Title of Invention

THERAPEUTICALLY USEFUL TRIETHYLENEGLYCOL CHOLESTERYL OLIGONUCLEOTIDES .

Abstract The instant invention discloses a composition comprising a 5'-OH, 3'-TEG cholesteryl, synthetic sequence, wherein the sequence is SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, and optionally comprising a pharmaceutically acceptable carrier, or a therapeutic agent, or a combination thereof.
Full Text THERAPEUTICALLY USEFUL TRIETHYLENEGLYCOL
CHOLESTERYL OLIGONUCLEOTIDES
FIELD OF THE INVENTION
The present invention relates to cholesteryl-conjugated oligonucleotide compositions and
their use for the inhibition of cellular proliferation, induction of apoptosis, modification of cell
cycle progression and modulation of extracellular matrix-cell interaction.
BACKGROUND OF THE INVENTION
Proliferation is the culmination of a cell's progression through the cell cycle resulting in
the division of one cell into two cells. The five major phases of the cell cycle are G0, G1, S, G2,
and M. During the G0, phase, cells are quiescent. Most cells in the body, at one time, are in this
stage. During the G1 phase, cells, responding to signals to divide, produce the RNA and the
proteins necessary for DNA synthesis. During the S-phase (SE, early S-phase; SM, middle S-
phase; and SL, late S-phase) the cells replicate their DNA. During the G2 phase, proteins are
elaborated in preparation for cell division. During the mitotic (M) phase, the cell divides into two
daughter cells. Alterations in cell cycle progression occur in all cancers and may result from
over-expression of genes, mutation of regulatory genes, or abrogation of DNA damage
checkpoints (Hochhauser D., Anti-Cancer Chemotherapeutic Agents, 8:903,1997).
Apoptosis or programmed cell death is the physiological process for the killing and
removal of unwanted cells, and a mechanism whereby chemotherapeutic agents kill cancer cells.
Apoptosis is characterized by distinctive morphological changes within cells that include
condensation of nuclear chromatin, cell shrinkage, nuclear disintegration, plasma membrane
blebbing, and the formation of membrane-bound apoptotic bodies (Wyllie et al., Int. Rev. Cytol.,
68: 251, 1980). The translocarion of phosphatidylserine from the inner face of the plasma
membrane to the outer face coincides with chromatin condensation and is regarded as a cellular
hallmark of apoptosis (Kooptnan, G. et al., Blood, 84:1415, 1994). The mechanism of apoptosis
is known to be mediated by the activation of a family of cysteine proteases, known as caspases.
Caspases recognize three major peptide sequences as substrates (Thomberry et al., J.
Biol. Chem. 272:17907, 1997): (i) Tyr-Val-Ala-Asp (YVAD, caspase-1, -4), (ii) Asp-Glu-Val-
Asp (DEVD, caspase-2, -3 and -7), and, (iii) Ile-(Leu)-Glu-X-Asp (I(L)EXD; caspase-8 and -10).
Sequence recognition in a protein target results in a limited and specific proteolysis of the target,

such as activation of caspase-7 by caspase-3, degradation of structural protein targets including,
but not limited to, lamins, or activation of enzymes including, but not limited to, poly(ADP-
ribose) polymerase. Caspase-3 was reported to be cleaved into its catalyrically active subunits
(17 and 13 kDa) following pro-apoptotic signals, leading to apoptosis (Susin et al., J. Exp. Med.
186:25, 3997).
During apoptosis, the activation of caspases results in proteolytic cleavage of numerous
substrates. Poly(ADP-ribose) polymerase (PARP), a nuclear enzyme involved in DNA repair, is
a well-known substrate for caspase-3 cleavage during apoptosis. Its cleavage is considered to be
a hallmark of apoptosis (O'Brien et al., Biotechniques 30:886,2001).
The extracellular matrix (ECM) impacts behavior of normal and tumor cells (Radisky et
al., Seminars Cancer Biol., 11:87, 2001). Therefore, the interaction between tumor cells and the
ECM components, when tumor cells are plated on the ECM, will activate signal transduction
events mimicking several biopathological characteristics of tumors in vivo, such as modulation
of cell-cell contacts (Weaver et al., J. Cell Biol., 137:231, 1997).
Synthetic oligonucleotides are polyanionic sequences that are internalized in cells
(Vlassov et al., Biochim. Biophys. Acta, 11197:95, 1994). Synthetic oligonucleotides were
reported that bind selectively to nucleic acids (Wagner, R-, Nature, 372:333, 1994), to specific
cellular proteins (Bates et al., J. Biol. Chem., 274:26369, 1999) and to specific nuclear proteins
(Scaggiante et al., Eur. J. Biochem, 252:207, 1998) in order to inhibit proliferation of cancer
cells.
Synthesis and physical properties of oligonucleotides with a cholesteryl moiety have been
described. The attachment of a cholesteryl moiety to the 3'-end of antisense oligonucleotides
enhances their activities (Letsinger et al., Proc. Natl. Acad. Sci. USA, 86:6553, 1989;
Boutorin et al., FEBS Letter, 254:129, 1989; Comas et al., J. Neurooncol. 31:171, 1997; US
Patent No. 4,958,013; WO Patent No. 9714440). The attachment of a cholesteryl moiety to the
3'-end enhances the uptake of antisense molecules by cells (Comas et al., J. Neurooncol. 31:171,
1997), and increases antisense vascular retention in vivo (Fleser et al.. Circulation 92:1296,
1995). Intemucleoside cholesteryl side chains linked to phosphorous via phosphoramidate bonds
have been described as a modification to increase the activity of antisense molecules (US Patent
No. 4,958,013). Homopolymers of 15 cytidine or thymidine residues with a cholesteryl moiety at
the 5'-end were found to modulate cytosolic Ca2+ levels in pro-myelocytic leukemia cells, while
heteropolymeric sequences with a cholesteryl moiety at the 5'-end or cholesteryl-modified
phosphorothioate sequences were inactive (Saxonetal., Antisense Res. Dev. 2:243, 1992).
Heteropolymers consisting of 15 phosphorothioate deoxynucleotides with alternating cytosine

and adenosine residues, or homopolymers with 15 cytosine or thymidine residues, were shown to
be potent inhibitors of methotrexate transport when a cholesteryl group was linked to the 5'-end
(Henderonetal., NucJ. Acids Res. 25:3726, 1995). The covalent modification of a 10 base
homocytidine phosphorothioate oligonucleotide with a cholesteryl moiety at the 5'-end blocked
the formation of syncitia in T lymphocytes infected with HIV-1 or HIV-2 through inhibition of
HIV reverse transcriptase (Stein et al., Biochemistry 5:2439, 1991).
The attachment of a cholesteryl moiety to oligonucleotides has minimal effects on the
growth of cancer cells (Henderon et al., Nucl. Acids Res. 25:3726, 1995). Typical features of
apoptotic cell death were not observed in cancer cell lines treated with 3'-end cholesteryl
oligonucleotides (Corrias et al., J. Neurooncol. 31:171, 1997).
Most anti-cancer therapies, whether directed to inhibition of proliferation, induction of
cell cycle arrest, induction of apoptosis, stimulation of the immune system or modulation of
extracellular matrix-cell interaction have proven to be less than adequate for clinical
applications. Many of these therapies are inefficient or toxic, have significant adverse effects,
result in development of drug resistance or immunosensitization, and are debilitating for the
recipient.
Therefore, there is a continuing need for novel compositions and methods that induce cell
cycle arrest in cancer cells, that induce apoptosis in cancer cells, and that modulate extracellular
matrix-cell interactions.
SUMMARY OF THE INVENTION
The present invention fulfills this need by providing a composition, wherein a
triethyleneglycol (TEG) cholesteryl moiety is attached to the 3' end of synthetic oligonucleotide
sequences SEQ ID NO: 1 (5' OH-GGGTGG-OH 3'), SEQ ID NO:2 (5' OH-GGGAGG-OH 3'),
SEQ ID NO:3 (5' OH-CCACCC-OH 3'), or SEQ ID NO:4 (5' OH-GTG-OH 3'), resulting in
corresponding 5'-OH, 3' TEG cholesteryl novel synthetic oligonucleotide sequences
SEQ ID NO:5 (5' OH-GGGTGG(TEG-cholesteryl) 3'), SEQ ID NO:6 (5' OH-GGGAGG(TEG-
cholesteryl) 3'), SEQ ID NO:7 (5' OH-CCACCC(TEG-cholesteryl) 3'), or SEQ ID NO:8 (5' OH-
GTG(TEG-cholesteryl) 3'). The present invention also provides methods tor using these novel
synthetic oligonucleotide sequences by combining them with an acceptable carrier to make a
composition, and administering the composition in vitro or in vivo. The composition is
administered to an animal, including a human, in order to induce a response in a cell. Such
responses include, but are not limited to, inhibition of cellular proliferation, induction of cell
cycle arrest, induction of apoptosis, activation of caspase, cleavage of poly(ADP-ribose)

polymerase, or modulation of extracellular matrix-cell interactions, or a combination thereof. A
preferred cell for induction of the response is a cancer cell or a synovial cell. Any disease or
condition characterized by undesired cellular proliferation may be treated with the compositions
of the present invention. Such diseases or conditions characterized by undesired cellular
proliferation include, but are not limited to, autoimmune disease, inflammation,
lymphoproliferative disease, arthritis and cancer.
The present invention also provides for the use of these novel synthetic oligonucleotide
sequences in the preparation of a medicament. Such medicaments are useful for treating a
disease or condition characterized by undesired cellular proliferation, including but not limited
to, autoimmune disease, inflammation, lymphoproliferative disease, arthritis or cancer.
One or more novel sequences of the present invention may be combined with an
acceptable carrier and administered as a composition in vitro in cells or tissues in culture, or in
vivo to an animal or human. Further, the compositions of the present invention may be
administered together with one or more therapeutic agent. Such administration of the
compositions of the present invention may occur before, during or after administration of one or
more therapeutic agents known to one of ordinary skill in the medical or veterinary arts. Any
therapeutic agent known to one of ordinary skill in the medical or veterinary arts, and employed
to treat diseases, may be used in combination with these novel sequences. Such combinations
may permit use of lower dosages of therapeutic agents, thereby decreasing unwanted side effects.
Administration of a composition comprising an effective amount of one or more of the
sequences of the present invention to an animal or human is a therapeutic treatment that prevents,
treats or eliminates a disease or condition characterized by undesired cellular proliferation. Such
diseases and conditions are known to one of skill in the medical or veterinary arts and include,
but are not limited to, cancer, inflammation, arthritis, lymphoproliferative disorders, asthma and
restenosis of arteries following angioplasty. Cancers include, but are not limited to, squamous
cell carcinoma, fibrosarcoma, sarcoid carcinoma, melanoma, breast cancer, lung cancer,
colorectal cancer, renal cancer, osteosarcoma, cutaneous melanoma, basal cell carcinoma,
pancreatic cancer, bladder cancer, brain cancer, ovarian cancer, prostate cancer, leukemia,
lymphoma, and metastases derived therefrom.
Methods and routes of administration of therapeutic agents to animals and humans are
known to one of ordinary skill in the art and may be employed to administer compositions
comprising the sequences of the present invention and a pharmaceutically acceptable carrier.
The unexpected and surprising ability of the covalent attachment of a cholesteryl-TEG
phosphoramidite moiety to the 3'-oxygen of functionally inert 3'-OH oligonucleotides to inhibit

the proliferation of cancer cells and synovial cells, to induce apoptosis in cancer cells and
synovial cells, to modulate extracellular matrix-cell interactions in cancer cells, and to modify
cell cycle progression of cancer cells addresses long-felt and unfulfilled needs in the medical arts
and provides an important benefit for animals, including humans.
Accordingly, it is an object of the present invention to provide a novel composition
comprising a 5'-OH, 3'-TEG cholesteryl synthetic sequence.
Another object of the present invention is to provide a composition and method effective
to treat a disease in an animal, including a human.
Still another object of the present invention is to provide a composition and method
effective to treat a disease or a condition characterized by undesired cellular proliferation.
Yet another object of the present invention is to provide a composition and method
effective to treat cancer.
Yet another object of the present invention is to provide a composition and method
effective to treat arthritis.
Still another object of the present invention is to provide a composition and method that
induces a response in cells, including but not limited to inhibition of cellular proliferation,
induction of cell cycle arrest, induction of caspase activation, cleavage of poly(ADP-ribose)
polymerase, induction of apoptosis or modulation of extracellular matrix-cell interactions, or
combinations thereof.
Still another object of the present invention is to provide a composition and method that
induces a response, including but not limited to inhibition of cellular proliferation, induction of
cell cycle arrest, induction of caspase activation, cleavage of poly(ADP-ribose) polymerase,
induction of apoptosis or modulation of extracellular matrix-cell interactions, or combinations
thereof, in cancer or synovial cells, including drug-resistant cancel or synovial cells.
Another object of the present invention is to provide a composition and method that
induces apoptosis in cells independent of BCR-ABL (a fusion of the BCR gene on chromosome
22 and ABL gene on chromosome 9).
Yet another object of the present invention is to provide a composition and method that
induces apoptosis in cells independent of p53 mutation,
Another object of the present invention is to provide a composition that is simple to
prepare.
Still another object of the present invention is to provide a composition that is minimally
toxic to the recipient.

Yet another object of the present invention is to provide the use of these novel synthetic
oligonucleotide sequences in the preparation of a medicament, the medicament being useful for
treating a disease or condition characterized by undesired cellular proliferation.
These and other objects, features and advantages of the present invention will become
apparent after a review of the following detailed description of the disclosed non-limiting
embodiment and the appended claims.
ACCOMPANYING
BRIEF DESCRIPTION OF THE ACCOMPANYING DRAWINGS
Figure 1. Photographs of growth of MCF-7, MDA-MB-231 (MDA-231), Hs578T and
Mpanc-96 cells on MATRIGEL® following pre-incubation with regular culture medium (RCM)
alone, or with added SEQ ID NO:1 or SEQ ID NO.5.
Figure 2. Photographs of growth of human breast cancer cells on MATRIGEL®
following pre-incubation with regular culture medium (RCM) alone, with added SEQ ID NO: 4
or SEQ ID NO:8.
Figure 3. Photographs of MCF-7 cells that were allowed to grow on MATRIGEL®-
coated wells for 48 hrs. Then, the resulting 3-dimensional cell structures were exposed to regular
culture medium (RCM) alone, or with added cholesteryl-TEG phosphoramidite, to SEQ ID NO:3
or to SEQ ID NO:7.
Figure 4. Photographs of MDA-231 cells that were allowed to grow on MATRIGEL®-
coated wells for 48 hrs. Then, the resulting three-dimensional cell structures were exposed to
regular culture medium (RCM) alone, with added cholesteryl-TEG phosphoramidite, SEQ ID
NO:3 or SEQ ID NO:7.
Figure 5. Photographs of Hs578T cells that were grown as spheroids and exposed for 3
days to regular culture medium (RCM) with or without addition of cholesteryl-TEG
phosphoramidite (chol-TEG), SEQ ID NO:3, SEQ ID NO:7, or to the corresponding controls
(RCM plus water (RCMW) and RCM plus acetonitrile (RCMA).
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides novel compositions comprising 5'-OH, 3'-TEG
cholesteryl synthetic sequences, wherein the sequence is SEQ ID N0:5 (5' OH-GGGTGG(TEG-
cholesteryl) 3'), SEQ ID NO:6 (5' OH-GGGAGG(TEG-cholesteryl) 3'), SEQ ID NO.7 (5' OH-
CCACCC(TEG-cholesteryl) 31) or SEQ ID NO:8 (51 OH-GTG(TEG-cholesteryl) 3').
The present invention also provides methods for using these novel compositions. The
compositions of the present invention are useful for inducing a response in a cell when
administrated to animals OT humans, in an amount effective to induce a response in the cell.

These responses include but are not limited to inhibition of cellular proliferation, cell cycle
arrest, induction of apoptosis, activation of caspase, cleavage of poly(ADP-ribose) polymerase in
the cell, or modulation of extracellular matrix-cell interactions, or a combination thereof. In one
embodiment, the animal or human has cancer or arthritis. In a preferred embodiment, the cells
are cancer cells. In another preferred embodiment, the cells are synovial cells.
The compositions of the present invention may be used to treat diseases or conditions
characterized by undesired cellular proliferation. In one embodiment, a composition of the
present invention is administered to an animal or human having cancer in an amount effective to
treat the cancer in the animal or the human.
In another embodiment, the composition of the present is administered to an animal or
human having arthritis in an amount effective to treat arthritis in the animal or the human.
The unexpected and surprising ability of the 3'-TEG cholesteryl oligonucleotides to
inhibit proliferation, induce cell cycle arrest, induce apoptosis, activate caspases, or modulate
extracellular matrix-cell interactions in cells, or induce a combination these responses in cells
fulfills a long-felt unfulfilled need in the medical arts and provides an important benefit for
animals and humans.
As used herein, the word "sequence" refers to a 3'-OH, 5'-OH synthetic oligonucleotide
comprising SEQ ID NO: 1 (5' OH-GGGTGG-OH 3'), SEQ ID NO:2 (5' OH-GGGAGG-OH 3'),
SEQ ID NO:3 (5' OH-CCACCC-OH 3'), or SEQ ID NO.4 (5' OH-GTG-OH 3'), or to a 5'-OH,
3'-TEG cholesteryl synthetic oligonucleotide comprising SEQ ID NO:5 (5' OH-GGGTGG(TEG-
cholesteryl) 3'), SEQ ID NO:6 (5' OH-GGGAGG(TEG-cholesteryl) 3'), SEQ ID NO.7 (5' OH-
CCACCC(TEG-cholesteryl) 3'), or SEQ ID NO:8 (5' OH-GTG(TEG-cholesteryl) 3').
As used herein, the terms "3'-TEG cholesteryl oligonucleotide" and "3'-TEG cholesteryl
synthetic oligonucleotide" refer to a 3'-triethyleneglycol cholesteryl-modified oligonucleotide, a
5'-OH oligonucleotide with a TEG cholesteryl moiety attached at the 3' end. For illustrative
purposes, the chemical structure of SEQ ID NO.7, an example of a 5'-OH, 3'-TEG cholesteryl
synthetic oligonucleotide, is shown below.

As used herein, the word "response" refers to induction of a response, including but not
limited to inhibition of cellular proliferation, induction of cell cycle arrest, activation of caspases,

cleavage of poly(ADP-ribose) polymerase, induction of apoptosis in cells or modulation of
extracellular matrix-cell interactions, or a combination thereof.
As used herein, the phrase "effective in responsive cells" refers to the ability of a
sequence to induce a response, including but not limited to ability of the sequence to inhibit
cellular proliferation, induce cell cycle arrest, induce activation of caspases, induce cleavage of
poly(ADP-ribose) polymerase, induce apoptosis in cells or modulate extracellular matrix-cell
interactions, or a combination thereof.
As used herein, the phrases "therapeutic treatment", "effective amount" and "amount
effective to" refer to an amount of a sequence effective to induce a response, including but not
limited to inhibition of cellular proliferation, cell cycle arrest, activate caspases, cleave
poly(ADP-ribose) polymerase, induce apoptosis in cells, modulate extracellular matrix-cell
interactions, or a combination thereof.
As used herein, the word "disease" relates to a condition wherein bodily health is
impaired.
As used herein, the phrase "therapeutic agent" is any agent, including radiation, approved
by a regulatory agency of a country or a state government OT listed in the U.S. Pharmacopoeia or
other generally recognized pharmacopoeia for use to treat a disease in an animal, including a
human.
As used herein, the phrase "chemotherapeutic" is any agent approved by a regulatory
agency of a country or a state government, or listed in the U.S. Pharmacopoeia or other generally
recognized pharmacopoeia to treat disease in an animal, including a human.
As used herein, the phrase "anti-arthritic" is any agent approved by a regulatory agency
of a country or a state government or listed in the U.S. Pharmacopoeia or other generally
recognized pharmacopoeia for use in the treatment of arthritis in an animal, including a human.
As used herein, the word "antineoplastic" refers to preventing the development,
progression, proliferation or spread of cancer cells.
Administration of an effective amount of a composition of the present invention to an
animal, or human, is a therapeutic treatment that induces a response, prevents, treats, or
eliminates a disease, or a combination thereof. The response includes but is not limited to,
inhibition of cellular proliferation, cell cycle arrest, activation of caspases, cleavage of
poVy(ADP-ribose) polymerase, induction of apoptosis in cells, modulation of extracellular
matrix-cell interactions, or a combination thereof. The disease includes, but is not limited to,
cancer, arthritis, lymphoproliferative disorders and inflammation. Cancers include, but are not
limited to, squamous cell carcinoma, fibrosarcoma, hemangiosarcoma, lymphangiosarcoma,

rhabdomyosarcoma, leiomyosarcoma, liposarcoma, chondrosarcoma, sarcoid carcinoma,
melanoma, breast cancer, lung cancer, colorectal cancer, renal cancer, osteosarcoma, cutaneous
melanoma, basal cell carcinoma, pancreatic cancer, bladder cancer, brain cancer, ovarian cancer,
prostate cancer, leukemia, lymphoma, myeloma and metastases derived therefrom. Forms of
arthritis include, but are not limited to, juvenile arthritis, osteoarthritis and rheumatoid arthritis.
The therapeutic effectiveness of a sequence may be increased by methods including, but
not limited to, chemically modifying the base, sugar or phosphate backbone, chemically
supplementing or biotechnologically amplifying the sequences using bacterial plasmids
containing the appropriate sequences, complexing the sequences to biological or chemical
carriers, or coupling the sequences to tissue-type or cell-type directed ligands or antibodies.
Compositions comprising one or more sequences and a pharmaceutically acceptable
carrier are prepared by uniformly and intimately bringing into association the sequence and the
pharmaceutically acceptable carrier. The terms "pharmaceutically acceptable carrier" or
"pharmaceutically acceptable vehicle" are used herein to mean, without limitation, any liquid,
solid or semi-solid, including, but not limited to, water or saline, a gel, cream, salve, solvent,
diluent, fluid ointment base, ointment, paste, implant, liposome, micelle, giant micelle, and the
like, which is suitable for use in contact with living animal or human tissue without causing
adverse physiological responses, and which does not interact with the other components of the
composition in a deleterious manner. Other pharmaceutically acceptable carriers or vehicles
known to one of skill in the art may be employed to make compositions for delivering the
oligonucleotide sequences of the present invention. Liquid carriers are aqueous carriers, non-
aqueous carriers or both and include, but are not limited to, aqueous suspensions, dimethyl
sulfoxide, ethanol, oil emulsions, water in oil emulsions, water-in-oil-in-water emulsions, site-
specific emulsions, long-residence emulsions, sticky-emulsions, microemulsions and
nanoemulsions. Solid carriers are biological carriers, chemical carriers or both and include, but
are not limited to, viral vector systems, particles, microparticles, nanoparticles, microspheres,
nanospheres, minipumps, bacterial cell wall extracts and biodegradable or non-biodegradable
natural or synthetic polymers that allow for sustained Telease of the sequences. Emulsions,
minipumps and polymers can be implanted in the vicinity of where delivery is required. Methods
used to complex a sequence(s) to a solid carrier include, but are not limited to, direct adsorption
to the surface of the solid carrier, covalent coupling to the surface of the solid carrier, either
directly or via a linking moiety, and covalent coupling or electrostatic coupling to the polymer
used to make the solid carrier. Optionally, a sequence(s) can be stabilized by the addition of non-
ionic or ionic polymers such as polyoxyethylenesorbitan monooleates (Tweens), hyahironic acid

or aluminum hydroxide. Other carriers known to one of ordinary skill in the art may be
employed.
Preferred aqueous carriers include, but are not limited to, water, saline and
pharmaceutically acceptable buffers. Preferred non-aqueous carriers include, but are not limited
to, a mineral oil or a neutral oil including, but not limited to, a diglyceride, a triglyceride, a
phospholipid, a lipid, an oil and mixtures thereof, wherein the oil contains an appropriate mix of
polyunsaturated and saturated fatty acids. Examples include, but are not limited to, soybean oil,
canola oil, palm oil, olive oil and myglyol, wherein the fatty acids can be saturated or
unsaturated. Optionally, excipients may be included regardless of the pharmaceutically
acceptable carrier used to present the sequence to the responding cells. These excipients include,
but are not limited to, anti-oxidants, buffers, and bacteriostats, and may include suspending
agents and thickening agents.
The sequences of the present invention may be combined with pharmaceutically
acceptable carriers and administered as compositions in vitro to cells or tissues in culture, or in
vivo to animals or humans. Forms of administration include, but are not limited to, injections,
solutions, creams, gels, implants, pumps, ointments, emulsions, suspensions, microspheres,
particles, microparticles, nanoparticles, liposomes, pastes, patches, tablets, transdermal delivery
devices, sprays, aerosols, or other means familiar to one of ordinary skill in the art. Such
pharmaceutically acceptable carriers are commonly known to one of ordinary skill in the art.
Pharmaceutical formulations of the present invention can be prepared by procedures known in
the art using well known and readily available ingredients. For example, the compounds can be
formulated with common excipients, diluents, or carriers, and formed into tablets, capsules,
suspensions, powders, and the like. Examples of excipients, diluents, and carriers that are
suitable for such formulations include the following: fillers and extenders (e.g., starch, sugars,
mannitol, and silicic derivatives); binding agents (e.g., carboxymethyl cellulose and other
cellulose derivatives, alginates, gelatin, and polyvinylpyrrolidone); moisturizing agents (e.g.,
glycerol); disintegrating agents (e.g., calcium carbonate and sodium bicarbonate); agents for
retarding dissolution (e.g., paraffin); resorption accelerators (e.g., quaternary ammonium
compounds); surface active agents (e.g., cetyl alcohol, glycerol monostearate); adsorptive
carriers (e.g., kaolin and bentonite); emulsifiers; preservatives; sweeteners; stabilizers; coloring
agents; perfuming agents; flavoring agents; lubricants (e.g., talc, calcium and magnesium
stearate); solid polyethyl glycols; and mixtures thereof.
The formulations can be so constituted that they release the active ingredient only or
preferably in a particular location, possibly over a period of time. Such combinations provide yet

a farther mechanism for controlling release kinetics. The coalings, envelopes, and protective
matrices may be made, for example, from polymeric substances or waxes.
One or more sequences may be administered alone, or in combination with other
therapeutic modalities including, but not limited to, chemotherapeutic agents, anti-arthritic
agents, immunotherapeutic agents, antimicrobial agents, or antiviral agents, or in combination
with radiation therapy, or any combination thereof. Chemotherapeutic agents include, but are
not limited to, anti-metabolites, DNA damaging, microtubule destabilizing, microtubule
stabilizing, actin depolymerizing, growth inhibiting, topoisomerase inhibiting, HMG-CoA (3-
hydroxy-3-methylglutaryl coenzyme A) reductase inhibiting, purine synthesis inhibiting,
pyrimidine synthesis inhibiting, metalloproteinase inhibiting, CDK (cyclin-dependent protein
kinase) inhibiting, angiogenesis inhibiting, differentiation enhancing, and immunotherapeutic
agents. Anti-arthritic agents include, but are not limited to, anti-inflammatory agents, including
non-steroidal anti-inflammatory agents (NSAlDs), analgesics, biologic response modifiers,
disease-modifying antirheumatic drugs (DMARDs), anti-metabolic, pro-apoptotic, DNA
damaging, microtubule destabilizing, microtubule stabilizing, actin depolymerizing, growth
inhibiting, topoisomerase inhibiting, purine synthesis inhibiting, pyrimidine synthesis inhibiting,
metalloproteinase inhibiting, CDK inhibiting, or angiogenesis inhibiting agents. NSAIDs include
but are not limited to traditional NSAIDs, such as diclofenac potassium, diclofenac sodium,
diclofenac sodium with misoprostol, diflunisal, etodolac, fenoprofen, calcium flurbiprofen,
lbuprofen, indomethacin, ketoprofen, meclofenamate, sodium mefenamic, acid meloxicam,
nabumetone, naproxen, naproxen sodium, oxaprozin, piroxicam, sulindac, and tolmetin sodium,
cyclooxygenase-2 (COX-2) inhibitors, such as celecoxib and rofecoxib, salicylates, such as
aspirin, choline salicylate, magnesium salicylate, salsalate and sodium salicylate. Analgesics
include but are not limited to acetaminophen, acetaminophen with codeine, hydrocodone with
acetaminophen, oxycodone, propoxyphene hydrochloride, and tramadol. Biologic response
modifiers include but are not limited to etanercept and infliximab. Glucocorticoids include but
are not limited to cortisone, dexamethasone, hydrocortisone, methylprednisolone, predmsolone,
prednisolone sodium phosphate and prednisone triamcinolone. DMARDs include but are not
limited to auranofm (oral gold), azathioprine, cyclophosphamide, cyclosporine,
hydroxychloroquine sulfate, leflunomide, methotrexate, minocycline, penicillamine,
sulfasalazine, aurothioglucose and gold sodium thiomalate.
Routes of administration are known to one of ordinary skill in the art and include, but are
not limited to, oral (e.g. buccal or sublmgual), rectal, as a suppository OT an enema, topical,
parenteral, subcutaneous, transdermal, sub-dermal, intramuscular, intraperitoneal, intravesicular,

intraarticular, intravenous, intradermal, intracranial, intralesional, intrathecal, intratumoral,
intraocular, ocular, aerosol, intrapulmonary, intraspinal, intraprostatic, sublingual, placement
within cavities of the body, nasal inhalation, pulmonary inhalation, impression into the skin and
electroporation, intrauterine, vaginal, into a body cavity, surgical administration at the location
of a tumor or internal injury, directly into tumors, into the lumen or parenchyma of an organ, and
into bone marrow. Techniques useful in the various forms of administrations mentioned above
include but are not limited to, topical application, ingestion, surgical administration, injections,
sprays, transdermal delivery devices, osmotic pumps, electrodepositing directly on a desired site,
or other means familiar to one of ordinary skill in the art. Sites of application can be external,
such as on the epidermis, or internal, for example a joint capsule, a tumor, a gastric ulcer, a
surgical field, or elsewhere.
The compositions of the present invention can be applied in the form of creams, gels,
solutions, suspensions, liposomes, particles, or other means known to one of skill in the art of
formulation and delivery of compositions. Ultrafme particle sizes can be used for inhalation
delivery of therapeutics. Some examples of appropriate formulations for subcutaneous
administration include but are not limited to implants, depot, needles, capsules, and osmotic
pumps. Some examples of appropriate formulations for vaginal administration include but are
not limited to creams, suppositories, sponges, gels, foams, and rings. Some examples of
appropriate formulations for oral administration include but are not limited to: pills, capsules,
liquids, syrups, and suspensions. Some examples of appropriate formulations for transdermal and
transmucosal administration include but are not limited to creams, pastes, patches, sprays, and
gels. Some examples of appropriate delivery mechanisms for subcutaneous administration
include but are not limited to implants, depots, needles, capsules, and osmotic pumps.
Formulations suitable for parenteral administration include but are not limited to aqueous and
non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats
and solutes which render the formulation isotonic with the blood of the intended recipient, and
aqueous and non-aqueous sterile suspensions which may include suspending agents and
thickening agents. Extemporaneous injection solutions and suspensions may be prepared from
sterile powders, granules and tablets commonly used by one of ordinary skill in the art.
The sequences of the invention may be combined with one or more pharmaceutically
acceptable carriers or excipients to form a composition. These compositions may conveniently
be presented in unit dosage form and may be prepared by conventional pharmaceutical
techniques. Such techniques include the step of bringing into association the compositions
containing the active ingredient and the pharmaceutical carrier(s) or excipient(s). In general, the

formulations are prepared by uniformly and intimately bringing into association the active
ingredient with liquid carriers. Preferred unit dosage formulations are those containing a dose or
unit, or an appropriate fraction thereof, of the administered ingredient. It should be understood
that in addition to the ingredients particularly mentioned above, formulations comprising the
compositions of the present invention may include other agents commonly used by one of
ordinary skill in the art.
The volume of administration will vary depending on the route of administration. Such
volumes are known to one of ordinary skill in the art of administering compositions to animals or
humans. Depending on the route of administration, the volume per dose is preferably about 0.001
to 100 ml, more preferably about 0.01 to 50 ml, and most preferably about 0.1 to 30 ml.
Preferably, the amount of sequence administered per dose is from about 0.001 to 100 ing/kg of
body weight, more preferably from about 0.01 to 10 mg/kg and most preferably from about 0.1
to 5 mg/kg. The sequence, combination of sequences, and/or additional therapeutic agents can be
administered in a single dose treatment, in multiple dose treatments or continuously infused on a
schedule and over a period of time appropriate to the disease being treated, the condition of the
recipient and the route of administration. Moreover, the sequence can be administered before, at.
the same time as, or after the administration of the therapeutic agent. The particular sequence and
the particular therapeutic agent administered, the amount per dose, and the route of
administration should be decided by the practitioner using methods known to those skilled in the
art and will depend on the disease or condition being treated, for example the type of cancer, the
severity of the cancer, the location of the cancer and other clinical factors such as the size,
weight and physical condition of the recipient. In addition, various in vitro and in vivo assays
may optionally be employed to help identify optimal ranges for sequence and for sequence plus
therapeutic agent administration.
A sequence in combination with therapeutic agent, for example a chemotherapeutic agent
or an anti-arthritic agent, is administered to an animal, or human, having cancer or arthritis in an
amount effective to enhance the anti-neoplastic effect of a chemotherapeutic agent or the anti-
arthritic effect of an anti-arthritic agent. Preferably, the amount of therapeutic agent administered
per dose is from about 0.001 to 1000 mg/m2 of body surface OT from about 0.01 to 1000 mg/kg
of body weight, more preferably from about 0.01 to 500 mg/m2 or about 0.01 to 500 mg/kg and
most preferably from about 0.1 to 100 mg/m2 or about 0.1 to 100 mg/kg. The particular sequence
and the particular therapeutic agent administered, the amount per dose, the dose schedule and the
route of administration should be decided by the practitioner using methods known to those
skilled in the art and will depend on the type of disease, the severity of the disease, the location

of the disease and other clinical factors such as the size, weight and physical condition of the
recipient. In addition, various in vitro and in vivo assays may optionally be employed to help
identify optimal ranges for sequence and for sequence plus therapeutic agent administration.
Various assays useful for this purpose are described in PCT CA00/01467 (WO 01/44465).
Additional assays for evaluation of the efficacy of the sequences of the present invention, and for
evaluation of the efficacy of these sequences in combination with other therapeutic agents are
described by Oncogene Research Products, P.O. Box 12087, La Jolla, California, 92039
(Apoptosis Catalog and Technical Guide 2002-2003, especially pages 5-295). Such assays
include assays designed to analyze DNA fragmentation, apoptosis, mitochondrial markers,
endoplasmic reticulum markers, free nucleosomes, nuclear matrix proteins, detection and activity
of numerous caspases and related proteins, including but not limited to caspases 1 through 14,
glutathione, superoxide dismutase, members of the bcl-2 family, analysis of the Fas/TNR-R
super family, PARP related products, analysis of apoptotic signal transducers, analysis of various
signaling receptors including death receptors, Apo2, decoy receptors, analysis of apoptotic
membrane proteins, nervous system apoptotic markers, numerous markers for cell cycle and
cellular proliferation, mitotic kinases, bromodeoxyuridine assays, and p53 assays. The efficacy
of the sequences of the present invention may also be evaluated in terms of other agents,
including therapeutic agents, including but not limited to, anti-arthritic agents, or inducers of
apoptosis and cell synchronization reagents as described by Oncogene Research Products, P.O.
Box 12087, La Jolla, California, 92039 (Apoptosis Catalog and Technical Guide 2002-2003,
especially pages 99-104 and pages 214-255). Such agents include but are not limited to
actinomycin D, amphidocolin, A23187, caffeine, camptothecin, cycloheximide, dexamethasone,
doxorubicin, 5-fluorouracil, hydroxyurea, paclitaxel, staurosporine, thymidine, vmblastme,
retinoic acid, etoposide, okadaic acid, vincristine and methotrexate.
Various in vitro and in vivo assays and models known to one skilled in the art may be
employed for evaluation of the efficacy and optimal dose ranges of sequences, alone or in
combination with a therapeutic agent or agents, for the treatment of arthritis. Animal models
include but are not limited to adjuvant disease models, oily adjuvant-induced models,
microorganisms and their cell wall components-induced models, cartilage components-mduced
models, transgenic and knockout models, non-irnrmmologic osteoarthiitis models, and partial
syndromes models, as described in Waxman, B.H., Scand. J. Immunol., 56:12, 2002. Model
animals include but are not limited to rats, mice, primates, guinea pigs, and rabbits
To determine a cell cycle stage, various assays and procedures known to one skilled in
the art may be employed. One such procedure uses a CYCLETEST™ PLUS DNA commercial

kit (Becton Dickinson, Franklin Lakes, NJ). Briefly, nuclei from cells are obtained by dissolving
the cell membrane in a nonionic detergent, eliminating the cell cytoskeleton and nuclear proteins
with trypsin, digesting the cellular KNA with RNase, and stabilizing the nuclear chromatin with
spermine. Propidhun iodide is added to the cell nuclei and their fluorescence was analyzed in a
flow cytometer equipped with electronic doublet discrimination capability (FACSCalibur,
Becton Dickinson, Franklin Lakes, NT). Accumulation of cells in G0/G1, early S (SE), mid S
(SM), late S (SL) or G2/M phases of the cell cycle may be analyzed using MODFIT LT software
(Verity Software House Inc., Topsham, MA), or other appropriate software.
Various in vitro and in vivo assays may be used to evaluate the influence of the
extracellular microenvironment on behavior of normal cells and tumor cells. Such assays may
employ MATRIGEL® (Becton Dickinson, Franklin Lakes, NJ),which is a solubilized basement
membrane preparation extracted from the Engelbreth-Holm-Swarm murine sarcoma.
Multicellular spheroids (MS) is an example of a special in vitro assay, in which tumor
cells are cultured in a 3 -dimensional manner to form a "tumor-like" structure. In this system,
there is a reinforcement of cell-cell interactions that mimic microenvironmental conditions of
malignant cells in solid tumors in vivo. In this type of assay, no extracellular matrix components
are added. Cells cultured in this MS system differ from those in 2-dimensional systems
(monolayer culture conditions). Some of these differences are related to structural and functional
differentiation of tumor cells, changes in the cell cycle of tumor cells, "multicellular drug
resistance", and changes in the diffusion and penetration of drugs throughout layers of tumor
cells (reviewed in Green et al., Anticancer Drug Des. 14:153, 1999).
The following examples will serve to further illustrate the present invention without, at
the same time, however, constituting any limitation thereof. On the contrary, it is to be clearly
understood that resort may be had to various other embodiments, modifications, and equivalents
thereof which, after reading the description herein, may suggest themselves to those skilled in
the art without departing from the spirit of the invention.
Example 1
Preparation of nucleotide sequences
Phosphodiester synthetic nucleotide sequences and conjugated 3'-TEG cholesteryl
synthetic nucleotide sequences were prepared by Sigma-Genosys (Woodlands, TX, USA) using
Abacus Segmented Synthesis Technology. Sequences terminating at their 3'-ends with TEG
cholesteryl were synthesized on TEG CPG support (Glen Research, Sterling, VA, USA). The
sequences were dispersed in water or in dimethyl sulfoxide (DMSO) immediately prior to use.

All cell lines were obtained from the American Type Culture Collection (ATCC,
Rockville, MD) and were cultured in the medium recommended by the ATCC. Breast cancer cell
lines were cultured in medium recommended by the ATCC or described in published articles
(Herrera-Gayol and Jothy, Int. J. Exp. Path., 82:193, 2001). Table 1 shows the cell lines, their
origin and their biopathological characteristics as described in the literature (Hackett et al.,
Cancer Inst, 58:1795, 1977; Price et al., Cancer Res., 50:717, 1990; Thompson et al., J. Cell
Physiol., 150:534,1992; and Peiper M et al., Int. J. Cancer 71: 993, 1997).

Example 3
Induction ofapoptosis in MEG-01 cells by SEO ID NO: 5 and SEQ ID NO: 6.
Redistribution of plasma membrane phosphatidylserine is a characteristic of cells
undergoing apoptosis (Martin et al., J. Exp. Med., 182:1545, 1995). The redistribution of
phosphatidylserine in the plasma membrane during apoptosis was measured by flow cytometry
using FITC (fluorescein isothiocyanate)-conjugated annexin V (BD Pharmingen, San Diego,

CA). MEG-01 cells, a human chronic myelogeneous leukemia cell line positive for the
Philadelphia chromosome and having a BCR-ABL gene fusion, were incubated at 2.5x105
cells/ml for 48 hours with 5.3, 26.5 and 53.0 uM final concentrations of SEQ ID NO:1,
SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6 and cholesteryl-TEG phosphoramidite molecule.
The percentage of cells in apoptosis after exposure to the SEQ ID NOs:1, 2, 5, 6, or cholesteryl-
TEG phosphoramidite treatment is reported in Table 2. The percentage of apoptosis in untreated
MEG-01 cells was 12%.

As shown in Table 2, SEQ ID NO: 1, SEQ ID NO:2 and cholesteryl-TEG
phosphoramidite are inactive against MEG-01. Unexpectedly the addition of a cholesteryl-TEG
phosphoramidite at the 3'-end of SEQ ID NO:1, resulting in SEQ ED NO: 5, and at the 3'-end of
SEQ ED NO:2, resulting in SEQ ED NO:6, conferred to these inert oligonucleotides the capacity
to induce apoptosis in MEG-01 cells as measured by the translocation of phosphandylserine at
the cell surface.
Example 4
Induction of apoptosis in EL-4 cells by SEQ ID NO:7
EL-4 cells, a murine T lymphoma cell line, were incubated at 2.5X105 cells/ml for
24 hours with 0.53, 5.3 and 53.0 M concentrations of SEQ ID NO:3, SEQ ID NO:7 or
cholesteryl-TEG phosphoramidite. The percentage of cells in apoptosis after exposure to SEQ ID
NO:3, SEQ ID NO:7 or cholesteryl-TEG phosphoramidite treatment is reported in Table 3. The
percentage of apoptosis in untreated EL-4 cells was 7%.


As shown in Table 3, neither SEQ ID NO:3 nor cholesteryl-TEG phosphoramidite caused
apoptosis in EL-4 cells. Unexpectedly, the addition of a cholesteryl-TEG phosphoramidite at the
3'-end of SEQ ID NO:3, resulting in SEQ ID NO:7, conferred to this inert oligonucleotide the
capacity to induce apoptosis in EL-4 cells as measured by the translocation of phosphatidylserine
at the cell surface.
Example 5
Activation of caspase 3 by SEQ ID NO: 7
EL-4 cells (2.5x105 cells/ml) were incubated for 72 hrs with 0 M (control), 53 M of
SEQ ID NO:3 or 53 M of SEQ ID NO:7. After incubation, both control and treated cells were
washed, fixed, permeabilized and incubated with a Phycoerythrin (PE)-conjugated antibody that
recognizes the active catalytic unit of caspase 3 (Clone: C92-605; BD Pharmingen, San Diego,
CA, USA) using the conditions recommended by the manufacturer. Fluorescence associated with
active caspase 3 was analyzed by flow cytometry on a FACSCALIBUR using the program
CellQUEST (both from Becton Dickinson, San Jose, CA, USA). The percentage of cells
containing active caspase 3 in EL-4 cells treated with 53 M of sequences is reported in the
Table 4.


As shown in Table 4, SEQ ID NO:3 was inactive against EL-4. Unexpectedly the
addition of a cholesteryl-TEG phosphoramidite at the 3'-end of SEQ ID NO:3, resulting in
SEQ ID NO: 7 conferred to this inert oligonucleotide the capacity to induce apoptosis as
measured by the activation of caspase-3.
Example 6
Cleavage of poly(ADP-ribose) polymerase by SEQ ID NO: 7
EL-4 cells (2.5X105 cells/ml) were incubated for 72 h with 0 uM (control), 53 M of
SEQ ID NO.3 or 53 uM of SEQ ID NO:7. After incubation, both control and treated cells were
washed, fixed, permeabilized and incubated with an FITC -conjugated antibody that recognizes
specifically the S5 kDa fragments of cleaved PARP (BioSource, Camarillo, CA, USA) using the
conditions recommended by the manufacturer. Fluorescence associated with cleaved PARP was
analyzed by flow cytometry on a FACSCalibur using the program CellQUEST (both from
Becton Dickinson). The percentage of cells containing cleaved PARP in EL-4 cells treated with
53 M final concentration of sequences is shown in Table 5.

As shown in Table 5, SEQ ID NO:3 was inactive against EL-4. Unexpectedly the
addition of a cholesteryl-TEG phosphoramidite at the 3'-end of SEQ ID NO.3, resulting in
SEQ ID NO.7, conferred to this inert oligonucleotide the capacity to induce apoptosis as
measured by cleavage of PARP.
Example 7
Effect of SEQ ID NO:2 SEQ ID NO.3, SEQ ID N0:4. SEQ ID N0.6, SEQ ID N0:7, and
SEQ ID NO:8 on proliferation of synovial cells
Adherent HIG-82 cells, a synovial cell line, were incubated at 1.0x105 cells/ml for 48
hours with 53 M (final concentration) of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID
NO:6, SEQ ID NO:7, or SEQ ID NO:8. Cellular proliferation was measured using
dimethylthiazol-diphenyl-tetrazolium (MTT) reduction (Mosman et al., J. Immunol. Methods


As shown in Table 6, SEQ ID NO.2, SEQ ID NO:3 and SEQ ID NO:4 did not inhibit
proliferation of synovial HIG-82 cells. Unexpectedly the addition of a cholesteryl-TEG
phosphoramidite at the 3'-ends of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:4, resulting in
SEQ ID NOs:6, 7, and 8, respectively, conferred the capacity to inhibit the cellular proliferation
of HIG-82 cells.
Example 8
Induction ofapoptosis in proliferating synovial cells by SEQ ID NO:5 and SEQ ID NO:6
Adherent HIG-82 cells were incubated at l.OxlO5 cells/ml for 48 hours with 53 M final
concentration of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:5 or SEQ ID NO.6. Since
phosphatidylserine/annexin V detection of apoptosis was not reliable after adherent cell
harvesting techniques, such as trypsinization (van Engeland, Cytometry, 31:1, 1998), apoptosis
in HIG-82 cells was evaluated using flow cytometry by the detection of fragmented DNA by
terminal deoxynucleotidyl transferase enzyme-mediated bromodeoxyuridine triphosphate-biotm
nick end-labeling (TUNEL) using a commercial assay (APO-BRDU™ kit; BD Pharmingen).
The percentage of cells containing nuclear DNA fragmentation was determined. After 24 hours,
untreated HIG-82 cells were essentially negative for nuclear DNA fragmentation.


As shown in Table 7, SEQ ID NO: 1 and SEQ ID NO:2 were inactive against
exponentially growing synovial cells. Unexpectedly the addition of a cholesteryl-TEG
phosphoramidite at the 3'-end of SEQ ID NO: 1 and SEQ ID NO:2, resulting in SEQ ID NO:5
and SEQ ID NO:6, respectively, conferred the capacity to induce apoptosis in HIG-82 cells as
measured by the percentage of cells showing fragmented nuclear DNA.
Example 9
Induction of cell cycle arrest by SEQ ID NO: 6
Exponentially growing MEG-01 cells (2xlO5 cells/ml) were incubated for 24 h with 0
M (control), 53 M of SEQ ID NO:2 or 53 uM of SEQ ID NO:6. The cells were collected,
centrifiiged, and cell cycle stage was determined.

As shown in Table 8, SEQ ID NO:2 was inactive against MEG-01 when compared to
untreated control cells. Unexpectedly the addition of a cholesteryl-TEG phosphoramidite at the
3'-end of SEQ ID NO:2, resulting in SEQ ID NO:6, conferred the capacity to induce cell cycle
arrest at the SL + G2/M phase in MEG-01 cells.

Example 10
Effect of SEQ ID NO: 3 and SEQ ID NO:7 on cellular proliferation of human breast cancer cells.
Either 20x103 MDA-MB-231 (MDA-231) or Hs578T cells were plated into individual
wells of 24-well plates in regular culture medium (RCM) presence or absence (control) of 53 M
(final concentration) of SEQ ID NO:3, SEQ ID NO:7, 53 M cholesteryl-TEG phosphoramidite,
or corresponding control media (regular culture medium (RCM) for SEQ ID NO:3, RCM with
the same amount of water as the amount added with the SEQ ID NO:7, and RCM with the same
amount of acetonitrile as the amount added with cholesteryl-TEG phosphoramidite). Cells were
cultured for 72 hrs, removed with trypsin and counted with an hemocytometer using the Trypan
blue exclusion technique. Results of three independent assays (mean and standard deviation
(s.d.) of percentage of changes compared to controls) are shown in Table 9.

As shown in Table 9, SEQ ID NO:3 and cholesteryl-TEG phosphoramidite did not
significantly affect cellular proliferation. Unexpectedly, the addition of cholesteryl-TEG
phosphoramidite at the 3' end of SEQ ID NO:3, resulting in SEQ ID NO:7, conferred the
capacity to inhibit cellular proliferation of two highly aggressive toman breast cancer cells.
Example 11
Changes in 3-dimensional structure formation induced by SEQ ID NO:5 m MATRIGEL®
outgrowth experiments '
MCF-7, MDA-MB-231 (MDA-231), Hs578T and Mpanc-96 cells were cultured
separately in regular culture medium, trypsinized, and counted. 100x103 of MDA-231 cells,
100x103 of Hs578T cells, 150xl03 of MCF-7 cells and 150xl03 of Mpanc-96 cells were

separately pre-incubated for 1 hr at 37°C in a final concentration of 53 uM of SEQ ID NO:1, 53
M of SEQ ID NO:5 or RCM, and plated on top of MATRIGEL®-coated plates (MATRIGEL®
Basement membrane matrix coated cellware 24-well plate,) for 3 days. Plates were fixed with
10% formalin. Digital photographs of the cells in the 24-well plates were taken using a Nikon
Coolpix 990 digital camera (Nikon Corporation, Tokyo, Japan) connected to a Nikon inverted
microscope model TMS. While SEQ ID NO:1 did not change cell morphology, SEQ ID NO:5
prevented the formation of 3-dimensional structures similar to those formed when cells were
cultured in the regular culture medium on MATRIGEL® (see Figure 1).
As shown in Figure 1, SEQ ID NO: 1 was inactive while, unexpectedly, the addition of
cholesteryl-TEG phosphoramidite at the 3'-end of SEQ ID NO:1, resulting in SEQ ID NO:5,
conferred the capability to prevent formation of 3-dimensional structures similar to those formed
when cells were cultured in regular culture medium on MATRIGEL®. It is believed that SEQ
ID NO:5 interfered with cell-extracellular matrix interactions thereby modulating cell-cell and
cell-extracellular matrix adhesion mechanisms.
Example 12
Changes in 3-dimensional structure formation induced by SEQ ID NO:8 in MATRIGEL®
(Beckton Dickinson, Franklin Lakes, NJ) outgrowth experiments /'
MDA-MB-231 (MDA-231) and Hs578T were cultured in regular culture medium,
trypsinized and counted. 100x103 of MDA-MB-231 cells or 100x103 of Hs578T cells, were
separately pre-incubated for 1 hr at 37°C in a final concentration of 53 uM of SEQ ID NO:4, 53
uM of SEQ ID NO: 8 or RCM and plated on MATRIGEL®-coated plates for 3 days. Plates were
fixed with 10% formalin. Digital photographs of the cells in the 24-well plates were taken using
a Nikon Coolpix 990 digital camera (Nikon Corporation, Tokyo, Japan) connected to a Nikon
inverted microscope model TMS. While SEQ ID NO:4 did not change the cellular morphology,
SEQ ID NO: 8 disrupted the growth pattern of tumor cells plated on MATRIGEL® (see Figure
2).
As shown in Figure 2, SEQ ID NO:4 was inactive while, unexpectedly, the addition of
cholesteryl-TEG phosphoramidite at the 3'-end of SEQ ID NO:4, resulting in SEQ ID NO:8,
conferred the capability to prevent formation of 3-dimension structures, similar to those formed
when cells were cultured in the regular culture medium on MATRIGEL®-coated wells. It is
believed that SEQ ID NO:8 interfered with cell-extracellular matrix interactions thereby
modulating interactions between tumor cells and the ECM components.

Example 13
Changes in 3-dimensional structure formation of MCF-7 cells induced by SEQ ID NO:7 in
MATRIGEL® outgrowth experiments
MCF-7 cells were cultured in regular culture medium (RCM), trypsinized and counted.
15OxlO3 of MCF-7 cells, in wells of 24-well plates coated with 350 ul of MATRIGEL®. After
the formation of 3-dimensional structures during 48 hrs without any treatment, the medium was
changed and the structures were exposed to a final concentration of 53 uM of SEQ ID NO.3, 53
M of SEQ ID NO:7, 53 uM of cholesteryl-TEG phosphoramidite, RCM or their respective
control media (RCM with water, RCM with DMSO, or RCM with acetonitrile). The treatments
were repeated every 3-4 days until a maximum time in culture of 19-20 days. The experiment
was repeated three times. Digital photographs of the cells in the 24-well plates were taken using
a Nikon Coolpix 990 digital camera connected to a Nikon inverted microscope model TMS.
While the respective control media (data not shown), SEQ ID NO:3 and cholesteryl-TEG
phosphoramidite did not affect the 3-dimensional structures compared to controls, SEQ ID NO:7
disrupted the growth pattern of the structures thereby affecting cell-cell and cell-extracellular
matrix interactions (see Figure 3).
As shown in Figure 3, SEQ ID NO:3 and cholesteryl-TEG phosphoramidite were inactive while,
unexpectedly, the addition of cholesteryl-TEG phosphoramidite at the 3'-end of SEQ ID NO:3,
resulting in SEQ ID NO.7, conferred the capability to disrupt pre-formed 3-dimensional
structures.
Example 14
Changes in 3-dimensional structure formation of MDA-MB-231 cells induced by SEQ ID NO:7
in MATRIGEL® outgrowth experiments
The MDA-MB-231 (MDA-231) cells were cultured in regular culture medium,
trypsinized and counted. 100x103 of MDA-231 cells were plated in regular culture medium
(RCM), in wells of 24-well plates coated with 350 ul of MATRIGEL®. After the formation of 3-
dimensional structures during 48 hrs without any treatment, the medium was changed, and
structures were exposed to a final concentration of 53 uM of SEQ ID NO:3, 53 M of
SEQ ID NO:7, 53 M of cholesteryl-TEG phosphoramidite, RCM, or their respective control
media (RCM with water, RCM with DMSO or RCM with acetonitrile). The treatments were
repeated every 3-4 days until a maximum time in culture of 17-21 days. The experiment was
repeated three times. Digital photographs of the cells in the 24-well plates were taken using a
Nikon Coolpix 990 digital camera connected to a Nikon inverted microscope model TMS. While

the respective control media (data not shown), SEQ ID NO:3 and cholesteryl-TEG
phosphoramidite did not affect the 3-dimensional structures, being similar to the structures
cultured in the RCM (negative control medium), SEQ ID NO:7 disrupted the growth pattern of
the structures thereby affecting cell-cell and cell-extracellulaT matrix interactions (see Figure 4).
As shown in Figure 4, SEQ ID NO:3 and cholesteryl-TEG phosphoramidite were inactive while,
unexpectedly, the addition of cholesteryl-TEG phosphoramidite at the 3'-end of SEQ ID NO:3,
resulting in SEQ ID NO:7, conferred the capability to disrupt 3-dimensional structures by
interfering with cell-cell and cell-extracellular matrix interactions.
Example 15
Changes in cell cycle induced by SEQ ID NO: 7 when the Hs578T cells were cultured as
multicelhdar spheroids /
About 100x103 Hs578T cells per spheroid were cultured in presence of 53 M final
concentration of SEQ ID NO:3, SEQ ID NO:7, 53 M final concentration of cholesteryl-TEG
phosphoramidite (cholTEG) or corresponding control media (regular culture medium (RCM),
RCM with the same amount of water (RCMW) as the amount added with the SEQ ID NO: 7, and
RCM with the same amount of acetonitrile (RCMA) as the amount added with cholesteryl-TEG
phosphoramidite). Five spheroids per each experimental condition were cultured for 72 hrs.
Afterwards, cell cycle progression was evaluated by propidium iodide (PI) staining (Calbiochem,
Novabiochem Corporation, San Diego, CA) using a FACScalibur flow cytometer (Becton
Dickinson, Franklin Lakes, NJ). Changes in the percentage of cells in the different phases of the
cell cycle were analyzed using MODFIT LT software (Verity Software House Inc). Results are
shown in Figure 5.
As shown in Figure 5, SEQ ID NO:3, cholesteryl-TEG phosphoramidite or control media did not
significantly modify cell cycle progression compared to those spheroids exposed to the regular
culture medium alone. Unexpectedly, exposure to SEQ ID NO:7 increased the percentage of
cells in G2M and S-phase and decrease the percentage of cells in Go/G, (p test). The addition of cholesteryl-TEG phosphoramidite conferred to an inactive oligonucleottde
tested in the MS assay the capacity to modify cell cycle progression in a complex 3-dimensional
system that mimics several biopathological characteristics of in vivo tumors.

Example 16
Changes in the release of nuclear mitotic apparatus protein (NuMA) by MDA-MB-231 human
breast cancer cells wiien incubated with SEQ ID NO: 5
MDA-MB-231 cells were cultured as mono-layers in respective control media, with 53
M final concentration of SEQ ID NO:1 or 53 M final concentration of SEQ ED NO: 5 for 72
hrs. The release of nuclear mitotic apparatus protein (NuMA) was used as a measure of
apoptosis. NuMA was determined using a commercial (ELISA kit (Oncogene, Cambridge, MA)
following the manufacturer's protocol. Results are shown in Table 10 and are expressed as the
percentage increase in NuMA release compared to respective controls based on optical density
measurements.
Table 10
Changes in the release of nuclear mitotic apparatus protein (NuMA) in MDA-MB-231 human
breast cancer cells

As shown in Table 10, the release of nuclear mitotic apparatus protein (NuMA) increased
by 430% after cells were incubated with SEQ ID NO:5. Unexpectedly, the addition of
cholesteryl-TEG phosphoramidite to the 3' end of SEQ ID NO: 1, resulting in SEQ ID NO:5,
conferred the capacity to induce apoptosis.
Example 17
Changes in the release of nuclear mitotic apparatus protein (NuMA) by Hs578T human breast
cancer cells when incubated with SEQ ID NO:6
Hs578T cells were cultured as monolayer in negative control conditions or with 53 uM
final concentraition of SEQ ID NO:2, 53 M of SEQ ID NO:6 for 72 hrs. The release of nuclear
mitotic apparatus protein (NuMA) was used as a measure of apoptosis. NuMA was determined
using a commercial ELISA kit following the manufacturer's protocol. Results are shown in Table
11 and are expressed as the percentage increase in NuMA release compared to control conditions
based on optical density measurements.


Table 11
Changes in the release of nuclear mitotic apparatus protein (NuMA) by Hs578T human breast
cancer cells
As shown in Table 11, the release of nuclear mitotic apparatus protein (NuMA) increased
by 288% after cells were incubated with SEQ ID NO:6 Unexpectedly, the addition of
cholesteryl-TEG phosphoramidite to the 31 end of SEQ ID NO:2 conferred to an inactive
oligonucleotide the capacity to induce apoptosis.
Example 18
Effect of SEQ ID NO: 1 SEQ ID NO.2, SEQ ID N0:5, and SEQ ID NO: 6 on MEG-01 cells in
athymic nude mice
MEG-01 cells are inoculated subcutaneously into athymic nude mice as previously
described (Takeo et al., Leukemia 7:1286, 1993). The mice are divided into 13 groups of 10
mice. On day 0, group 1 mice receive saline, group 2 mice receive 1 mg/kg SEQ ID NO:1, group
3 mice receive 10 mg/kg SEQ ID NO:1, group 4 mice receive 100 mg/kg SEQ ID NO:1, group 5
mice receive 1 mg/kg SEQ ID NO:2, group 6 mice receive 10 mg/kg SEQ ID NO:2, group 7
mice receive 100 mg/kg SEQ ID NO.2, group 8 mice receive 1 mg/kg, SEQ ID NO:5, group 9
mice receive 10 mg/kg SEQ ID NO:5, group 10 mice receive 100 mg/kg SEQ ID NO.5, group
11 mice receive 1 mg/kg SEQ ID NO:6, group 12 mice receive 10 mg/kg SEQ ID NO.6 and
group 13 mice receive 100 mg/kg SEQ ID NO:6 After 4 weeks of treatment, the mice are
sacrificed and tumor mass is determined. Mice in groups 8-13 have less tumor mass than mice in
groups 1-7. Mice in groups 8-13 display less tumor mass in a dose-dependent fashion.
Example 19
Effect of SEQ ID NO: 3 and SEQ ID NO: 7 on growth of lymphoma cells in mice
EL-4 murine T lymphoma cells are implanted subcutaneously into C57/BL6 mice as
previously described (Krawczyk et al., Cancer Immunol. Immunother. 40:347, 1995). The mice
are divided into 7 groups of 10 mice. On day 0, group 1 mice receive saline, group 2 mice
receive 1 mg/kg SEQ ID NO:3, group 3 mice receive 10 mg/kg SEQ ID NO:3, group 4 mice
receive 100 mg/kg SEQ ID NO:3, group 5 mice receive 1 mg/kg SEQ ID NO:7, group 6 mice

receive 10 mg/kg SEQ ID NO:7, group 7 mice receive 100 mg/kg SEQ ID NO:7. After 4 weeks
of treatment, the mice are sacrificed and tumor mass is determined. Groups 5-7 have less tumor
mass than mice in groups 1-4. Mice in groups 5-7 display less tumor mass in a dose-dependent
fashion.
Example 20
Effect of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:5 and SEQ ID NO:6 on rats with
streptococcal cell wall-induced arthritis s^
Streptococcal cell wall-induced arthritis in LEW/N rats resembles a localized neoplasm
consisting of, in part, of a proliferative and invasive population of fibroblast-like synovial cells
(Yocum et al., Am. J. Pathol. 132:38, 1988). The arthritis is induced in LEW/N rats by intra-
articular injection of streptocococcal cell wall (SCW) from group A Streptococcus pyogenes.
The rats are divided into 13 groups of 10 rats. On day 0, group 1 rats receive SCW, group 2 rats
receive SCW + 1 mg/kg SEQ ED NO:1, group 3 rats receive SCW + 10 mg/kg SEQ ID NO:1,
group 4 rats receive SCW + 100 mg/kg SEQ ID NO: 1, group 5 rats receive SCW + 1 mg/kg
SEQ ID NO:2, group 6 rats receive SCW + 10 mg/kg SEQ ID NO:2, group 7 rats receive SCW +
100 mg/kg SEQ ID NO.-2, group 8 rats receive SCW + 1 mg/kg SEQ ID NO.5, group 9 rats
receive SCW + 10 mg/kg SEQ ID NO:5, group 10 rats receive SCW + 100 mg/kg SEQ ID NO:5,
group 11 rats receive SCW + 1 mg/kg SEQ ID NO:6, group 12 rats receive SCW + 10 mg/kg
SEQ ID NO:6, group 13 rats receive SCW + SEQ ID NO:6. The joint inflammation is monitored
daily for two weeks. Group 8-13 rats show less inflammation than group 1-7 rats. Rats in groups
8-13 have less inflammation in a dose-dependent fashion.
Example 21
Effect of sequences conjugated with TEG cholesteryl on cell morphology and cell cycle when
cancer cells are grown as monolayers, on MATRIGEL® or as multicelhdar spheroids
Different types of malignant cell lines from breast, pancreas, colon, ovary and prostate
are cultured as monolayers, on MATRIGEL®-coated wells or as multicelmlar spheroids (MS).
Cells are treated individually with oligonucleotide sequences of different lengths (3 and 6 bases)
with or without conjugated cholesteryl-TEG phosphoramidite for at least 1-3 days. Such
sequences include, but are not limited to SEQ ID NO:1, SEQ ID NO.5, SEQ ID NO:2,
SEQ ID NO:6, SEQ ID NO:3, SEQ ID NO:7; SEQ ID NO.4, or SEQ ID NO:8. Cell
proliferation/necrosis (measured by Trypan blue exclusion), apoptosis (measured by flow
cytometry, release of nuclear mitotic apparatus protein (NuMA), detection of fragmented DNA
by terminal deoxynucleotidyl transferase enzyme-mediated bromodeoxyuridine triphosphate-

biotin nick end-labeling (TUNEL)), cell cycle progression studied by flow cytometry (PI
staining) and morphology of tumor cells plated on MATRIGEL®-coated wells or as
multicellular spheroids (MS) are studied.
Oligonucleotide sequences conjugated with cholesteryl-TEG phosphoramidite increase
cell death (necrosis and apoptosis), modify cell cycle progression when cells are cultured as MS
or on MATRIGEL®-coated plates, and change cell morphology when cells are cultured as MS
or on MATRIGEL®-coated wells. Unconjugated oligonucleotides are inactive.
Example 22
Effect of SEQ ID NO: 3 and SEQ ID NO:7 on MDA-MB-231 xenotransplanted tumors
MDA-MB-231 cells are xenotransplanted subcutaneously into nude mice. The mice are
divided into 7 groups of 10 mice. After the tumors reach 5 mm in diameter, group 1 mice receive
saline, group 2 mice receive 0.5 mg/kg SEQ ID NO:3, group 3 mice receive 5 mg/kg
SEQ ID NO:3, group 4 mice receive 50 mg/kg SEQ ID NO:3, group 5 mice receive 0.5 mg/kg
SEQ ID NO:7, group 6 mice receive 5 mg/kg SEQ ID NO.7, group 7 mice receive 50 mg/kg
SEQ ID NO:7. Treatments are given intravenously every 3 days for 6 doses maximum. Mice are
sacrificed when tumor reach 1 cm in diameter, at any sign of distress or at the end of the study (3
months from cell injection). Complete autopsies are performed. Tumor mass, presence of
invasion and metastasis are determined. Groups 5-7 have less tumor mass than group 1-4 mice.
Mice in groups 5-7 display less tumor mass in a dose-dependent fashion.
Example 23
Effect of SEQ ID NO: 3 and SEQ ID NO:7 on MDA-MB-231 xenotransplanted tumors
Breast cancer MDA-MB-231 cells are xenotransplanted subcutaneously in nude mice
(lx107 cells). The mice are divided into 7 groups of 10 mice. After the tumors reach 5 mm in
diameter, group 1 mice receive saline, group 2 mice receive 0.4 mg/kg SEQ ID NO:3, group 3
mice receive 4 mg/kg SEQ ID NO:3, group 4 mice receive 40 mg/kg SEQ ID NO.3, group 5
mice receive 0.4 mg/kg SEQ ID NO:7, group 6 mice receive 4 mg/kg SEQ ID NO:7, group 7
mice receive 40 mg/kg SEQ ID NO:7. Treatments are given intravenously every 3 days for 6
doses maximum. Mice are sacrificed when tumor reach 1 cm in diameter, at any sign of distress
or at the end of the study (3 months from cell injection). Complete autopsies are performed.
Tumor mass, presence of invasion and metastasis are determined. Groups 5-7 have less tumor
mass and metastasis than group 1-4 mice. Mice in groups 5-7 display less tumor mass and
metastasis in a dose-dependent fashion.

All patents, publications and abstracts cited above are incorporated herein by reference in their
entirety. It should be understood, of course, that the foregoing relates only to preferred
embodiments of the present invention and that numerous modifications or alterations may be
made therein without departing from the spirit and the scope of the invention as set forth in the
appended claims.

WE CLAIM :
1. A composition comprising a 5'-OH, 3-TEG cholesteryl, synthetic sequence, wherein the
sequence is SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, and optionally
comprising a pharmaceutically acceptable carrier, or a therapeutic agent, or a combination thereof.
2. A composition comprising a 5'-OH, 3'-TEG cholesteryl, synthetic sequence,in an amount
effective to induce a response in a cell, wherein the sequence is SEQ ID NO:5, SEQ ID NO:6, SEQ
ID NO:7 or SEQ ID NO:8, and wherein the response is inhibition of cell proliferation, cell cycle
arrest, induction of apoptosis, activation of caspase, cleavage of poly(ADP- ribose)polymerase in the
cell, or modulation of extracellular matrix cell interactions, or a combination thereof, and optionally
comprising a pharmaceutically acceptable carrier, or a therapeutic agent or a combination thereof..
3. A composition as claimed in any one of claims 1 or 2, for the preparation of a medicament.
4. A composition as claimed in claim 3 wherein the medicament is effective to induce a
response in a cell.
5. A composition as claimed in claim 3, wherein the medicament is useful to administer to an
animal or a human.
6. A composition as claimed in claim 2, wherein the cell is a cancer cell or a synovial cell.
7. A composition as claimed in claim 3, 4 or 5, wherein the medicament is effective to treat a
disease.
8. A composition as claimed in claim 7, wherein the disease is cancer or arthiritis.
9. A composition as claimed in claim 8, wherein cancer is lymphoma, leukemia, or breast
cancer.

The instant invention discloses a composition comprising a 5'-OH, 3'-TEG cholesteryl,
synthetic sequence, wherein the sequence is SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID
NO:8, and optionally comprising a pharmaceutically acceptable carrier, or a therapeutic agent, or a
combination thereof.

Documents:

350-KOLNP-2004-FORM-27.pdf

350-kolnp-2004-granted-abstract.pdf

350-kolnp-2004-granted-assignment.pdf

350-kolnp-2004-granted-claims.pdf

350-kolnp-2004-granted-correspondence.pdf

350-kolnp-2004-granted-description (complete).pdf

350-kolnp-2004-granted-drawings.pdf

350-kolnp-2004-granted-examination report.pdf

350-kolnp-2004-granted-form 1.pdf

350-kolnp-2004-granted-form 18.pdf

350-kolnp-2004-granted-form 2.pdf

350-kolnp-2004-granted-form 3.pdf

350-kolnp-2004-granted-form 5.pdf

350-kolnp-2004-granted-form 6.pdf

350-kolnp-2004-granted-gpa.pdf

350-kolnp-2004-granted-reply to examination report.pdf

350-kolnp-2004-granted-sequence listing.pdf

350-kolnp-2004-granted-specification.pdf


Patent Number 226189
Indian Patent Application Number 350/KOLNP/2004
PG Journal Number 50/2008
Publication Date 12-Dec-2008
Grant Date 08-Dec-2008
Date of Filing 15-Mar-2004
Name of Patentee HERRERA-GAYOL ANDREA CRISTINA
Applicant Address 27 DE CASSON, WESTMOUNT, QUEBEC H3Y 2G9
Inventors:
# Inventor's Name Inventor's Address
1 HERRERA-GAYOL ANDREA CRISTINA 27 DE CASSON, WESTMOUNT, QUEBEC H3Y 2G9
2 PHILLIPS NIGEL C. 101 SEIGNIORY AVENUE, POINTE-CLAIRE, QUEBEC, H9R 1J6
3 FILION MARIO C 1145, JEAN-DE BREBEUF STREET LAVAL, QUEBEC, H7E 3Y6
PCT International Classification Number A61K 47/48
PCT International Application Number PCT/IB2002/004065
PCT International Filing date 2002-10-03
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 NA