pdf

1791-KOLNP-2007-(08-09-2011)-PETITION UNDER RULE 137.pdf

1791-KOLNP-2007-(12-06-2012)-CORRESPONDENCE.pdf

1791-KOLNP-2007-(12-06-2012)-OTHERS.pdf

1791-KOLNP-2007-(12-06-2012)-PA-CERTIFIED COPIES.pdf

1791-KOLNP-2007-(17-02-2012)-EXAMINATION REPORT REPLY RECIEVED.PDF

1791-KOLNP-2007-(22-02-2010)FORM 13.pdf

1791-KOLNP-2007-ASSIGNMENT.pdf

1791-KOLNP-2007-CORRESPONDENCE 1.1.pdf

1791-KOLNP-2007-CORRESPONDENCE.pdf

1791-KOLNP-2007-FORM 13.1.1.pdf

1791-KOLNP-2007-FORM 13.pdf

1791-KOLNP-2007-FORM 6.pdf

1791-kolnp-2007-form-18.pdf

1791-KOLNP-2007-PA.pdf

1791-KOLNP-2007-REPLY TO EXAMINATION REPORT-1.2.pdf

1791-KOLNP-2007-REPLY TO EXAMINATION REPORT.pdf

1791-KOLNP-2007-REPLY TO EXAMINATION REPORT1.1.pdf

abstract-01791-kolnp-2007.jpg


Patent Number 253578
Indian Patent Application Number 1791/KOLNP/2007
PG Journal Number 31/2012
Publication Date 03-Aug-2012
Grant Date 01-Aug-2012
Date of Filing 18-May-2007
Name of Patentee SANTARIS PHARMA A/S
Applicant Address 6 KOGLE ALLÉ, HØRSHOLM, DK
Inventors:
# Inventor's Name Inventor's Address
1 RASMUSSEN, FRANK WINTHER SOLSORTEVEJ 6, DK-4000, ROSKILDE
2 HANSEN, HENRIK FRYDENLUND TARNVEJ 33 A, ST., DK-2610, RODOVRE
3 THRUE, CHARLOTTE ALBÆK KRONPRINSESSEGADE 80 ST., DK-1306 COPENHAGEN K
4 WESTERGAARD, MAJKEN ELLEBAKKEN 5, DK-3460 BIRKERØD
PCT International Classification Number C07H 21/04
PCT International Application Number PCT/DK2005/000721
PCT International Filing date 2005-11-09
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/724,621 2005-10-07 U.S.A.
2 60/699,721 2005-07-15 U.S.A.
3 60/626,563 2004-11-09 U.S.A.
4 60/647,186 2005-01-25 U.S.A.