WO2007131237A2 - Compounds and methods for modulating expression of ptp1b - Google Patents

Compounds and methods for modulating expression of ptp1b Download PDF

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Publication number
WO2007131237A2
WO2007131237A2 PCT/US2007/068402 US2007068402W WO2007131237A2 WO 2007131237 A2 WO2007131237 A2 WO 2007131237A2 US 2007068402 W US2007068402 W US 2007068402W WO 2007131237 A2 WO2007131237 A2 WO 2007131237A2
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Prior art keywords
short antisense
antisense compound
certain embodiments
monomers
certain
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English (en)
French (fr)
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WO2007131237A3 (en
Inventor
Sanjay Bhanot
Richard S. Geary
Robert Mckay
Brett P. Monia
Punit P. Seth
Andrew M. Siwkowski
Eric E. Swayze
Edward Wancewicz
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Ionis Pharmaceuticals Inc
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Isis Pharmaceuticals Inc
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Priority claimed from PCT/US2007/061183 external-priority patent/WO2007090071A2/en
Application filed by Isis Pharmaceuticals Inc filed Critical Isis Pharmaceuticals Inc
Priority to US12/299,607 priority Critical patent/US8586554B2/en
Publication of WO2007131237A2 publication Critical patent/WO2007131237A2/en
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Definitions

  • RNAi RNA interference
  • Sequence-specificity makes antisense compounds extremely attractive as tools for target validation and gene functionalization, as well as research tools for identifying and characterizing nucleases and as therapeutics to selectively modulate the expression of genes involved in the pathogenesis of any one of a variety of diseases.
  • Antisense technology is an effective means for reducing the expression of one or more specific gene products and can therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications.
  • Chemically modified nucleosides are routinely used for incorporation into antisense compounds to enhance one or more properties, such as nuclease resistance, pharmacokinetics or affinity for a target RNA.
  • the present disclosure describes incorporation of chemically-modified high-affinity nucleotides into antisense compounds allows for short antisense compounds about 8-16 nucleobases in length useful in the reduction of target RNAs in animals with increased potency and improved therapeutic index.
  • short antisense compounds comprising high-affinity nucleotide modifications useful for reducing a target RNA in vivo.
  • Such short antisense compounds are effective at lower doses than previously described antisense compounds, allowing for a reduction in toxicity and cost of treatment.
  • short antisense compounds and methods of using said compounds to reduce target RNA expression in cells or tissues.
  • a method of reducing expression of a target in an animal comprising administering to the animal a short antisense compound targeted to a nucleic acid of such target.
  • shorts antisense compounds are oligonucleotide compounds.
  • short antisense oligonucleotides are about 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length and comprises a gap region flanked on each side by a wing, wherein each wing independently consists of 1 to 3 nucleotides.
  • Preferred motifs include but are not limited to wing - deoxy gap -wing motifs selected from 3-10-3, 2-10-3, 2-10-2, 1-10-1, 2-8-2, 1-8-1, 3-6-3 or 1-6-1.
  • the short antisense oligonucleotide comprise at least one high-affinity modification.
  • the high-affinity modification includes chemically-modified high-affinity nucleotides.
  • each wing independently consists of 1 to 3 high-affinity modified nucleotides.
  • the high affinity modified nucleotides are sugar-modified nucleotides.
  • short antisense compounds exhibit greater uptake in the gut as compared to antisense compounds of greater length.
  • methods of reducing a target in an animal comprising orally administering the short antisense compounds of the present invention.
  • short antisense compounds are targeted to a nucleic acid encoding a protein selected from ApoB, SGLT2, PCSK9, SODl, CRP, GCCR, GCGR, DGAT2, PTPlB and PTEN.
  • a metabolic disorder in an animal comprising administering to an animal in need of such therapy a short antisense compound targeted to a nucleic acid involved in regulating glucose metabolism or clearance, lipid metabolism, cholesterol metabolism, or insulin signaling.
  • a short antisense compound targeted to a nucleic acid encoding a target that is involved in regulating glucose metabolism or clearance, lipid metabolism, cholesterol metabolism, or insulin signaling wherein said short antisense compound is 8 to 16 nucleotides in length and comprises a gap region flanked on each side by a wing, wherein each wing independently consists of 1 to 3 high-affinity modified nucleotides.
  • Certain targets involved in regulating glucose metabolism or clearance, lipid metabolism, cholesterol metabolism, or insulin signaling include, but are not limited to, GCGR and ApoB-100.
  • short antisense compounds targeting nucleic acids encoding GCGR and ApoB-100 and methods of reducing expression of said targets and/or target nucleic acids in animal.
  • short antisense compounds targeting nucleic acids encoding GCGR, and ApoB-100 for the treatment of a metabolic or cardiovascular disease or condition.
  • short antisense compounds further comprise a conjugate group.
  • Conjugate groups include, but are not limited to, Ci 6 and cholesterol.
  • short antisense compounds comprise at least one modified nucleobase, internucleoside linkage or sugar moiety.
  • such modified internucleoside linkage is a phosphorothioate internucleoside linkage.
  • each internucleoside linkage is a phosphorothioate internucleoside linkage.
  • short antisense compounds comprise at least one high affinity modification.
  • the high-affinity modification is a chemically-modified high-affinity nucleotide.
  • chemically-modified high affinity nucleotides are sugar-modified nucleotides.
  • at least one of the sugar-modified nucleotides comprises a bridge between the 4' and the 2' position of the sugar.
  • Each of the sugar-modified nucleotides is, independently, in the ⁇ -D or ⁇ -L sugar conformation.
  • each of said high-affinity modified nucleotides confers a T m of at least 1 to 4 degrees per nucleotide.
  • each of said sugar-modified nucleotides comprises a 2'-substituent group that is other than H or OH.
  • Such sugar-modified nucleotides include those having a 4' to 2' bridged bicyclic sugar moiety.
  • each of the T- substituent groups is, independently, alkoxy, substituted alkoxy, or halogen.
  • each of the 2'-substituent groups is OCH 2 CH 2 OCH 3 (2'-MOE).
  • each of said bridges is, independently, -[C(Ri )(R 2 )] n -, -[C(Ri)(R 2 )J n -O-, -C(R]R 2 )- N(RO-O- or -C(R]R 2 )-0-N(Ri)-.
  • each of said bridges is, independently, 4'-(CH 2 ) 3 -2', 4'- (CH 2 ) 2 -2 ⁇ 4'-CH 2 -O-2', 4'-(CH 2 ) 2 -O-2 T , 4'-CH 2 -O-N(R,)-2' and 4'-CH 2 -N(R, )-0-2'- wherein each R, is, 5 independently, H, a protecting group or Ci-C] 2 alkyl.
  • provided herein are short antisense compounds useful in the reduction of targets and/or target RNAs associated with disease states in animals. In certain embodiments, provided are methods of using the short antisense compounds for reducing expression of a target RNA in an animal. In certain embodiments, provided herein is the use of a short antisense compound in the preparation of a O medicament for the treatment of a metabolic disorder in an animal. In certain embodiments, provided herein is the use of a short antisense compound in the preparation of a medicament for increasing insulin sensitivity, decreasing blood glucose or decreasing HbA ]c in an animal.
  • short antisense compounds provided herein exhibit equal or increased potency with regard to target RNA knockdown as compared to longer parent antisense oligonucleotide at least 20 nucleotides in length.
  • short antisense compounds exhibit a faster onset of action (target RNA reduction) as compared to the parent antisense oligonucleotide.
  • increased potency is in the kidney.
  • target RNA is predominately expressed in the 50 kidney.
  • increased potency is in the liver.
  • target RNA is predominately expressed in the liver.
  • GenBank and other data bases referred to throughout in the disclosure herein are incorporated by reference in their entirety.
  • nucleoside means a glycosylamine comprising a nucleobase and a sugar.
  • Nucleosides includes, but are not limited to, naturally occurring nucleosides, abasic nucleosides, modified nucleosides, and nucleosides having mimetic bases and/or sugar groups.
  • nucleotide refers to a glycosomine comprising a nucleobase and a sugur having a phosphate group covalently linked to the sugar. Nucleotides may be modified with any of a variety of substituents. i0 As used herein, the term “nucleobase” refers to the base portion of a nucleoside or nucleotide. A nucleobase may comprise any atom or group of atoms capable of hydrogen bonding to a base of another nucleic acid.
  • heterocyclic base moiety refers to a nucleobase comprising a heterocycle.
  • deoxyribonucleotide means a nucleotide having a hydrogen at the 2' position of the sugar portion of the nucleotide. Deoxyribonucleotides may be modified with any of a variety of substituents.
  • ribonucleotide means a nucleotide having a hydroxy at the 2' position of the sugar portion of the nucleotide. Ribonucleotides may be modified with any of a variety of substituents. 5
  • the term “oligomeric compound” refers to a polymeric structure comprising two or more sub-structures and capable of hybridizing to a region of a nucleic acid molecule. In certain embodiments, oligomeric compounds are oligonucleosides. In certain embodiments, oligomeric compounds are oligonucleotides. In certain embodiments, oligomeric compounds are antisense compounds.
  • oligomeric compounds are antisense oligonucleotides. In certain embodiments, oligomeric 0 compounds are short antisense compounds. In certain embodiments, oligomeric compounds are short antisense oligonucleotides. In certain embodiments, oligomeric compounds are chimeric oligonucleotides.
  • monomer refers to a single unit of an oligomer. Monomers include, but are not limited to, nucleosides and nucleotides, whether naturally occuring or modified.
  • oligonucleoside refers to an oligonucleotide in which the internucleoside linkages 5 do not contain a phosphorus atom.
  • oligonucleotide refers to an oligomeric compound comprising a plurality of linked nucleotides. In certain embodiment, one or more nucleotides of an oligonucleotide is modified. In certain embodiments, an oligonucleotide comprises ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). In certain embodiments, oligonucleotides are composed of naturally- and/or non-naturally-occurring .0 nucleobases, sugars and covalent internucleotide linkages, and may further include non-nucleic acid conjugates.
  • RNA ribonucleic acid
  • DNA deoxyribonucleic acid
  • internucleotide linkage refers to a covalent linkage between adjacent nucleotides.
  • monomelic linkage refers to a covalent linkage between two monmers.
  • Monomelic linkages include, but are not limited to internucleotide linkages and internucleoside linkages. >5
  • naturally occuring internucleotide linkage refers to a 3' to 5' phosphodiester linkage.
  • antisense compound refers to an oligomeric compound that is at least partially complementary to a target nucleic acid molecule to which it hybridizes. In certain embodiments, an antisense compound modulates (increases or decreases) expression of a target nucleic acid.
  • Antisense compounds include, but are not limited to, compounds that are oligonucleotides, oligonucleosides, »0 oligonucleotide analogs, oligonucleotide mimetics, and chimeric combinations of these. Consequently, while all antisense compounds are oligomeric compounds, not all oligomeric compounds are antisense compounds.
  • antisense oligonucleotide refers to an antisense compound that is an oligonucleotide.
  • parent antisense oligonucleotide refers to an oligonucleotide 20 i5 nucleotides in length having a deoxy gap region having ten 2'-deoxyribonucleotides, flanked by a first and a second wing region each having five 2'-O-(2-methoxyethyl) ribonucleotides (a 5-10-5 MOE gapmer) and comprising the sequence of the corresponding short antisense compound to which it is a parent.
  • short antisense compound refers to an antisense compound about 8, 9, 10, 11, 12, 13, 14, 15 or 16 monomers in length.
  • a short antisense compound has at least one high-affinity modification.
  • short antisense oligonucleotide or refers to an antisense oligonucleotide about 8, 9, 10, 11, 12, 13, 14, 15 or 16 nucleotides in length.
  • a short antisense oligonucleotide has at least one high-affinity modification.
  • short gapmer refers to a short antisense oligonucleotide having a first and a second wing region each independently 1 to 3 nucleotides in length and a gap region 2 to 14 nucleobase in length.
  • motif refers to the pattern of unmodified and modified nucleotides in a short antisense compound
  • chimeric antisense oligomer refers to an antisense oligomeric compound, having at least one sugar, nucleobase or internucleoside linkage that is differentially modified as compared to at least on other sugar, nucleobase or internucleoside linkage within the same antisense oligomeric compound.
  • the remainder of the sugars, nucleobases and internucleoside linkages can be independently modified or unmodified, the same or different.
  • chimeric antisense oligonucleotide refers to an antisense oligonucleotide, having at least one sugar, nucleobase or internucleoside linkage that is differentially modified as compared to at least on other sugar, nucleobase or internucleoside linkage within the same antisense oligonucleotide.
  • the remainder of the sugars, nucleobases and internucleoside linkages can be independently modified or unmodified, the same or different.
  • mixed-backbone antisense oligonucleotide refers to an antisense oligonucleotide wherein at least one internucleoside linkage of the antisense oligonucleotide is different from at least one other internucleotide linkage of the antisense oligonucleotide.
  • target refers to a protein, the modulation of which is desired.
  • target gene refers to a gene encoding a target.
  • target nucleic acid and “nucleic acid molecule encoding a target” refer to any nucleic acid molecule the expression or activity of which is capable of being modulated by an antisense compound.
  • Target nucleic acids include, but are not limited to, RNA (including, but not limited to pre- mRNA and mRNA or portions thereof) transcribed from DNA encoding a target, and also cDNA derived from such RNA, and miRNA.
  • the target nucleic acid can be a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent.
  • targeting or “targeted to” refers to the association of an antisense compound to a particular target nucleic acid molecule or a particular region of nucleotides within a target nucleic acid molecule.
  • 5' target site refers to the nucleotide of a target nucleic acid which is 5 complementary to the 5 ' -most nucleotide of a particular antisense compound.
  • 3' target site refers to the nucleotide of a target nucleic acid which is complementary to the 3 '-most nucleotide of a particular antisense compound.
  • target region refers to a portion of a target nucleic acid to which one or more antisense compounds is complementary.
  • target segment refers to a smaller or sub-portions of a region within a target nucleic acid.
  • nucleobase complementarity refers to a nucleobase that is capable of base pairing with another nucleobase.
  • adenine (A) is complementary to thymine (T).
  • adenine (A) is complementary to uracil (U).
  • complementary 5 nucleobase refers to a nucleobase of an antisense compound that is capable of base pairing with a nucleobase of its target nucleic acid.
  • nucleobase at a certain position of an antisense compound is capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid
  • the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be complementary at that nucleobase pair.
  • non-complementary nucleobase refers to a pair of nucleobases that do not form hydrogen bonds with one another or otherwise support hybridization.
  • the term "complementary” refers to the capacity of an oligomeric compound to hybridize to another oligomeric compound or nucleic acid through nucleobase complementarity.
  • an antisense compound and its target are complementary to each other when a sufficient 5 number of corresponding positions in each molecule are occupied by nucleobases that can bond with each other to allow stable association between the antisense compound and the target.
  • antisense compounds may comprise up to about 20% nucleotides that are mismatched (i.e., are not nucleobase complementary to the
  • the antisense compounds contain no more than about
  • nucleotides are nucleobase complementary or otherwise do not disrupt hybridization (e.g., universal bases).
  • mismatch refers to a non-complementary nucleobase within a complementary oligomeric compound.
  • hybridization means the pairing of complementary oligomeric compounds (e.g., an antisense compound and its target nucleic acid). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases
  • nucleobases are nucleobase complementary to the natural nucleobases thymidine and uracil which pair through the formation of hydrogen bonds.
  • the natural base guanine is nucleobase complementary to the natural bases cytosine and 5 -methyl cytosine. Hybridization can occur under varying circumstances.
  • the term “specifically hybridizes” refers to the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site.
  • an antisense oligonucleotide specifically hybridizes to more than one target site.
  • design or “designed to” refer to the process of designing an oligomeric compound that specifically hybridizes with a selected nucleic acid molecule.
  • modulation refers to a perturbation of function or activity when compared to the level of the function or activity prior to modulation.
  • modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression.
  • modulation of expression can include perturbing splice site selection of pre-mRNA processing.
  • expression refers to all the functions and steps by which a gene's coded information is converted into structures present and operating in a cell. Such structures include, but are not limited to the products of transcription and translation.
  • variant refers to an alternative RNA transcript that can be produced from the same genomic region of DNA. Variants include, but are not limited to “pre-mRNA variants” which are transcripts produced from the same genomic DNA that differ from other transcripts produced from the same genomic DNA in either their start or stop position and contain both intronic and exonic sequence. Variants also include, but are not limited to, those with alternate splice junctions, or alternate initiation and termination codons.
  • high-affinity modified monomer refers to a monomer having at least one modified nucleobase, internucleoside linkage or sugar moiety, when compared to naturally occurring monomers, such that the modification increases the affinity of an antisense compound comprising the high-affinity modified monomer to its target nucleic acid.
  • High-affinity modifications include, but are not limited to, monomers (e.g., nucleosides and nucleotides) comprising 2'-modifed sugars.
  • the term “2 '-modified” or "2 '-substituted” means a sugar comprising substituent at the T position other than H or OH.
  • T- substituents such as allyl, amino, azido, thio, O-allyl, 0-C 1 -C 10 alkyl, -OCF 3 , O-(CH 2
  • short antisense compounds comprise a 2'modified monomer that does not have the formula T- O(CH 2 ) n H, wherein n is one to six. In certain embodiments, short antisense compounds comprise a 2'modified monomer that does not have the formula 2'-OCH 3 . In certain embodiments, short antisense compounds comprise a 2'modified monomer that does not have the formula or, in the alternative, T- O(CH 2 ) 2 OCH 3 .
  • bicyclic nucleic acid or "BNA” or "bicyclic nucleoside” or “bicyclic nucleotide” refers to a nucleoside or nucleotide wherein the furanose portion of the nucleoside includes a bridge connecting two carbon atoms on the furanose ring, thereby forming a bicyclic ring system.
  • methyleneoxy BNA alone refers to ⁇ -D- methyleneoxy BNA.
  • MOE refers to a 2'-methoxyethyl substituent.
  • the term “gapmer” refers to a chimeric oligomeric compound comprising a central region (a "gap") and a region on either side of the central region (the “wings”), wherein the gap comprises at least one modification that is different from that of each wing.
  • modifications include nucleobase, monomelic linkage, and sugar modifications as well as the absence of modification (unmodified).
  • the nucleotide linkages in each of the wings are different than the nucleotide linkages in the gap.
  • each wing comprises nucleotides with high affinity modifications and the gap comprises nucleotides that do not comprise that modification.
  • nucleotides in the gap and the nucleotides in the wings all comprise high affinity modifications, but the high affinity modifications in the gap are different than the high affinity modifications in the wings.
  • the modifications in the wings are the same as one another. In certain embodiments, the modifications in the wings are different from each other. In certain embodiments, nucleotides in the gap are unmodified and nucleotides in the wings are modified. In certain embodiments, the modifications) in each wing are the same. In certain embodiments, the modification(s) in one wing are different from the modification(s) in the other wing.
  • short antisense compounds are gapmers having 2'-deoxynucleotides in the gap and nucleotides with high-affinity modifications in the wing.
  • prodrug refers to a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions.
  • pharmaceutically acceptable salts refers to salts of active compounds that retain the desired biological activity of the active compound and do not impart undesired toxicological effects thereto.
  • cap structure or “terminal cap moiety” refers to chemical modifications, which have been incorporated at either terminus of an antisense compound.
  • prevention refers to delaying or forestalling the onset or development of a condition or disease for a period of time from hours to days, preferably weeks to months.
  • the term “amelioration” refers to a lessening of at least one indicator of the severity of a condition or disease.
  • the severity of indicators may be determined by subjective or objective measures which are known to those skilled in the art.
  • treatment refers to administering a composition of the invention to effect an alteration or improvement of the disease or condition.
  • Prevention, amelioration, and/or treatment may require administration of multiple doses at regular intervals, or prior to onset of the disease or condition to alter the course of the disease or condition.
  • a single agent may be used in a single individual for each prevention, amelioration, and treatment of a condition or disease sequentially, or concurrently.
  • the term "pharmaceutical agent” refers to a substance provides a therapeutic benefit when administered to a subject.
  • terapéuticaally effective amount refers to an amount of a pharmaceutical agent that provides a therapeutic benefit to an animal.
  • administering means providing a pharmaceutical agent to an animal, and includes, but is not limited to administering by a medical professional and self-administering.
  • co-administration refers to administration of two or more pharmaceutical agents to an animal.
  • the two or more pharmaceutical agents may be in a single pharmaceutical composition, or may be in separate pharmaceutical compositions. Each of the two or more pharmaceutical agents may be administered through the same or different routes of administration. Co-administration encompasses administration in parallel or sequentially.
  • pharmaceutical composition refers to a mixture of substances suitable for administering to an individual.
  • a pharmaceutical composition may comprise an antisense oligonucleotide and a sterile aqueous solution.
  • the term "individual” refers to a human or non-human animal selected for treatment or therapy.
  • the term “animal” refers to a human or non-human animal, including, but not limited to, mice, rats, rabbits, dogs, cats, pigs, and non-human primates, including, but not limited to, monkeys and chimpanzees.
  • the term “subject” refers to an animal, including, but not limited to a human, to whom a pharmaceutical composition is administered.
  • the term “duration” refers to the period of time during which an activity or event continues. In certain embodiments, the duration of treatment is the period of time during which doses of a pharmaceutical agent are administered.
  • parenteral administration refers to administration through injection or infusion.
  • Parenteral administration includes, but is not limited to, subcutaneous administration, intravenous administration, or intramuscular administration.
  • subcutaneous administration refers to administration just below the skin.
  • Intravenous administration means administration into a vein.
  • a dose refers to a specified quantity of a pharmaceutical agent provided in a single administration.
  • a dose may be administered in two or more boluses, tablets, or injections.
  • the desired dose requires a volume not easily accommodated by a single injection.
  • two or more injections may be used to achieve the desired dose.
  • a dose may be administered in two or more injections to minimize injection site reaction in an individual.
  • a dosage unit refers to a form in which a pharmaceutical agent is provided.
  • a dosage unit is a vial comprising lyophilized antisense oligonucleotide.
  • a dosage unit is a vial comprising reconstituted antisense oligonucleotide.
  • the term “pharmaceutical agent” refers to a substance provides a therapeutic benefit when administered to an individual.
  • an antisense oligonucleotide is a pharmaceutical agent.
  • active pharmaceutical ingredient refers to the substance in a pharmaceutical composition that provides a desired effect.
  • a therapeutically effective amount refers to an amount of a pharmaceutical agent that provides a therapeutic benefit to an individual.
  • a therapeutically effective amount of an antisense compound is the amount that needs to be administered to result in an observable benefit.
  • hypocholesterolemia refers to a condition characterized by elevated serum cholesterol.
  • hypolipidemia refers to a condition characterized by elevated serum lipids.
  • hypotriglyceridemia refers to a condition characterized by elevated triglyceride levels.
  • non-familial hypercholesterolemia refers to a condition characterized by elevated cholesterol that is not the result of a single inherited gene mutation.
  • polygenic hypercholesterolemia refers to a condition characterized by elevated cholesterol that results from the influence of a variety of genetic factors. In certain embodiments, polygenic hypercholesterolemia may be exacerbated by dietary intake of lipids.
  • FH familial hypercholesterolemia
  • a diagnosis of familial hypercholesterolemia is made when a individual meets one or more of the following criteria: genetic testing confirming 2 mutated LDL-receptor genes; genetic testing confirming one mutated LDL-receptor gene; document history of untreated serum LDL-cholesterol greater than 500 mg/dL; tendinous and/or cutaneous xanthoma prior to age 10 years; or, both parents have documented elevated serum LDL-cholesterol prior to lipid-lowering therapy consistent with heterozygous familial hypercholesterolemia.
  • the term "homozygous familial hypercholesterolemia” or "HoFH” refers to a condition characterized by a mutation in both maternal and paternal LDL-R genes.
  • heterozygous familial hypercholesterolemia or “HeFH” refers to a condition characterized by a mutation in either the maternal or paternal LDL-R gene.
  • mixed dyslipidemia refers to a condition characterized by elevated serum cholesterol and elevated serum triglycerides.
  • diabetes dyslipidemia or “Type II diabetes with dyslipidemia” refers to a condition characterized by Type II diabetes, reduced HDL-C, elevated serum triglycerides, and elevated small, dense LDL particles.
  • CHD risk equivalents refers to indicators of clinical atherosclerotic disease that confer a high risk for coronary heart disease.
  • CHD risk equivalents include, without limitation, clinical coronary heart disease, symptomatic carotid artery disease, peripheral arterial disease, and/or abdominal aortic aneurysm.
  • non-alcoholic fatty liver disease refers to a condition characterized by fatty inflammation of the liver that is not due to excessive alcohol use (for example, alcohol consumption of over 20 g/day).
  • NAFLD is related to insulin resistance and the metabolic syndrome.
  • non-alcoholic steatohepatitis refers to a condition characterized by inflammation and the accumulation of fat and fibrous tissue in the liver, that is not due to excessive alcohol use. NASH is an extreme form of NAFLD.
  • major risk factors refers to factors that contribute to a high risk for a particular disease or condition. In certain embodiments, major risk factors for coronary heart disease include, without limitation, cigarette smoking, hypertension, low HDL-C, family history of coronary heart disease, and age.
  • CHD risk factors refers to CHD risk equivalents and major risk factors.
  • coronary heart disease refers to a narrowing of the small blood vessels that supply blood and oxygen to the heart, which is often a result of atherosclerosis.
  • reduced coronary heart disease risk refers to a reduction in the likelihood that a individual will develop coronary heart disease.
  • a reduction in coronary heart disease risk is measured by an improvement in one or more CHD risk factors, for example, a decrease in LDL-C levels.
  • the term “atherosclerosis” refers to a hardening of the arteries affecting large and medium-sized arteries and is characterized by the presence of fatty deposits.
  • the fatty deposits are called “atheromas” or “plaques,” which consist mainly of cholesterol and other fats, calcium and scar tissue, and damage the lining of arteries.
  • plaque consist mainly of cholesterol and other fats, calcium and scar tissue, and damage the lining of arteries.
  • the term “history of coronary heart disease” refers to the occurrence of clinically evident coronary heart disease in the medical history of a individual or a individual's family member.
  • Early onset coronary heart disease refers to a diagnosis of coronary heart disease prior to age 50.
  • statin intolerant individual refers to a individual who as a result of statin therapy experiences one or more of creatine kinase increases, liver function test abnormalities, muscle aches, or central nervous system side effects.
  • efficacy refers to the ability to produce a desired effect.
  • efficacy of a lipid-lowering therapy may be reduction in the concentration of one or more of LDL-C, VLDL- C, IDL-C, non-HDL-C, ApoB, lipoprotein(a), or triglycerides.
  • acceptable safety profile refers to a pattern of side effects that is within clinically acceptable limits.
  • side effects refers to physiological responses attributable to a treatment other than desired effects.
  • side effects include, without limitation, injection site reactions, liver function test abnormalities, renal function abnormalities, liver toxicity, renal toxicity, central nervous system abnormalities, and myopathies.
  • increased aminotransferase levels in serum may indicate liver toxicity or liver function abnormality.
  • increased bilirubin may indicate liver toxicity or liver function abnormality.
  • injection site reaction refers to inflammation or abnormal redness of skin at a site of injection in an individual.
  • individual compliance refers to adherence to a recommended or prescribed therapy by an individual.
  • lipid-lowering therapy refers to a therapeutic regimen provided to a individual to reduce one or more lipids in a individual.
  • a lipid-lowering therapy is provide to reduce one or more of ApoB, total cholesterol, LDL-C, VLDL-C, IDL-C, non-HDL-C, triglycerides, small dense LDL particles, and Lp(a) in an individual.
  • lipid-lowering agent refers to a pharmaceutical agent provided to a individual to achieve a lowering of lipids in the individual.
  • a lipid-lowering agent is provided to an individual to reduce one or more of ApoB, LDL-C, total cholesterol, and triglycerides.
  • LDL-C target refers to an LDL-C level that is desired following lipid- lowering therapy.
  • the term “comply” refers to the adherence with a recommended therapy by an individual.
  • the term "recommended therapy” refers to a therapeutic regimen recommended by a medical professional for the treatment, amelioration, or prevention of a disease.
  • low LDL-receptor activity refers to LDL-receptor activity that is not sufficiently high to maintain clinically acceptable levels of LDL-C in the bloodstream.
  • cardiovascular outcome refers to the occurrence of major adverse cardiovascular events.
  • improved cardiovascular outcome refers to a reduction in the occurrence of major adverse cardiovascular events, or the risk thereof. Examples of major adverse cardiovascular events include, without limitation, death, reinfarction, stroke, cardiogenic shock, pulmonary edema, cardiac arrest, and atrial dysrhythmia.
  • surrogate markers of cardiovascular outcome refers to indirect indicators of cardiovascular events, or the risk thereof.
  • surrogate markers of cardiovascular outcome include carotid intimal media thickness (CMT).
  • CMT carotid intimal media thickness
  • Atheroma size may be determined by intravascular ultrasound (FVUS).
  • the term “increased HDL-C” refers to an increase in serum HDL-C in an individual over time.
  • lipid-lowering refers to a reduction in one or more serum lipids in an individual over time.
  • Metabolic disorder refers to a condition characterized by an alteration or disturbance in metabolic function.
  • Metabolic and “metabolism” are terms well know in the art and generally include the whole range of biochemical processes that occur within a living organism. Metabolic disorders include, but are not limited to, hyperglycemia, prediabetes, diabetes (type I and type II), obesity, insulin resistance and metabolic syndrome.
  • metabolic syndrome refers to a clustering of lipid and non-lipid cardiovascular risk factors of metabolic origin. It has been closely linked to the generalized metabolic disorder known as insulin resistance.
  • NCEP National Cholesterol Education Program
  • ATPIII Adult Treatment Panel III established criteria for diagnosis of metabolic syndrome when three or more of five risk determinants are present.
  • the five risk determinants are abdominal obesity defined as waist circumference of greater than 102 cm for men or greater than 88cm for women, triglyceride levels greater than or equal to 150 mg/dL, HDL cholesterol levels of less than 40 mg/dL for men and less than 50 mg/dL for women, blood pressure greater than or equal to 130/85 mm Hg and fasting glucose levels greater than or equal to 110 5 mg/dL. These determinants can be readily measured in clinical practice (JAMA, 2001, 285: 2486-2497).
  • alkyl refers to a saturated straight or branched hydrocarbon radical containing up to twenty four carbon atoms.
  • alkyl groups include, but are not limited to, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl, dodecyl and the like.
  • Alkyl groups typically include from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms (Ci-Ci 2 alkyl) with from 1 0 to about 6 carbon atoms being more preferred.
  • the term "lower alkyl” as used herein includes from 1 to about 6 carbon atoms.
  • Alkyl groups as used herein may optionally include one or more further substituent groups.
  • alkenyl refers to a straight or branched hydrocarbon chain radical containing up to twenty four carbon atoms and having at least one carbon-carbon double bond.
  • alkenyl groups include, but are not limited to, ethenyl, propenyl, butenyl, l-methyl-2-buten-l-yl, dienes such as 1 ,3-butadiene and the like.
  • Alkenyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred.
  • Alkenyl groups as used herein may optionally include one or more further substituent groups.
  • alkynyl refers to a straight or branched hydrocarbon radical containing up .0 to twenty four carbon atoms and having at least one carbon-carbon triple bond.
  • alkynyl groups include, but are not limited to, ethynyl, 1 -propynyl, 1 -butynyl, and the like.
  • Alkynyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred.
  • Alkynyl groups as used herein may optionally include one or more further substitutent groups.
  • aminoalkyl refers to an amino substituted alkyl radical. This term is meant to include CpCi 2 alkyl groups having an amino substituent at any position and wherein the alkyl group attaches the aminoalkyl group to the parent molecule. The alkyl and/or amino portions of the aminoalkyl group can be further substituted with substituent groups.
  • aliphatic refers to a straight or branched hydrocarbon radical containing K) up to twenty four carbon atoms wherein the saturation between any two carbon atoms is a single, double or triple bond.
  • An aliphatic group preferably contains from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms with from 1 to about 6 carbon atoms being more preferred.
  • the straight or branched chain of an aliphatic group may be interrupted with one or more heteroatoms that include nitrogen, oxygen, sulfur and phosphorus.
  • Such aliphatic groups interrupted by heteroatoms include without limitation >5 polyalkoxys, such as polyalkylene glycols, polyamines, and polyimines.
  • Aliphatic groups as used herein may optionally include further substitutent groups.
  • alicyclic refers to a cyclic ring system wherein the ring is aliphatic.
  • the ring system can comprise one or more rings wherein at least one ring is aliphatic.
  • Preferred alicyclics include rings having from about 5 to about 9 carbon atoms in the ring.
  • Alicyclic as used herein may 5 optionally include further substitutent groups.
  • alkoxy refers to a radical formed between an alkyl group and an oxygen atom wherein the oxygen atom is used to attach the alkoxy group to a parent molecule.
  • alkoxy groups include, but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, M-butoxy, sec-butoxy, tert- butoxy, n-pentoxy, neopentoxy, n-hexoxy and the like.
  • Alkoxy groups as used herein may optionally 0 include further substitutent groups.
  • halo and halogen, as used herein, refer to an atom selected from fluorine, chlorine, bromine and iodine.
  • aryl and aromatic refer to a mono- or polycyclic carbocyclic ring system radicals having one or more aromatic rings.
  • aryl groups include, but are not limited to, 5 phenyl, naphthyl, tetrahydronaphthyl, indanyl, idenyl and the like.
  • Preferred aryl ring systems have from about 5 to about 20 carbon atoms in one or more rings.
  • Aryl groups as used herein may optionally include further substitutent groups.
  • aralkyl and arylalkyl refer to a radical formed between an alkyl group and an aryl group wherein the alkyl group is used to attach the aralkyl group to a parent molecule. Examples .0 include, but are not limited to, benzyl, phenethyl and the like.
  • Aralkyl groups as used herein may optionally include further substitutent groups attached to the alkyl, the aryl or both groups that form the radical group.
  • heterocyclic radical refers to a radical mono-, or poly-cyclic ring system that includes at least one heteroatom and is unsaturated, partially saturated or fully saturated, thereby including heteroaryl groups. Heterocyclic is also meant to include fused ring systems wherein one or more ⁇ 5 of the fused rings contain at least one heteroatom and the other rings can contain one or more heteroatoms or optionally contain no heteroatoms.
  • a heterocyclic group typically includes at least one atom selected from sulfur, nitrogen or oxygen.
  • heterocyclic groups include, [l,3]dioxolane, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and 10 the like.
  • Heterocyclic groups as used herein may optionally include further substitutent groups.
  • heteroaryl refers to a radical comprising a mono- or poly-cyclic aromatic ring, ring system or fused ring system wherein at least one of the rings is aromatic and includes one or more heteroatom. Heteroaryl is also meant to include fused ring systems including systems where one or more of the fused rings contain no heteroatoms. Heteroaryl groups typically include 5 one ring atom selected from sulfur, nitrogen or oxygen.
  • heteroaryl groups include, but are not limited to, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzooxazolyl, quinoxalinyl, and the like.
  • Heteroaryl radicals can be attached to a parent molecule directly or through a linking moiety such as an aliphatic group or hetero atom.
  • Heteroaryl groups as used herein may optionally include further substituted groups.
  • heteroarylalkyl refers to a heteroaryl group as previously defined having an alky radical that can attach the heteroarylalkyl group to a parent molecule. Examples include, but are not limited to, pyridinylmethyl, pyrimidinylethyl, napthyridinylpropyl and the like. Heteroarylalkyl groups as used herein may optionally include further substituted groups on one or both of the heteroaryl or alkyl portions.
  • mono or poly cyclic structure includes all ring systems that are single or polycyclic having rings that are fused or linked and is meant to be inclusive of single and mixed ring systems individually selected from aliphatic, alicyclic, aryl, heteroaryl, aralkyl, arylalkyl, heterocyclic, heteroaryl, heteroaromatic, heteroarylalkyl.
  • Such mono and poly cyclic structures can contain rings that are uniform or have varying degrees of saturation including fully saturated, partially saturated or fully unsaturated.
  • Each ring can comprise ring atoms selected from C, N, O and S to give rise to heterocyclic rings as well as rings comprising only C ring atoms which can be present in a mixed motif such as for example benzimidazole wherein one ring has only carbon ring atoms and the fused ring has two nitrogen atoms.
  • mono or poly cyclic structures can be attached to a parent molecule directly through a ring atom, through a substituent group or a bifunctional linking moiety.
  • acyl refers to a radical formed by removal of a hydroxyl group from an organic acid an d has the general formula -C(O)-X where X is typically aliphatic, alicyclic or aromatic. Examples include aliphatic carbonyls, aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphatic sulfinyls, aromatic phosphates, aliphatic phosphates and the like. Acyl groups as used herein may optionally include further substitutent groups.
  • hydrocarbyl includes groups comprising C, O and H. Included are straight, branched and cyclic groups having any degree of saturation. Such hydrocarbyl groups can include one or more heteroatoms selected from N, O and S and can be further mono or poly substituted with one or more substituent groups.
  • substituted and substituteduent group include groups that are typically added to other groups or parent compounds to enhance desired properties or give desired effects. Substituent groups can be protected or unprotected and can be added to one available site or to many available sites in a parent compound. Substituent groups may also be further substituted with other substituent groups and may be attached directly or via a linking group such as an alkyl or hydrocarbyl group to a parent compound.
  • each R aa , R bb and R 00 is, independently, H, an optionally linked chemical functional group or a further substituent group with a 0 preferred list including without limitation H, alkyl, alkenyl, alkynyl, aliphatic, alkoxy, acyl, aryl, aralkyl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl.
  • oligomeric compounds compared to 5 naturally occuring oligomers, such as DNA or RNA.
  • Certain such modifications alter the activity of the oligomeric compound.
  • Certain such chemical modifications can alter activity by, for example: increasing affinity of an antisense compound for its target nucleic acid, increasing its resistance to one or more nucleases, and/or altering the pharmacokinetics or tissue distribution of the oligomeric compound.
  • the use of chemistries that increase the affinity of an oligomeric compound for its target can allow .0 for the use of shorter oligomeric compounds. 1.
  • oligomeric compounds comprise one or more modified monomer.
  • oligomeric compounds comprise one or more high affinity monomer.
  • the oligomeric compounds including, but no limited to short antisense iO compounds of the present invention, comprise one or more high affinity monomers provided that the oligomeric compound does not comprise a nucleotide comprising a 2'-O(CH 2 ) n H, wherein n is one to six.
  • the oligomeric compounds including, but no limited to short antisense compounds of the present invention comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a nucleotide comprising a 2'-OCH 3 or a 2'-O(CH 2 ) 2 OCH 3 . '5 In certain embodiments, the oligomeric compounds including, but no limited to short antisense compounds of the present invention, comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA.
  • the oligomeric compounds including, but no limited to short antisense compounds of the present invention, comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA.
  • the oligomeric compounds including, but no limited to short antisense compounds of the present invention, comprise one or more high affinity monomer provided that the oligomeric compound does not comprise a ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA or a ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA.
  • the naturally occurring base portion of a nucleoside is typically a heterocyclic base.
  • the two most common classes of such heterocyclic bases are the purines and the pyrimidines.
  • a phosphate group can be linked to the 2', 3' or 5' hydroxyl moiety of the sugar.
  • those phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound.
  • the phosphate groups are commonly referred to as forming the internucleotide backbone of the oligonucleotide.
  • the naturally occurring linkage or backbone of RNA and of DNA is a 3' to 5' phosphodiester linkage.
  • a modified nucleobase is a nucleobase that is fairly similar in structure to the parent nucleobase, such as for example a 7-deaza purine, a 5-methyl cytosine, or a G-clamp.
  • nucleobase mimetic include more complicated structures, such as for example a tricyclic phenoxazine nucleobase mimetic. Methods for preparation of the above noted modified nucleobases are well known to those skilled in the art. b. Certain sugars
  • Oligomeric compounds provided herein may comprise one or more monomer, including a nucleoside or nucleotide, having a modified sugar moiety.
  • the furanosyl sugar ring of a nucleoside can be modified in a number of ways including, but not limited to, addition of a substituent group, bridging of two non-geminal ring atoms to form a bicyclic nucleic acid (BNA).
  • BNA bicyclic nucleic acid
  • oligomeric compounds comprise one or more monomers that is a BNA.
  • BNA s include, but are not limited to, (A) ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , (B) ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , (C) Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , (D) Aminooxy (4'- CH 2 -O-N(R)-2') BNA and (E) Oxyamino (4'-CH 2 -N(R)-O-2') BNA, as depicted in Figure 1.
  • each of the bridges of the BNA compounds is, independently, -[C(R 1 )(R 2 )J n -, -[C(RO(R 2 )J n -O-, or -C(RiR 2 )-O-N(R,)-.
  • each of said bridges is, independently, 4'-CH 2 -2 I , 4'-(CH 2 ) 2 -2', 4'-(CH 2 ) 3 -2', 4'-CH 2 -O-2', 4'-(CH 2 ) 2 -O-2', 4'-CH 2 -O-N(Ri)-2' and 4'- CH 2 -N(Ri)-O-2'- wherein each R] is, independently, H, a protecting group or C r C 12 alkyl.
  • BNAs in which the 2'-hydroxyl group of the ribosyl sugar ring is linked to the 4' carbon atom of the sugar ring thereby forming a methyleneoxy (4'-CH 2 -O-2') linkage to form the bicyclic sugar moiety
  • methyleneoxy (4'-CH 2 -O-2') linkage to form the bicyclic sugar moiety
  • the linkage can be a methylene (-CH 2 -) group bridging the 2' oxygen atom and the 4' carbon atom, for which the term methyleneoxy (4'-CH 2 -O-2') BNA is used for the bicyclic moiety; in the case of an ethylene group in this position, the term ethyleneoxy (4'-CH 2 CH 2 -O-2') BNA is used (Singh et al., Chem. Commun., 1998, 4, 455-456: Morita et al., Bioorganic Medicinal Chemistry, 2003, 0 11, 2211-2226).
  • Potent and nontoxic antisense oligonucleotides compriseing BNAs have been described (Wahlestedt et al., Proc. Natl. Acad. ScL U. S. A., 2000, 97, 5633-5638).
  • alpha-L- methyleneoxy (4'-CH 2 -O-2') BNA An isomer of methyleneoxy (4'-CH 2 -O-2') BNA that has also been discussed is alpha-L- methyleneoxy (4'-CH 2 -O-2') BNA which has been shown to have superior stability against a 3'-exonuclease.
  • the alpha-L- methyleneoxy (4'-CH 2 -O-2') BNA's were incorporated into antisense gapmers and chimeras that showed potent antisense activity (Frieden et al, Nucleic Acids Research, 2003, 21, 6365-6372).
  • Modified sugar moieties are well known and can be used to alter, typically increase, the affinity of the antisense compound for its target and/or increase nuclease resistance.
  • a representative list of preferred modified sugars includes but is not limited to bicyclic modified sugars (BNA's), including methyleneoxy (4'- CH 2 -O-2') BNA and ethyleneoxy (4'-(CH 2 ) 2 -O-2' bridge) BNA ; substituted sugars, especially 2'-substituted
  • Patents 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; 5,792,747; 5,700,920; 6,531,584; and 6,600,032; and WO 2005/121371.
  • BNA' s include bicyclic nucleoside having the formula:
  • Bx is a heterocyclic base moiety
  • Ti is H or a hydroxyl protecting group
  • T 2 is H, a hydroxyl protecting group or a reactive phosphorus group
  • Z is Ci-C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C, -C 6 alkyl, substituted C 2 -C 6 alkenyl, substituted C 2 -C 6 alkynyl, acyl, substituted acyl, or substituted amide.
  • the Z group is C 1 -C 6 alkyl substituted with one or more X x , wherein each X x is independently halo (e.g., fluoro), hydroxyl, alkoxy
  • the Z group is -CH 2 X X , wherein X x is halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O-) or azido.
  • the Z group is in the (R)-conf ⁇ guration:
  • the Z group is in the ( ⁇ -configuration:
  • each Ti and T 2 is a hydroxyl protecting group.
  • hydroxyl protecting groups includes benzyl, benzoyl, 2,6-dichlorobenzyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, mesylate, tosylate, dimethoxytrityl (DMT), 9-phenylxanthine-9-yl (Pixyl) and 9-(p-methoxyphenyl)xanthine- 9-yl (MOX).
  • Ti is a hydroxyl protecting group selected from acetyl, benzyl, t- butyldimethylsilyl, t-butyldiphenylsilyl and dimethoxytrityl wherein a more preferred hydroxyl protecting group is Ti is 4,4'-dimethoxytrityl.
  • T 2 is a reactive phosphorus group wherein preferred reactive phosphorus groups include diisopropylcyanoethoxy phosphoramidite and H-phosphonate.
  • Ti is 4,4'-dimethoxytrityl and T 2 is diisopropylcyanoethoxy phosphoramidite.
  • oligomeric compounds have at least one monomer of the formula:
  • Bx is a heterocyclic base moiety
  • T 3 is H, a hydroxyl protecting group, a linked conjugate group or an internucleoside linking group attached to a nucleoside, a nucleotide, an oligonucleoside, an oligonucleotide, a monomelic subunit or an 5 oligomeric compound;
  • T 4 is H, a hydroxyl protecting group, a linked conjugate group or an internucleoside linking group attached to a nucleoside, a nucleotide, an oligonucleoside, an oligonucleotide, a monomelic subunit or an oligomeric compound; wherein at least one of T 3 and T 4 is an internucleoside linking group attached to a nucleoside, a 0 nucleotide, an oligonucleoside, an oligonucleotide, a monomelic subunit or an oligomeric compound; and
  • Z is C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C r C 6 alkyl, substituted C 2 -C 6 alkenyl, substituted C 2 -C 6 alkynyl, acyl, substituted acyl, or substituted amide.
  • at least one Z is CpC 6 alkyl or substituted Ci-C 6 alkyl.
  • each Z is, independently, Q-C 6 alkyl or substituted Ci-C 6 alkyl.
  • At least one Z is Ci-C 6 alkyl. In certain embodiments, each Z is, independently, C 1 -C 6 alkyl. In certain embodiments, at least one Z is methyl. In certain embodiments, each Z is methyl. In certain embodiments, at least one Z is ethyl. In certain embodiments, each Z is ethyl. In certain embodiments, at least one Z is J5 substituted C]-C 6 alkyl. In certain embodiments, each Z is, independently, substituted CpC 6 alkyl. In certain embodiments, at least one Z is substituted methyl. In certain embodiments, each Z is substituted methyl. In certain embodiments, at least one Z is substituted ethyl. In certain embodiments, each Z is substituted ethyl.
  • At least one substituent group is Ci-C 6 alkoxy (e.g., at least one Z is C r C 6 alkyl substituted with one or more Ci-C 6 alkoxy).
  • each substituent group is, iO independently, C]-C 6 alkoxy (e.g., each Z is, independently, Ci-C 6 alkyl substituted with one or more CpC 6 alkoxy).
  • At least one Cj-C 6 alkoxy substituent group is CH 3 O- (e.g., at least one Z is CH 3 OCH 2 -).
  • each Ci-C 6 alkoxy substituent group is CH 3 O- (e.g., each Z is CH 3 OCH 2 -).
  • at least one substituent group is halogen (e.g., at least one Z is C r C 6 alkyl substituted with one or more halogen).
  • each substituent group is, independently, halogen (e.g., each Z is, independently, C r C 6 alkyl substituted with one or more halogen).
  • At least one halogen substituent group is fluoro (e.g., at least one Z is CH 2 FCH 2 -, CHF 2 CH 2 - or CF 3 CH 2 -).
  • each halo substituent group is fluoro (e.g., each Z is, independently, CH 2 FCH 2 -, CHF 2 CH 2 - or CF 3 CH 2 -).
  • At least one substituent group is hydroxyl (e.g., at least one Z is Ci-C 6 alkyl substituted with one or more hydroxyl).
  • each substituent group is, independently, hydroxyl (e.g., each Z is, independently, C 1 -C 6 alkyl substituted with one or more hydroxyl).
  • at least one Z is HOCH 2 -.
  • each Z is HOCH 2 -.
  • at least one Z is CH 3 -, CH 3 CH 2 -, CH 2 OCH 3 -, CH 2 F- or HOCH 2 -.
  • each Z is, independently, CH 3 -, CH 3 CH 2 -, CH 2 OCH 3 -, CH 2 F- or HOCH 2 -.
  • Ji, J 2 and J 3 is, independently, H or C 1 -Q alkyl, and X is O, S or NJ 1 .
  • at least one Z group is C 1 -C 6 alkyl substituted with one or more X x , wherein each X" is, independently, halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O-) or azido.
  • each Z group is, independently, C 1 -C 6 alkyl substituted with one or more X", wherein each X x is independently halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O-) or azido.
  • X x is independently halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O-) or azido.
  • at least one Z group is -CH 2 X", wherein X x is halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O-) or azido.
  • each Z group is, independently, -CH 2 X", wherein each X x is, independently,
  • each Z group is, independently, -CH 2 X", wherein each X x is, independently, halo (e.g., fluoro), hydroxyl, alkoxy (e.g., CH 3 O- ) or azido.
  • At least one Z is CH 3 -. In another embodiment, each Z is, CH 3 -.
  • the Z group of at least one monomer is in the (R)- configuration represented by the formula: or the formula:
  • the Z group of each monomer of the formula is in the (R)- configuration.
  • the Z group of at least one monomer is in the (S)- configuration represented by the formula:
  • the Z group of each monomer of the formula is in the (S)- configuration.
  • T 3 is H or a hydroxyl protecting group. In certain embodiments, T 4 is H or a hydroxyl protecting group. In a further embodiment T 3 is an internucleoside linking group attached to a nucleoside, a nucleotide or a monomelic subunit. hi certain embodiments, T 4 is an internucleoside linking group attached to a nucleoside, a nucleotide or a monomelic subunit. In certain embodiments,T 3 is an internucleoside linking group attached to an oligonucleoside or an oligonucleotide, hi certain embodiments,
  • T 4 is an internucleoside linking group attached to an oligonucleoside or an oligonucleotide, hi certain embodiments, T 3 is an internucleoside linking group attached to an oligomeric compound, hi certain embodiments, T 4 is an internucleoside linking group attached to an oligomeric compound, hi hi certain embodiments, at least one of T 3 and T 4 comprises an internucleoside linking group selected from phosphodiester or phosphorothioate.
  • oligomeric compounds have at least one region of at least two contiguous monomers of the formula:
  • the oligomeric compound comprises at least two regions of at least two contiguous monomers of the above formula.
  • the oligomeric compound comprises a gapped oligomeric compound
  • the oligmeric compound comprises at least one region of from about 8 to about 14 contiguous ⁇ -D-2'-deoxyribofuranosyl nucleosides
  • the oligomeric compound comprises at least one region of from about 9 to about 12 contiguous ⁇ -D-2'-deoxyribofuranosyl nucleosides.
  • monmers include sugar mimetics.
  • a mimetic is used in place of the sugar or sugar-internucleoside linkage combination, and the nucleobase is maintained for hybridization to a selected target.
  • Representative examples of a sugar mimetics include, but are not limited to, cyclohexenyl or morpholino.
  • Representative examples of a mimetic for a sugar-internucleoside linkage combination include, but are not limited to, peptide nucleic acids (PNA) and morpholino groups linked by uncharged achiral linkages. In some instances a mimetic is used in place of the nucleobase.
  • nucleobase mimetics are well known in the art and include, but are not limited to, tricyclic phenoxazine analogs and universal bases (Berger et al., Nuc Acid Res. 2000, 28:2911-14, incorporated herein by reference). Methods of synthesis of sugar, nucleoside and nucleobase mimetics are well known to those skilled in the art.
  • linking groups that link monomers (including, but not limited to, modified and unmodified nucleosides and nucleotides) together, thereby forming an oligomeric compound.
  • the two main classes of linking groups are defined by the presence or absence of a phosphorus atom.
  • Non-phosphorus containing linking groups include, but are not limited to, methylenemethylimino (-CH 2 -N(CHa)-O-CH 2 -), thiodiester (-O-C(O)-S-), thionocarbamate (-0-C(O)(NH)-S-); siloxane (-O-Si(H)2-O-); and N,N'- dimethylhydrazine (-CH 2 -N(CH 3 )-N(CH 3 )-). Oligomeric compounds having non-phosphorus linking groups are referred to as oligonucleosides.
  • Modified linkages compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligomeric compound.
  • linkages having a chiral atom can be prepared a racemic mixtures, as separate enantomers.
  • Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing linkages are well known to those skilled in the art.
  • oligomeric compounds described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), a or ⁇ such as for sugar anomers, or as (D) or (L) such as for amino acids et al. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms. 4. Oligomeric Compounds
  • oligomeric compounds having reactive phosphorus groups useful for forming linkages including for example phosphodiester and phosphorothioate internucleoside linkages.
  • Methods of preparation and/or purification of precursors or oligomeric compounds are not a limitation of the compositions or methods provided herein.
  • Methods for synthesis and purification of oligomeric compounds including DNA, RNA, oligonucleotides, oligonucleosides, and antisense compounds are well known to those skilled in the art.
  • oligomeric compounds comprise a plurality of monomeric subunits linked together by linking groups.
  • Nonlimiting examples of oligomeric compounds include primers, probes, antisense compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, and siRNAs.
  • these compounds can be introduced in the form of single-stranded, double-stranded, circular, branched or hairpins and can contain structural elements such as internal or terminal bulges or loops.
  • Oligomeric double-stranded compounds can be two strands hybridized to form double-stranded compounds or a single strand with sufficient self complementarity to allow for hybridization and formation of a fully or partially double-stranded compound.
  • the present invention provides chimeric oligomeric compounds.
  • chimeric oligomeric compounds are chimeric oligonucleotides.
  • the chimeric oligonucleotides comprise differently modified nucleotides.
  • chimeric oligonucleotides are mixed-backbone antisense oligonucleotides.
  • a chimeric oligomeric compound will have modified nucleosides that can be in isolated positions or grouped together in regions that will define a particular motif. Any combination of modifications and/or mimetic groups can comprise a chimeric oligomeric compound as described herein.
  • chimeric oligomeric compounds typically comprise at least one region modified so as to confer increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid.
  • an additional region of the oligomeric compound may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids.
  • RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA: DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of inhibition of gene expression.
  • RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.
  • chimeric oligomeric compounds are gapmers. In certain embodiments, chimeric compounds are short antisense compounds. In certain embodiments, short antisense compounds are gapmers. In certain such embodiments, a mixed-backbone antisense oligomer has one type of internucleotide linkages in one or both wings and a different type of internucleotide linkages in the gap. In certain such embodiments, the mixed-backbone antisense oligonucleotide has phosphodiester linkages in the wings and phosphorothioate linkages in the gap.
  • the internucleotide linkage bridging that wing and the gap is the same as the internucleotide linkage in the wing.
  • the intemucleotide linkage bridging that wing and the gap is the same as the intemucleotide linkage in the gap.
  • short antisense compounds are 9 to 14 nucleotides in length.
  • short antisense compounds are 10 to 14 nucleotides in length.
  • such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds comprise one or more chemical modifications.
  • short antisense compounds comprise at least one modified nucleotide. In certain embodiments short antisense compounds comprise at least two or more modified nucleotides. In certain embodiments, short antisense compounds comprise at least one modified internucleotide linkage. In certain embodiments, short antisense compounds are mixed-backbone oligonucleotides. In certain embodiments, short antisense compounds are chimeric oligonucleotides. In certain embodiments, short antisense oligonucleotides are uniformly modified. In certain embodiments, short antisense oligonucleotides comprise modifications independently selected at each nucleobase and at each linkage.
  • short antisense compounds are short gapmers.
  • short gapmers comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds comprise 1 to 3 high-affinity modifications in each wing.
  • high affinity modifications of the short antisense compounds allow for a target affinity similar to, or even greater than, the target affinity of longer antisense compounds.
  • the high-affinity modified nucleotides are sugar modified nucleotides. Such sugar modified nucleotides include those comprising a bridge between the 4' and 2' position of the sugar. Exemplary high affinity sugar modifications include, but are not limited to, BNA s and other 2'-modifications such as T- MOE.
  • the high affinity modified nucleotide is not a 2'-OCH 3 or a 2'-OCH 2 CH 2 OCH 3 nucleotide.
  • the high-affinity modified nucleotides confer a T n , of at least 1, at least 1.5, at least 2, at least 2.5, at least 3.0, at least 3.5 or at least 4.0 degrees per nucleotide.
  • short antisense compounds having a limited number (generally 2 to 6) of high affinity modifications exhibit little to no increase in toxicity but retain or increase affinity for the target RNA, while also significantly reducing expression of the RNA target.
  • Short antisense compounds of the invention may optionally comprise a conjugate group, such as, for example, cholesterol or Ci 6 .
  • the short antisense compounds comprise a 5' wing and/or a 3' wing.
  • the features of the 3' wing and the features of the 5' wing are selected independently.
  • the number of monomers in the 5' wing and the number of monomers (length) in the 3' wing may be the same or may be different;
  • the modifications, if any, in the 5' wing may be the same as the modifications, if any, in the 3' wing or such modifications, if any, may be different;
  • the monomelic linkages in the 5' wing and the monomelic linkages in the 3' wing may be the same or they may be different.
  • a wing comprises one, two or three monomers (i.e. has a length of 1, 2, or 3).
  • the monomers of a wing are modified. In certain such embodiments, the monomers of the wing are modified to increase affinity of the antisense compound for its target nucleic acid. In certain embodiments, the monomers of a wing are nucleosides or nucleotides. In certain such embodiments, the nucleosides or nucleotides of the wing comprise a 2' modification. In certain such embodiments, the monomers (nucleosides or nucleotides) of the wing are BNA 's.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 - N(R)-O-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • a wing comprises two, three or four monomers
  • those two, three or four monomers all comprise the same modifications, if any.
  • one or more of those two, three or four nucleobases comprises one or more modifications that is different from one or more of the modifications of one or more of the remaining monomers.
  • the short antisense compounds comprise a gap between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen,
  • the monomers of the gap are unmodified deoxyribonucleotides. In certain embodiments, the monomers of the gap are unmodified ribonucleotides. In certain embodiments, gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • the wings and the gaps discussed above may be selected and then combined in a variety of combinations to generate gapped oligomeric compounds, including, but not limited to, gapped antisense oligomeric compounds, and gapped antisense oligonucleotides.
  • the features (length, modifications, linkages) of the 5' wing and the 3' wing may be selected independently of one another.
  • the features of the gap include at least one difference in modification compared to the features of the 5' wing and at least one difference compared to the features of the 3' wing
  • the features of the gap may otherwise be selected independently.
  • 3' wings, 5' wings, gaps, and linkages discussed above may be used in any combination to prepare a gapmer.
  • the table below provides non-limiting examples showing how one might prepare a gapmer by selecting a certain 5' wing, a gap, a 3' wing and certain linkages bridging the gap and each wing.
  • the oligomeric compounds disclosed herein may comprise from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • oligomeric compounds are antisense compounds.
  • short antisense compounds are 8 nucleobases in length. In certain embodiments, short antisense compounds are 9 nucleobases in length. In certain embodiments, short antisense compounds are 10 nucleobases in length. In certain embodiments, short antisense compounds are 11 nucleobases in length.
  • short antisense compounds are 12 nucleobases in length. In certain embodiments, short antisense compounds are 13 nucleobases in length. In certain embodiments, short antisense compounds are 14 nucleobases in length. In certain embodiments, short antisense compounds are 15 nucleobases in length. In certain embodiments, short antisense compounds are 16 nucleobases in length.
  • short antisense compounds are 8 monomers in length. In certain embodiments, short antisense compounds are 9 monomers in length. In certain embodiments, short antisense compounds are 10 monomers in length. In certain embodiments, short antisense compounds are 11 monomers in length. In certain embodiments, short antisense compounds are monomers in length. In certain embodiments, short antisense compounds are 13 monomers in length. In certain embodiments, short antisense compounds are 14 monomers in length. In certain embodiments, short antisense compounds are 15 monomers in length. In certain embodiments, short antisense compounds are 16 monomers in length. In certain embodiments, short antisense compounds comprise 9 to 15 monomers. In certain embodiments, short antisense compounds comprise 10 to 15 monomers. In certain embodiments, short antisense compounds comprise 12 to 14 monomers. In certain embodiments, short antisense compounds comprise 12 to 14 nucleotides or nucleosides.
  • short antisense compounds comprise a gap flanked by more than one wing on either or both sides.
  • a short antisense compound comprises two or more 5' wings and two or more 3' wings.
  • a short antisense compound comprises one 5' wing and two or more 3' wings.
  • a short antisense compound comprises one 3' wing and two or more 5' wings.
  • Certain such embodiments comprise, for example, the following regions: a first 5' wing - a bridge - a second 5' wing - a bridge - a gap - a bridge - a second 3' wing - a bridge - a first 3 'wing.
  • each region has at least one difference in modification when compared to its neighboring region.
  • the second 5' wing and the second 3' wing each independently comprises one or more differences in modification compared to the gap and compared to the first 5' wing and the first 3' wing.
  • the modifications of the first 3' wing and first 5' wing may either or both be the same or different from the modifications of the gap, if any. 4.
  • oligomeric compounds are modified by covalent attachment of one or more conjugate groups.
  • conjugate groups modify one or more properties of the attached oligomeric compound including but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and clearance.
  • Conjugate groups are routinely used in the chemical arts and are linked directly or via an optional linking moiety or linking group to a parent compound such as an oligomeric compound.
  • conjugate groups includes without limitation, intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins and dyes.
  • Preferred conjugate groups amenable to the present invention include lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci.
  • cholic acid Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053
  • a thioether e.g., hexyl-S-tritylthiol
  • a thiocholesterol (Oberhauser et al., Nucl.
  • Linking groups or bifunctional linking moieties such as those known in the art are amenable to the compounds provided herein. Linking groups are useful for attachment of chemical functional groups, conjugate groups, reporter groups and other groups to selective sites in a parent compound such as for example an oligomeric compound.
  • a bifunctional linking moiety comprises a hydrocarbyl moiety having two functional groups. One of the functional groups is selected to bind to a parent molecule or compound of interest and the other is selected to bind essentially any selected group such as chemical functional group or a conjugate group.
  • the linker comprises a chain structure or an oligomer of repeating units such as ethylene glycol or amino acid units.
  • bifunctional linking moieties include amino, hydroxyl, carboxylic acid, thiol, unsaturations (e.g., double or triple bonds), and the like.
  • bifunctional linking moieties include 8-amino- 3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA).
  • linking groups include, but are not limited to, substituted Ci-Cio alkyl, substituted or unsubstituted C 2 -Ci 0 alkenyl or substituted or unsubstituted C 2 -Ci 0 alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl. 5. Synthesis. Purification and Analysis
  • Oligomerization of modified and unmodified nucleosides and nucleotides can be routinely performed according to literature procedures for DNA (Protocols for Oligonucleotides and Analogs, Ed. Agrawal (1993), Humana Press) and/or RNA (Scaringe, Methods (2001), 23, 206-217. Gait et al., Applications of Chemically synthesized RNA in RNA: Protein Interactions, Ed. Smith (1998), 1-36. Gallo et al., Tetrahedron (2001), 57, 5707-5713).
  • Oligomeric compounds provided herein can be conveniently and routinely made through the well- known technique of solid phase synthesis.
  • Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, CA). Any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives.
  • the invention is not limited by the method of antisense compound synthesis.
  • Antisense mechanisms are all those involving the hybridization of a compound with target nucleic acid, wherein the outcome or effect of the hybridization is either target degradation or target occupancy with concomitant stalling of the cellular machinery involving, for example, transcription or splicing.
  • One type of antisense mechanism involving target degradation includes an RNase H.
  • RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. It is known in the art that single-stranded antisense compounds which are "DNA-like" elicit RNAse H activity in mammalian cells.
  • Activation of RNase H results in cleavage of the RNA target, thereby greatly enhancing the efficiency of DNA-like oligonucleotide-mediated inhibition of gene expression.
  • chemically-modified antisense compounds have a higher affinity for target
  • RNAs than does non-modified DNA.
  • that higher affinity in turn provides increased potency allowing for the administration of lower doses of such compounds, reduced potential for toxicity and improvement in therapeutic index and decreased overall cost of therapy.
  • the present disclosure demonstrates that the incorporation of chemically-modified high-affinity nucleotides and nucleosides into antisense compounds allows for the design of short antisense compounds 8- 16 nucleobases in length useful for the reduction of target RNAs and/or target proteins in cells, tissues, and animals, including, but not limited to, humans with increased potency and improved therapeutic index.
  • short antisense compounds comprising high-affinity nucleotide modifications useful for reducing a target RNA in vivo.
  • Certain such short antisense compounds are effective at lower doses than previously described antisense compounds, allowing for a reduction in toxicity and cost of treatment.
  • certain short antisense compounds have greater potential for oral dosing.
  • short antisense compounds (8-16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length) with increased activity in vivo relative to longer compounds.
  • Certain short antisense compounds are gapmer compounds comprising high-affinity chemically-modified nucleotides on the 3' and 5' ends (wings) of the compound.
  • the addition of high-affinity modified nucleotides allows antisense compounds to be active against, and specific for, their intended target RNA in vivo despite being shorter in length.
  • Contemplated herein are short antisense compounds wherein each of the wings independently comprises 1 to 3 high-affinity modified nucleotides.
  • the high-affinity modifications are sugar modifications.
  • High-affinity modified nucleotides include, but are not limited to, BNA s or other 2'-modified nucleotides, such as 2'-MOE nucleotides.
  • short antisense compounds having at least one modified internucleotide linkage, such as a phosphorothioate internucleotide linkage.
  • the short antisense compounds of the present invention can have all phosphorothioate internucleoside linkages.
  • the short antisense compounds optionally comprise a conjugate group. As shown herein, short antisense compounds have greater affinity for target RNA than they have for DNA and are significantly more potent in vivo as shown by reduction of target mRNA as well as by amelioration of a variety of disease indications.
  • an RNA which is involved in regulating glucose metabolism or clearance, lipid metabolism, cholesterol metabolism or insulin metabolism is any RNA involved in the biochemical pathways that regulate these processes.
  • RNAs are well known in the art.
  • target genes include, but are not limited to, ApoB-100 (also known as APOB; Ag(x) antigen; apoB-48; apolipoprotein B; apolipoprotein B-IOO; apolipoprotein B-48) and GCGR (also known as glucagon receptor; GR), CRP, DGAT2, GCCR, PCSK9, PTEN, PTPlB, SGLT2, and SODl .
  • a target is identified and antisense oligonucleotides are designed to modulate that target or its expression.
  • designing an oligomeric compound to a target nucleic acid molecule can be a multistep process. Typically the process begins with the identification of a target protein, the activity of which is to be modulated, and then identifying the nucleic acid the expression of which yields the target protein.
  • designing of an antisense compound results in an antisense compound that is hybridizable to the targeted nucleic acid molecule.
  • the antisense compound is an antisense oligonucleotide or antisense oligonucleoside.
  • an antisense compound and a target nucleic acid are complementary to one another. In certain such embodiments, an antisense compound is perfectly complementary to a target nucleic acid. In certain embodiments, an antisense compound includes one mismatch. In certain embodiments, an antisense compound includes two mismatches. In certain embodiments, an antisense compound includes three or more mismatches.
  • RNA to be modulated include, but are not limited to, translocation functions, which include, but are not limited to, translocation of the RNA to a site of protein translation, translocation of the RNA to sites within the cell which are distant from the site of RNA synthesis, and translation of protein from the RNA.
  • RNA processing functions that can be modulated include, but are not limited to, splicing of the RNA to yield one or more RNA species, capping of the RNA, 3' maturation of the RNA and catalytic activity or complex formation involving the RNA which may be engaged in or facilitated by the RNA.
  • Modulation of expression can result in the increased level of one or more nucleic acid species or the decreased level of one or more nucleic acid species, either temporally or by net steady state level.
  • modulation of expression can mean increase or decrease in target RNA or protein levels.
  • modulation of expression can mean an increase or decrease of one or more RNA splice products, or a change in the ratio of two or more splice products.
  • expression of a target gene is modulated using an oligomeric compound comprising from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • an oligomeric compound comprising from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating a target gene comprises use of a short antisense compound that is 8 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 9 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 8 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 10 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 10 nucleobases in length.
  • 5 methods of modulating a target gene comprises use of a short antisense compound that is 11 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 12 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 13 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 14 nucleobases in 0 length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 15 nucleobases in length. In certain embodiments, methods of modulating a target gene comprises use of a short antisense compound that is 16 nucleobases in length.
  • methods of modulating expression of a target gene comprises use of a short antisense compound comprising 9 to 15 monomers. In certain embodiments, methods of modulating 5 expression of a target gene comprises use of a short antisense compound comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of a target gene comprises use of a short antisense compound comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of a target gene comprises use of a short antisense compound comprising 12 or 14 nucleotides or nucleosides.
  • antisense compounds specifically hybridize when there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays are performed in the
  • stringent hybridization conditions or “stringent conditions” refers to conditions under which an antisense compound will hybridize to its target sequence, but to a minimal number of other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances, and
  • nucleotide affinity modifications may allow for a greater number of mismatches compared to an unmodified compound.
  • certain oligonucleotide sequences may be more tolerant to mismatches than other oligonucleotide sequences.
  • T 1n melting temperature
  • T 1n or T m can be calculated by techniques that are familiar to one of ordinary skill in the art. For example, techniques described in Freier et al. ⁇ Nucleic Acids Research, 1997, 25, 22: 4429-4443) allow one of ordinary skill in the art to evaluate nucleotide modifications for their ability to increase the melting temperature of an 5 RNA:DNA duplex.
  • Antisense compounds, or a portion thereof, may have a defined percent identity to a SEQ ID NO, or a compound having a specific Isis number.
  • a sequence is identical to the sequence disclosed herein if it has the same nucleobase pairing ability.
  • an RNA which contains uracil in place of 0 thymidine in the disclosed sequences of the compounds described herein would be considered identical as they both, pair with adenine.
  • This identity may be over the entire length of the oligomeric compound, or in a portion of the antisense compound (e.g., nucleobases 1-20 of a 27-mer may be compared to a 20-mer to determine percent identity of the oligomeric compound to the SEQ ID NO.
  • an antisense compound need not have an identical sequence to those described herein to function 5 similarly to the antisense compound described herein.
  • Shortened versions of antisense compounds taught herein, or non-identical versions of the antisense compounds taught herein, are also provided herein.
  • Non- identical versions are those wherein each base does not have the same pairing activity as the antisense compounds disclosed herein. Bases do not have the same pairing activity by being shorter or having at least one abasic site.
  • a non-identical version can include at least one base replaced with a different 0 base with different pairing activity (e.g., G can be replaced by C, A, or T).
  • Percent identity is calculated according to the number of bases that have identical base pairing corresponding to the SEQ ID NO or antisense compound to which it is being compared.
  • the non-identical bases may be adjacent to each other, dispersed through out the oligonucleotide, or both.
  • a 16-mer having the same sequence as nucleobases 2-17 of a 20-mer is 80% identical to 5 the 20-mer.
  • a 20-mer containing four nucleobases not identical to the 20-mer is also 80% identical to the 20-mer.
  • a 14-mer having the same sequence as nucleobases 1-14 of an 18-mer is 78% identical to the 18-mer.
  • the percent identity is based on the percent of nucleobases in the original sequence present in a portion of the modified sequence. Therefore, a 30 nucleobase antisense compound comprising the full
  • the oligonucleotides provided herein are at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100%
  • short antisense compounds may be designed to target any target nucleic acid.
  • the target nucleic acid encodes a target that is clinically relevant. In such embodiments, modulation of the target nucleic acid results in clinical benefit.
  • Certain target nucleic acids include, but are not limited to, the target nucleic acids illustrated in Table 1.
  • a target nucleic acid is a nucleic acid molecule encoding ApoB.
  • Nucleic acid molecules that encode ApoB include, without limitation, SEQ ID NO: 1 and SEQ ID NO: 2.
  • a target nucleic acid is a nucleic acid molecule encoding SGLT2.
  • Nucleic acid molecules that encode SGLT2 include, without limitation, SEQ ID NO: 3.
  • a target nucleic acid is a nucleic acid molecule encoding PCSK9.
  • Nucleic acid molecules that encode PCSK9 include, without limitation, SEQ ID NO: 4.
  • a target nucleic acid is a nucleic acid molecule encoding SODl .
  • Nucleic acid molecules that encode SODl include, without limitation, SEQ DD NO: 5.
  • a target nucleic acid is a nucleic acid molecule encoding CRP.
  • Nucleic acid molecules that encode CRP include, without limitation, SEQ ID NO: 6.
  • a target nucleic acid is a nucleic acid molecule encoding GCCR.
  • Nucleic acid molecules that encode GCCR include, without limitation, SEQ ID NO: 7 and SEQ ID NO: 8.
  • a target nucleic acid is a nucleic acid molecule encoding GCGR.
  • Nucleic acid molecules that encode GCGR include, without limitation, SEQ ID NO: 9.
  • a target nucleic acid is a nucleic acid molecule encoding DGAT2.
  • Nucleic acid molecules that encode DGAT2 include, without limitation, SEQ ID NO: 10.
  • a target nucleic acid is a nucleic acid molecule encoding PTPlB.
  • Nucleic acid molecules that encode PTPlB include, without limitation, SEQ ID NO: 11 and SEQ ID NO: 12.
  • a target nucleic acid is a nucleic acid molecule encoding PTEN.
  • Nucleic acid molecules that encode PTEN include, without limitation, SEQ ED NO: 14 or SEQ ID NO: 15.
  • the targeting process usually includes determination of at least one target region, segment, or site within the target nucleic acid for the antisense interaction to occur such that the desired effect will result.
  • the 5 '-most nucleotide of a target region is the 5' target site of a short antisense compound and the 3 '-most nucleotide of a target region is the 3' target site of the same short antisense compound. In certain embodiments, the 5 '-most nucleotide of a target region is the 5' target site of a short antisense compound and the 3 '-most nucleotide of a target region is the 3' target site of a different short antisense compound. In certain embodiments, a target region comprises a nucleotide sequence within 10, 15, or 20 nucleotides of a 5' target site or a 3' target site.
  • a target region is a structurally defined region of the nucleic acid.
  • a target region may encompass a 3' UTR, a 5' UTR, an exon, an intron, a coding region, a translation initiation region, translation termination region, or other defined nucleic acid region.
  • the target nucleic acid having one or more active short antisense compounds targeted thereto is a target RNA.
  • the compounds are preferably separated by no more than about 10 nucleotides on the target sequence, more preferably no more than about 5 nucleotides on the target sequence, even more preferably the short antisense compounds are contiguous, most preferably the short antisense compounds are overlapping. There may be substantial variation in activity (e.g., as defined by percent inhibition) of the short antisense compounds within an active target segment.
  • Active short antisense compounds are those that modulate the expression of their target nucleic acid, including but not limited to a target RNA. Active short antisense compounds inhibit expression of their target RNA at least 10%, preferably 20%. In a preferred embodiment, at least about 50%, preferably about 70% of the short antisense compounds targeted to the active target segment modulate expression of their target RNA at least 40%. In a more preferred embodiment, the level of inhibition required to define an active short antisense compound is defined based on the results from the screen used to define the active target segments.
  • a suitable target segment is at least about an 8-nucleobase portion of a target region to which an active short antisense compound is targeted.
  • Target segments can include DNA or RNA sequences that comprise at least the 8 consecutive nucleobases from the 5 '-terminus of one of the illustrative target segments (the remaining nucleobases being a consecutive stretch of the same DNA or RNA beginning immediately upstream of the 5 '-terminus of the target segment and continuing until the DNA or RNA comprises about 8 to about 16 nucleobases).
  • Target segments are also represented by DNA or RNA sequences that comprise at least the 8 consecutive nucleobases from the 3 '-terminus of one of the illustrative target segments (the remaining nucleobases being a consecutive stretch of the same DNA or RNA beginning immediately downstream of the 3 '-terminus of the target segment and continuing until the DNA or RNA comprises about 8 to about 16 nucleobases).
  • antisense target segments may be represented by DNA or RNA sequences that comprise at least 8 consecutive nucleobases from an internal portion of the sequence of an illustrative target segment, and may extend in either or both directions until the short antisense compound comprises about 8 to about 16 nucleobases.
  • short antisense compounds are chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.
  • the short antisense compounds may also be targeted to regions of the target nucleobase sequence comprising any consecutive nucleobases 8 to 16 nucleobases in length along the target nucleic acid molecule.
  • Target segments 8-16 nucleobases in length comprising a stretch of at least eight (8) consecutive nucleobases selected from within the illustrative target segments are considered to be suitable for targeting as well.
  • the short antisense compounds may also encompass 8-16 nucleobases within those segments identified herein as beginning at a particular 5' target site. Any segment of 8, 9, 10, 11, or more preferably 12, 13, 14, 15 or 16 contiguous nucleobases in a 50, preferably 25, more preferably 16 nucleobase perimeter around these regions are also considered to be suitable for targeting.
  • the "suitable target segments” identified herein may be employed in a screen for additional short antisense compounds that modulate the expression of a target nucleic acid.
  • “Modulators” are those compounds that decrease or increase the expression of a target nucleic acid and which comprise at least an 8-nucleobase portion which is complementary to a target segment.
  • the screening method comprises the steps of contacting a target segment of a nucleic acid with one or more candidate modulators, and selecting for one or more candidate modulators which decrease or increase the expression of a target nucleic acid.
  • the candidate modulator or modulators are capable of modulating (e.g. either decreasing or increasing) the expression of a target nucleic acid, the modulator may then be employed in further investigative studies of the function of the target, or for use as a research, diagnostic, or therapeutic agent in accordance with the present invention.
  • sequence, monomer, monomelic modification, and monomelic linkage may each be selected independently.
  • short antisense compounds are described by a motif.
  • any motif may be used with any sequence, whether or not the sequence and/or the motif is specifically disclosed herein.
  • short antisense compounds comprise modifications that are not amenable to description by motif (for example, short antisense compounds comprising several different modifications and/or linkages at various positions throughout the compound). Such combinations may be incorporated for any sequence, whether or not it is disclosed herein.
  • sequence listing accompanying this filing provides certain nucleic acid sequences independent of chemical modification. Though that listing identifies each sequence as either "RNA" or "DNA” as required, in reality, those sequences may be modified with any combination of chemical modifications and/or motifs.
  • short antisense compounds comprise at least one high-affinity modified monomer.
  • short antisense compounds targeted to nucleic acid molecules encoding targets including, but not limited to, ApoB-100 (also known as APOB; Ag(x) antigen; apoB-48; apolipoprotein B; apolipoprotein B-IOO; apolipoprotein B-48), GCGR (also known as glucagon receptor; GR), CRP, DGAT2, GCCR, PCSK9, PTEN, PTPlB, SGLT2, and SODl .
  • ApoB-100 also known as APOB
  • Ag(x) antigen also known as APOB
  • apoB-48 apolipoprotein B
  • apolipoprotein B-IOO apolipoprotein B-48
  • GCGR also known as glucagon receptor
  • CRP CRP
  • DGAT2 DGAT2
  • GCCR PCSK9
  • PTEN PTPlB
  • short antisense compounds may be designed to modulate any target.
  • the target is clinically relevant. In such embodiments, modulation of the target results in clinical benefit.
  • Certain targets are preferentially expressed in the kidney.
  • Certain targets are preferentially expressed in the liver.
  • Certain targets are associated with a metabolic disorder.
  • Certain targets are associated to a cardiovascular disorder.
  • a target is selected from: ApoB, SGLT2, PCSK9, SODl, CRP, GCCR, GCGR, DGAT2, PTPlB, and PTEN.
  • a target is selected from: ApoB, SGLT2, PCSK9, SODl, CRP, GCCR, GCGR, DGAT2, and PTPlB.
  • a target is any protein other than SGLT2.
  • short antisense compounds exhibit liver and kidney-specific target RNA reduction in vivo. Such property renders those short antisense compounds particularly useful for inhibition of many target RNAs involved in metabolic and cardiovascular diseases.
  • methods of treating cardiovascular or metabolic disorders by contacting said kidney or liver tissues with short antisense compounds targeted to RNAs associated with said disorders.
  • methods for ameliorating any of a variety of metabolic or cardiovascular disease indications with the short antisense compounds of the present invention are provided.
  • ApoB also known as apolipoprotein B-IOO; ApoB-100, apolipoprotein B-48; ApoB-48 and Ag(x) antigen
  • ApoB-IOO apolipoprotein B-IOO
  • ApoB-100 apolipoprotein B-48
  • ApoB performs a variety of activities, from the absorption and processing of dietary lipids to the regulation of circulating lipoprotein levels (Davidson and Shelness, Annu. Rev. Nutr., 2000, 20, 169-193). This latter property underlies its relevance in terms of atherosclerosis susceptibility, which is highly correlated with the ambient concentration of ApoB-containing lipoproteins (Davidson and Shelness, Annu. Rev. Nutr., 2000, 20, 169- 0 193).
  • ApoB-100 is the major protein component of LDL-C and contains the domain required for interaction of this lipoprotein species with the LDL receptor. Elevated levels of LDL-C are a risk factor for cardiovascular disease, including atherosclerosis.
  • ApoB is the gene product or protein of which expression is to be modulated by administration of a short antisense compound.
  • ApoB nucleic acid means any nucleic acid encoding ApoB.
  • a nucleic acid encoding ApoB for example, in certain embodiments, a
  • ApoB nucleic acid includes, without limitation, a DNA sequence encoding ApoB, an RNA sequence transcribed from DNA encoding ApoB, and an mRNA sequence encoding ApoB.
  • JO "ApoB mRNA” means an mRNA encoding ApoB.
  • the invention provides methods of modulating the expression of ApoB in an individual comprising administering a short antisense compound targeted to an ApoB nucleic acid.
  • the invention provides methods of treating an individual comprising administering one or more pharmaceutical compositions comprising a short antisense compound targeted to an ApoB nucleic acid.
  • the individual has hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing atherosclerosis, coronary i0 heart disease, a history of coronary heart disease, early onset coronary heart disease, one or more risk factors for coronary heart disease, type II diabetes, type II diabetes with dyslipidemia, dyslipidemia, hypertriglyceridemia, hyperlipidemia, hyperfattyacidemia, hepatic steatosis, non-alcoholic steatohepatitis, or non-alcoholic fatty liver disease.
  • the guidelines include obtaining a complete lipoprotein profile, typically after a 9 to 12 hour fast, for determination of LDL-C, total cholesterol, and HDL-C levels.
  • LDL-C levels of 130-159 mg/dL, 160-189 mg/dL, and greater than or equal to 190 mg/dL are considered borderline high, high, and very high, respectively.
  • Total cholesterol levels of 200-239 5 and greater than or equal to 240 mg/dL are considered borderline high and high, respectively.
  • HDL-C levels of less than 40 mg/dL are considered low.
  • the individual has been identified as in need of lipid-lowering therapy. In certain such embodiments, the individual has been identified as in need of lipid-lowering therapy according to the guidelines established in 2001 by Adult Treatment Panel III (ATP III) of the National Cholesterol 0 Education Program (NCEP), and updated in 2004 (Grundy et al., Circulation, 2004, 110, 227-239).
  • the individual in need of lipid-lowering therapy has LDL-C above 190 mg/dL. In certain such embodiments, the individual in need of lipid-lowering therapy has LDL-C above 160 mg/dL. In certain such embodiments, the individual in need of lipid-lowering therapy has LDL-C above 130 mg/dL.
  • the individual in need of lipid-lowering therapy has LDL-C above 100 mg/dL. In certain 5 such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C below 160 mg/dL. In certain such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C below 130 mg/dL. In certain such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C below 100 mg/dL. In certain such embodiments the individual should maintain LDL-C below 70 mg/dL.
  • the invention provides methods for reducing ApoB in an individual. In certain embodiments the invention provides methods for reducing ApoB-containing lipoprotein in an individual. In certain embodiments the invention provides methods for reducing LDL-C in an individual. In certain embodiments the invention provides methods for reducing VLDL-C in an individual. In certain embodiments the invention provides methods for reducing IDL-C in an individual. In certain embodiments
  • the invention provides methods for reducing non-HDL-C in an individual.
  • the invention provides methods for reducing Lp(a) in an individual.
  • the invention provides methods for reducing serum triglyceride in an individual.
  • the invention provides methods for reducing liver triglyceride in an individual.
  • the invention provides methods for reducing Ox-LDL-C in an individual.
  • the invention provides
  • the invention provides methods for reducing small LDL particles in an individual. In certain embodiments the invention provides methods for reducing small VLDL particles in an individual. In certain embodiments the invention provides methods for reducing phospholipids in an individual. In certain embodiments the invention provides methods for reducing oxidized phospholipids in an individual.
  • the invention provides methods for reducing Ox-LDL-C concentration in a 5 subject.
  • the reduction in ApoB, LDL-C, VLDL-C, IDL-C, total cholesterol, non-HDL-C, Lp(a), triglyerides, or Ox-LDL-C is, independently, selected from at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, and at least 100%.
  • the reduction in ApoB, LDL-C, VLDL-C, IDL-C, total 5 cholesterol, non-HDL-C, Lp(a), triglyerides, or Ox-LDL-C is, independently, selected from at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, and at least 70%.
  • the reduction in ApoB, LDL-C, VLDL-C, EDL-C, total cholesterol, non-HDL-C, Lp(a), triglyerides, or Ox-LDL- C is, independently, selected from at least 40%, at least 50%, at least 60%, and at least 70%.
  • the invention provides method for raising HDL-C concentration in a subject. 0 In certain embodiments, the methods provided by the present invention do not lower HDL-C. In certain embodiments, the methods provided by the present invention do not result in accumulation of lipids in the liver. In certain embodiments, the methods provided by the present invention do not cause hepatic steatosis.
  • the invention provides methods for lowering ApoB concentration in a 5 subject while reducing side effects associated with treatment.
  • a side effect is liver toxicity.
  • a side effect is abnormal liver function.
  • a side effect is elevated alanine aminotransferase (ALT).
  • a side effect is elevated aspartate aminotransferase (AST).
  • the invention provides methods for lowering ApoB concentration in a .0 subject who is not reaching target LDL-C levels as a result of lipid-lowering therapy.
  • a short antisense compound targeted to an ApoB nucleic acid is the only lipid-lowering agent administered to the subject.
  • the subject has not complied with recommended lipid-lowering therapy.
  • a pharmaceutical composition of the invention is coadministered with an additional different lipid-lowering therapy.
  • an additional 15 lipid-lowering therapy is LDL-apheresis.
  • an additional lipid-lowering therapy is a statin.
  • an additional lipid-lowering therapy is ezetimibe.
  • the invention provides methods for lowering ApoB concentration in a statin- intolerant subject.
  • the subject has creatine kinase concentration increases as a result of statin administration.
  • the subject has liver function abnormalities as a i0 result of statin administration.
  • the subject has muscle aches as a result of statin administration.
  • the subject has central nervous system side effects as a result of statin administration.
  • the subject has not complied with recommended statin administration.
  • the invention provides methods for lowering liver triglycerides in a subject. >5 In certain such embodiments, the subject has elevated liver triglycerides. In certain such embodiments, the subject has steatohepatitis. In certain such embodiments, the subject has steatosis. In certain such embodiments, liver triglyceride levels are measured by magnetic resonance imaging.
  • the invention provides methods for reducing coronary heart disease risk in a subject. In certain embodiments the invention provides methods for slowing the progression of 5 atherosclerosis in a subject. In certain such embodiments the invention provides methods for stopping the progression of atherosclerosis in a subject. In certain such embodiments the invention provides methods for reducing the size and/or prevalence of atherosclerotic plaques in a subject. In certain embodiments the methods provided reduce a subject's risk of developing atherosclerosis.
  • the methods provided improve the cardiovascular outcome in a subject, hi
  • improved cardiovascular outcome is the reduction of the risk of developing coronary heart disease
  • improved cardiovascular outcome is a reduction in the occurrence of one or more major cardiovascular events, which include, but are not limited to, death, myocardial infarction, reinfarction, stroke, cardiogenic shock, pulmonary edema, cardiac arrest, and atrial dysrhythmia.
  • the improved cardiovascular outcome is evidenced by improved
  • improved carotid intimal media thickness is a decrease in thickness
  • improved carotid intimal media thickness is a prevention an increase of intimal media thickness.
  • a pharmaceutical composition comprising a short antisense compound targeted to an ApoB nucleic acid is for use in therapy. In certain embodiments, the therapy is the reduction of
  • the therapy is the treatment of hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing atherosclerosis, coronary
  • the therapy is the reduction of CHD risk, hi certain the therapy is prevention of atherosclerosis, hi certain embodiments, the therapy is the prevention of
  • a pharmaceutical composition comprising a short antisense compound targeted to an ApoB nucleic acid is used for the preparation of a medicament for reducing LDL-C, ApoB, VLDL-C, IDL-C, non-HDL-C, Lp(a) , serum triglyceride, liver triglyceride, Ox-LDL-C, small LDL particles, small VLDL, phospholipids, or oxidized phospholipids in an individual, hi certain embodiments
  • a short antisense compound targeted to an ApoB nucleic acid is used for the preparation of a medicament for reducing coronary heart disease risk.
  • a short antisense compound targeted to an ApoB nucleic acid is used for the preparation of a medicament for the treatment of hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, 5 atherosclerosis, a risk of developing atherosclerosis, coronary heart disease, a history of coronary heart disease, early onset coronary heart disease, one or more risk factors for coronary heart disease, type II diabetes, type II diabetes with dyslipidemia, dyslipidemia, hypertriglyceridemia, hyperlipidemia, hyperfattyacidemia, hepatic steatosis, non-alcoholic steatohepatitis, or non-alcoholic fatty liver disease.
  • one or more pharmaceutical compositions comprising a short antisense compound targeted to an ApoB nucleic acid are co-administered with one or more other pharmaceutical agents.
  • such one or more other pharmaceutical agents are designed to treat the same disease or condition as the one or more pharmaceutical compositions of the present invention.
  • the one or more pharmaceutical agents are lipid-lowering agents. In certain embodiments, such one or more other pharmaceutical agents are designed to treat a different disease or condition as the one or more pharmaceutical compositions of the present invention. In certain embodiments, such one or more other pharmaceutical agents are designed to treat an undesired effect of one or more pharmaceutical compositions of the present invention. In certain embodiments, one or more pharmaceutical compositions of the present
  • ⁇ O invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at the same time.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times.
  • compositions of the present invention and one or more other pharmaceutical agents are prepared together in a single formulation.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared separately.
  • pharmaceutical agents that may be co-administered with a pharmaceutical composition comprising a short antisense compound targeted to an ApoB nucleic acid include lipid-lowering
  • pharmaceutical agents that may be co-administered with a pharmaceutical composition of the present invention include, but are not limited to atorvastatin, simvastatin, rosuvastatin, and ezetimibe.
  • the lipid-lowering agent is administered prior to administration of a pharmaceutical composition of the present invention.
  • the lipid-lowering agent is administered following administration of a pharmaceutical composition of the present
  • the lipid-lowering agent is administered at the same time as a pharmaceutical composition of the present invention.
  • the dose of a coadministered lipid-lowering agent is the same as the dose that would be administered if the lipid-lowering agent was administered alone.
  • the dose of a co-administered lipid-lowering agent is lower than the dose that would be administered if the lipid-lowering agent was administered alone.
  • the dose of a co-administered lipid-lowering agent is greater than the dose that would be administered if the lipid-lowering agent was administered alone.
  • a co-administered lipid-lowering agent is a HMG-CoA reductase inhibitor.
  • the HMG-CoA reductase inhibitor is a statin.
  • the statin is selected from atorvastatin, simvastatin, pravastatin, fluvastatin, and rosuvastatin.
  • a co-administered lipid-lowering agent is a cholesterol absorption inhibitor.
  • cholesterol absorption inhibitor is ezetimibe.
  • a co-administered lipid-lowering agent is a co-formulated HMG-CoA reductase inhibitor and cholesterol absorption inhibitor. In certain such embodiments the co-formulated lipid- lowering agent is ezetimibe/simvastatin. 5 In certain embodiments, a co-administered lipid-lowering agent is a microsomal triglyceride transfer protein inhibitor (MTP inhibitor).
  • MTP inhibitor microsomal triglyceride transfer protein inhibitor
  • a co-administered pharmaceutical agent is a bile acid sequestrant.
  • the bile acid sequestrant is selected from cholestyramine, colestipol, and colesevelam.
  • a co-administered pharmaceutical agent is a nicotinic acid.
  • the nicotinic acid is selected from immediate release nicotinic acid, extended release nicotinic acid, and sustained release nicotinic acid.
  • a co-administered pharmaceutical agent is a fibric acid.
  • a fibric acid is selected from gemfibrozil, fenofibrate, clofibrate, bezaf ⁇ brate, and ciprofibrate.
  • compositions comprising a short antisense compound targeted to an ApoB nucleic acid
  • corticosteroids including but not limited to prednisone
  • immunoglobulins including, but not limited to intravenous immunoglobulin (IVIg)
  • analgesics e.g., acetaminophen
  • anti-inflammatory agents including, but not limited to non-steroidal anti-inflammatory drugs (e.g., ibuprofen, COX-I inhibitors, and COX-2, inhibitors); salicylates; antibiotics; antivirals; antifungal agents; antidiabetic agents (e.g., biguanides, i O glucosidase inhibitors, insulins, sulfonylureas, and thiazolidenediones); adrenergic modifiers; diuretics; hormones (e.g., anabolic steroids, and
  • a pharmaceutical composition comprising a short antisense compound targeted to an ApoB nucleic acid may be administered in conjunction with a lipid-lowering therapy.
  • a lipid-lowering therapy is therapeutic lifestyle change.
  • a lipid-lowering therapy is LDL apheresis.
  • the antisense compounds provided herein can be used to lower the level of 5 apolipoprotein B-containing lipoproteins in a human subject.
  • apolipoprotein B-containing lipoprotein refers to any lipoprotein that has apolipoprotein B as its protein component, and is understood to include LDL, VLDL, IDL, and lipoprotein(a).
  • LDL, VLDL, IDL and lipoprotein(a) each contain one molecule of apolipoprotein B, thus a serum apolipoprotein B measurement reflects the total number of these lipoproteins.
  • each of the aforementioned lipoproteins is atherogenic.
  • lowering 0 one or more apolipoprotein B-containing lipoproteins in serum may provide a therapeutic benefit to a human subject.
  • Small LDL particles are considered to be particularly atherogenic relative to large LDL particles, thus lowering small LDL particles can provide a therapeutic benefit to a human subject.
  • Additional lipid parameters can also be determined in a subject. Reduction of total cholesterol:HDL ratio or LDL:HDL ratio is a clinically desirable improvement in cholesterol ratio. Similarly, it is clinically desirable to reduce serum 5 triglycerides in humans who exhibit elevated lipid levels.
  • serum LDL particle size refers to the classification of serum LDL particle size, which may be very small, O small, medium, or large, and is typically expressed in g/ ⁇ mol.
  • serum LDL cholesteryl ester concentration means the amount of cholesteryl ester present in LDL particles, and is typically measured as mg/dL.
  • serum LDL cholesteryl ester composition is a measurement of the percentage of saturated, monounsaturated and polyunsaturated cholesteryl ester fatty acids present in serum LDL particles.
  • .5 esters means the percentage of polyunsaturated cholesteryl ester fatty acids in serum LDL particles.
  • the antisense compounds provided herein can be used to treat metabolic disorders.
  • a variety of biomarkers can be used for evaluating metabolic disease. For example, blood glucose levels can be determined by a physician or even by the patient using a commonly available test kit or glucometer (for example, the Ascensia ELITETM kit, Ascensia (Bayer), Tarrytown NY, or Accucheck, Roche Diagnostics).
  • Glycated hemoglobin (HbAi 0 ) can also be measured.
  • HbA lc is a stable minor hemoglobin
  • HbAi 0 is often viewed as the "gold standard" for measuring sustained blood glucose control (Bunn, H.F. et al., 1978, Science. 200, 21-7).
  • HbAi 0 can be measured by ion-exchange HPLC or immunoassay; home blood collection and mailing kits for HbAi 0 measurement are 5 now widely available.
  • Serum fructosamine is another measure of stable glucose control and can be measured by a colorimetric method (Cobas Integra, Roche Diagnostics).
  • short antisense compounds are targeted to an ApoB nucleic acid having the 0 sequence of GENBANK® Accession No. NM 000384.1, incorporated herein as SEQ ID NO: 1.
  • a short antisense compound targeted to SEQ ID NO: 1 is at least 90% complementary to SEQ ID NO: 1.
  • a short antisense compound targeted to SEQ BD NO: 1 is at least 95% complementary to SEQ ID NO: 1.
  • a short antisense compound targeted to SEQ ID NO: 1 is 100% complementary to SEQ ID NO: 1.
  • a short antisense compounds are targeted to an ApoB nucleic acid having the 0 sequence of GENBANK® Accession No. NM 000384.1, incorporated herein as SEQ ID NO: 1.
  • a short antisense compound targeted to SEQ ID NO: 1 is at least 90% complementary to SEQ ID NO: 1.
  • a short antisense compound targeted to SEQ BD NO: 1 is at least 95% complementary to SEQ ID NO: 1.
  • antisense compound targeted to SEQ ID NO: 1 comprises a nucleotide sequence selected from the nucleotide sequences set forth in Table 2 and Table 3.
  • nucleotide sequence set forth in each SEQ ID NO in Tables 2 and 3 is independent of any modification to a sugar moiety, a monomelic linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an
  • Antisense compounds described by Isis Number indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Tables 2 and 3 illustrate examples of short antisense compounds targeted to SEQ ID NO: 1.
  • Table 2 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 1.
  • Table 3 illustrates
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2 '-modified sugar.
  • the particular 2'-modified sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing i0 segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines. For example, "5-mC in gap only" indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • Table 2 Short Antisense Compounds targeted to SEQ ID NO: 1
  • Table 3 Short antisense compounds targeted to SEQ ID NO: 1 and having 1 or 2 mismatches
  • a target region is nucleotides 263-278 of SEQ ID NO: 1.
  • short antisense compounds targeted to nucleotides 263-278 of SEQ ID NO: 1 comprise a nucleotide sequence selected from SEQ ID NO: 16 or 17.
  • a short antisense compound targeted to nucleotides 263-278 of SEQ ID NO: 1 is selected from Isis NO. 372816 or 372894.
  • a target region is nucleotides 428-483 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 428-483 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27.
  • a short antisense compound targeted to nucleotides 428-483 of SEQ ID NO: 1 is selected from Isis NO. 372817, 372895, 372818, 372896, 372819, 372897, 372820, 372898, 372821 , or 372899.
  • a target region is nucleotides 428-458 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 428-458 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 18, 19, 20, 21, 22, 23, 24, or 25.
  • a short antisense compound targeted to nucleotides 428-458 of SEQ ID NO: 1 is selected from Isis NO.
  • a target region is nucleotides 468-483 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 468-483 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 26 or 27.
  • a short antisense compound targeted to nucleotides 468-483 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 26 or 27.
  • a target region is nucleotides 587-607 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 587-607 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 28, 29, 30, or 31.
  • a short antisense compound targeted to nucleotides 587-607 of SEQ ID NO: 1 is selected from ISIS NO. 372822,
  • a target region is nucleotides 715-736 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 715-736 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 32, 33, 34, 35, 36, 37, 38, 39, or 40.
  • a short antisense compound targeted to nucleotides 715-736 of SEQ DD NO: 1 is selected from
  • a target region is nucleotides 929-944 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 929-944 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 41 or 42.
  • a short antisense compound targeted to nucleotides 929-944 of SEQ ID NO: 1 is selected from Isis NO. 372824 or 372902.
  • a target region is nucleotides 1256-1319 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 1256-1319 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 43, 44, 45, or 46.
  • a short antisense compound targeted to nucleotides 1256-1319 of SEQ ID NO: 1 is selected from Isis NO. 372825, 372903, 372826, or 372904.
  • a target region is nucleotides 1256-1271 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 1256-1271 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 43 or 44.
  • a short antisense compound targeted to nucleotides 1256-1271 of SEQ ID NO: 1 is selected from Isis NO. 372825 or 372903.
  • a target region is nucleotides 1304-1319 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 1304-1319 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 45 or 46.
  • a short antisense compound targeted to nucleotides 1304-1319 of SEQ ID NO: 1 is selected from Isis NO. 372826 or 372904.
  • a target region is nucleotides 2135-2150 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 2135-2150 of SEQ ID NO: 1 comprises a 5 nucleotide sequence selected from SEQ ID NO 47 or 48.
  • a short antisense compound targeted to nucleotides 2135-2150 of SEQ ID NO: 1 is selected from ISIS NO. 372829 or 372907.
  • a target region is nucleotides 2774-2794 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 2774-2794 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 49, 50, 51, or 52.
  • a short 0 antisense compound targeted to nucleotides 2774-2794 of SEQ ID NO: 1 is selected from ISIS NO. 372832,
  • a target region is nucleotides 2961-2976 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 2961-2976 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 53 or 54.
  • a short antisense 15 compound targeted to nucleotides 2961-2976 of SEQ ID NO: 1 is selected from ISIS NO. 372835 or 372913.
  • a target region is nucleotides 3248-3269 of SEQ DD NO: 1.
  • a short antisense compound targeted to nucleotides 3248-3269 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 55, 56, 57, 58, 59, 60, 61, 62, or 63.
  • a short antisense compound targeted to nucleotides 3248-3269 of SEQ ID NO: 1 is selected
  • a target region is nucleotides 3350-3375 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 3350-3375 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 64, 65, 66, 67, 68, or 69.
  • a short antisense compound targeted to nucleotides 3350-3375 of SEQ ID NO: 1 is selected from ISIS NO. 372836,
  • a target region is nucleotides 3409-3424 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 3409-3424 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 70 or 73.
  • a short antisense compound targeted to nucleotides 3409-3424 of SEQ ID NO: 1 is selected from ISIS NO. 372839, 387461,
  • a target region is nucleotides 3573-3588 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 3573-3588 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 74 or 75.
  • a short antisense compound targeted to nucleotides 3573-3588 of SEQ ID NO: 1 is selected from ISIS NO. 372840 or 372918.
  • a target region is nucleotides 3701-3716 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 3701-3716 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 76 or 77.
  • a short antisense compound targeted to nucleotides 3701-3716 of SEQ ID NO: 1 is selected from ISIS NO. 372841 or 372919.
  • a target region is nucleotides 4219-4234 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 4219-4234 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 78 or 79.
  • a short antisense compound targeted to nucleotides 4219-4234 of SEQ ID NO: 1 is selected from ISIS NO. 372843 or 372921.
  • a target region is nucleotides 4301-4323 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 4301-4323 of SEQ ED NO: 1 comprises a 0 nucleotide sequence selected from SEQ ID NO 80, 81, 82, or 83.
  • a short antisense compound targeted to nucleotides 4301-4323 of SEQ ID NO: 1 is selected from ISIS NO. 372844, 372922,
  • a target region is nucleotides 5588-5609 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 5588-5609 of SEQ ID NO: 1 comprises a 5 nucleotide sequence selected from SEQ ID NO 84, 85, 86, 87, 88, 89, 90, 91, or 92.
  • a short antisense compound targeted to nucleotides 5588-5609 of SEQ ED NO: 1 is selected from ISIS NO. 346601, 346602, 346603, 346604, 346605, 346606, 346607, 346608, or 346609.
  • a target region is nucleotides 5924-5939 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 5924-5939 of SEQ ED NO: 1 comprises a 20 nucleotide sequence selected from SEQ ED NO 93 or 94.
  • a short antisense compound targeted to nucleotides 5924-5939 of SEQ ED NO: 1 is selected from ISIS NO. 372851 or 372929.
  • a target region is nucleotides 6664-6679 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 6664-6679 of SEQ ED NO: 1 comprises a nucleotide sequence selected from SEQ ED NO 95 or 96.
  • a short antisense .5 compound targeted to nucleotides 6664-6679 of SEQ ED NO: 1 is selected from ISIS NO. 372854 or 372932.
  • a target region is nucleotides 6908-6923 of SEQ ED NO: 1.
  • a short antisense compound targeted to nucleotides 6908-6923 of SEQ ED NO: 1 comprises a nucleotide sequence selected from SEQ ED NO 97 or 98.
  • a short antisense compound targeted to nucleotides 6908-6923 of SEQ ED NO: 1 is selected from ISIS NO. 372855 or 372933. i0
  • a target region is nucleotides 7190-7205 of SEQ ED NO: 1.
  • a short antisense compound targeted to nucleotides 7190-7205 of SEQ ED NO: 1 comprises a nucleotide sequence selected from SEQ ED NO 99 or 100.
  • a short antisense compound targeted to nucleotides 7190-7205 of SEQ ED NO: 1 is selected from ISIS NO. 372856 or 372934.
  • a target region is nucleotides 7995-8010 of SEQ ED NO: 1.
  • a short antisense compound targeted to nucleotides 7995-8010 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 112 or 113.
  • a short antisense compound targeted to nucleotides 7995-8010 of SEQ ID NO: 1 is selected from ISIS NO. 372859 or 372937.
  • a target region is nucleotides 8336-8356 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 8336-8356 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 114, 115, 116, or 117.
  • a short antisense compound targeted to nucleotides 8336-8356 of SEQ ID NO: 1 is selected from ISIS NO. 372861 ,
  • a target region is nucleotides 8539-8554 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 8539-8554 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 118 or 119.
  • a short antisense compound targeted to nucleotides 8539-8554 of SEQ ID NO: 1 is selected from ISIS NO. 372863 or 372941.
  • a target region is nucleotides 9344-9359 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 9344-9359 of SEQ ID NO: 1 comprises a JO nucleotide sequence selected from SEQ ID NO 120 or 121.
  • a short antisense compound targeted to nucleotides 9344-9359 of SEQ ID NO: 1 is selected from ISIS NO. 372871 or 372949.
  • a target region is nucleotides 9515-9530 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 9515-9530 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 122 or 123.
  • a short antisense »5 compound targeted to nucleotides 9515-9530 of SEQ ID NO: 1 is selected from ISIS NO. 372872 or 372950.
  • a target region is nucleotides 9794-9809 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 9794-9809 of SEQ BD NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 124 or 125.
  • a short antisense compound targeted to nucleotides 9794-9809 of SEQ ID NO: 1 is selected from ISIS NO. 372875 or 372953. i0
  • a target region is nucleotides 10157-10187 of SEQ ED NO: 1.
  • a short antisense compound targeted to nucleotides 10157-10187 of SEQ ED NO: 1 comprises a nucleotide sequence selected from SEQ ED NO 126, 127, 128, 129, 130, 131, 132, or 133.
  • a short antisense compound targeted to nucleotides 10157-10187 of SEQ ED NO: 1 is selected from ISIS NO. 372877, 372955, 372878, 372956, 372879, 372957, 372880, or 372958.
  • a target region is nucleotides 10838-10859 of SEQ ED NO: 1.
  • a short antisense compound targeted to nucleotides 10838-10859 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 134, 135, 136, 137, 138, 139, 140, 141, or 142.
  • a short antisense compound targeted to nucleotides 10838-10859 of SEQ ID NO: 1 is selected from ISIS NO. 346619, 346620, 346621, 346622, 346623, 346624, 346625, 346626, or 346627.
  • a target region is nucleotides 13689-13714 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 13689-13714 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 143, 144, 145, 146, 147, or 148.
  • a short antisense compound targeted to nucleotides 13689-13714 of SEQ ID NO: 1 is selected from ISIS NO. 372890, 372968, 372891, 372969, 372892, or 372970.
  • a target region is nucleotides 13907-13928 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 13907-13928 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 149, 150, 151, 152, 153, 154, 155, 156, or 157.
  • a short antisense compound targeted to nucleotides 13907-13928 of SEQ ID NO: 1 is selected from ISIS NO. 346628, 346629, 346630, 346631, 346632, 346633, 346634, 346635, or 346636.
  • a target region is nucleotides 13963-13984 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 13963-13984 of SEQ DD NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 158, 159, 160, 161, 162, 163, 164, 165, or 166.
  • a short antisense compound targeted to nucleotides 13963-13984 of SEQ ID NO: 1 is selected from ISIS NO. 346637, 346638, 346639, 346640, 346641, 346642, 346643, 346644, or 346645.
  • a target region is nucleotides 14051-14072 of SEQ ID NO: 1.
  • a short antisense compound targeted to nucleotides 14051-14072 of SEQ ID NO: 1 comprises a nucleotide sequence selected from SEQ ID NO 167, 168, 169, 170, 171, 172, 173, 174, or 175.
  • a short antisense compound targeted to nucleotides 14051-14072 of SEQ ID NO: 1 is selected from ISIS NO. 346646, 346647, 346648, 346649, 346650, 346651, 346652, 346653, or 346654.
  • short antisense compounds targeted to an ApoB nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 9 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds targeted to an ApoB nucleic acid are short gapmers.
  • short gapmers targeted to an ApoB nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to an ApoB nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA's.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)- 0-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to an ApoB nucleic acid comprise a gap 0 between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides.
  • the monomers of the gap are unmodified ribonucleotides.
  • gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, 5 RNase H.
  • short antisense compounds targeted to an ApoB nucleic acid have uniform monomelic linkages. In certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid have mixed backbones.
  • short antisense compounds targeted to an ApoB nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to an ApoB
  • .5 ApoB nucleic acid are monomers in length.
  • short antisense compounds targeted to an ApoB nucleic acid are 13 monomers in length.
  • short antisense compounds targeted to an ApoB nucleic acid are 14 monomers in length.
  • short antisense compounds targeted to an ApoB nucleic acid are 15 monomers in length.
  • short antisense compounds targeted to an ApoB nucleic acid are 16 monomers in length.
  • SO short antisense compounds targeted to an ApoB nucleic acid comprise 9 to 15 monomers. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid comprise 10 to 15 monomers. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid comprise 12 to 14 monomers. In certain embodiments, short antisense compounds targeted to an ApoB nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of ApoB.
  • such methods comprise use of one or more short antisense compound targeted to an ApoB nucleic acid, wherein the short antisense compound targeted to an ApoB nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to an ApoB nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 11 monomers in length.
  • methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 14 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid that is 16 monomers in length.
  • methods of modulating expression of ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of ApoB comprise use of a short antisense compound targeted to an ApoB nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • short antisense compounds targeting a ApoB nucleic acid may have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a ApoB nucleic acid have a motif (wing - deoxy gap - wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-8-1, 3-6-3 or 1-6-1, more preferably 1-10-1, 2-10-2, 3-10-3, and 1-9-2. 2.
  • motif wing - deoxy gap - wing
  • SGLT-2 Sodium dependent glucose transporter 2
  • SGLT-2 is expressed in the kidney proximal tubule epithelial cells, and functions to reabsorb glucose preventing glucose loss in the urine.
  • SGLT-2 is a member of an 11-membered family of sodium substrate co-transporters. Many of these 5 family members share sequence homology, for example SGLT-I shares about 59% sequence identity with SGLT-2 and about 70% sequence identity with SGLT-3.
  • SGLT-I is a glucose transporter found in the heart and the CNS.
  • SGLT-3 is a glucose sensing sodium channel in the small intestine.
  • the separate localization patterns for these SGLTs is one point of distinction between the homologous family members.
  • Diabetes is a disorder characterized by hyperglycemia due to deficient insulin action.
  • Chronic hyperglycemia is a major risk factor for diabetes-associated complications, including heart disease, retinopathy, nephropathy and neuropathy.
  • heart disease retinopathy, nephropathy and neuropathy.
  • nephropathy nephropathy
  • neuropathy As the kidneys play a major role in the regulation of plasma
  • Diabetic nephropathy is the most common cause of end-stage renal disease that develops in many patients with diabetes. Glucotoxicity, which results from long-term hyperglycemia, induces tissue-dependent insulin resistance in diabetic patients (Nawano et al., Am. J. Physiol. Endocrinol. Metab., 2000, 278, E535-543).
  • Sodium dependent glucose transporter 2 is the gene product or protein of which expression is to be modulated by administration of a short antisense compound.
  • Sodium dependent glucose transporter 2 is generally referred to as SGLT2 but may also be referred to as SLC5A2; sodium-glucose transporter 2;
  • sodium-glucose cotransporter kidney low affinity; sodium-glucose cotransporter, renal; solute carrier family 5 (sodium/glucose cotransporter), member 2; SL52.
  • SGLT2 nucleic acid means any nucleic acid encoding SGLT2.
  • a SGLT2 nucleic acid includes, without limitation, a DNA sequence encoding SGLT2, an RNA sequence transcribed from DNA encoding SGLT2, and an mRNA sequence encoding SGLT2.
  • S 5 mRNA means an mRNA encoding a SGLT2 protein.
  • short antisense compounds are used to modulate expression of SGLT-2 and related proteins.
  • such modulation is accomplished by providing short antisense compounds that hybridize with one or more target nucleic acid molecules encoding SGLT-2, including, but is not limited to, SGLT2, SL52, SLC5A2, Sodium-Glucose Co-Transporter, Kidney Low Affinity Sodium- Glucose Co-Transporter, Renal Sodium-Glucose Co-Transporter 2 and Solute Carrier Family 5 Sodium/Glucose Co-Transporter Member 2. Also provided are methods of treating metabolic and/or cardiovascular disease and disorders as described herein.
  • short antisense compounds that inhibit the expression of SGLT2 are used in methods of lowering blood glucose levels in an animal and methods of delaying or preventing the onset of type 2 diabetes. Such methods comprise administering a therapeutically or prophylactically effective amount of one or more of the compounds of the invention to the animal, which may be in need of treatment.
  • the one or more compounds can be a short antisense compound targeting a nucleic acid encoding SGLT2.
  • short antisense compounds are chimeric oligomeric compounds having mixed phosphorothioate and phosphodiester backbones,.
  • Certain mixed backbone short antisense compounds have a central gap comprising at least 5 contiguous 2'-deoxy nucleosides flanked by two wings each of which comprises at least one 2'-O-methoxyethyl nucleoside.
  • the internucleoside linkages of the mixed backbone compounds are phosphorothioate linkages in the gap and phosphodiester linkages in the two wings.
  • mixed backbone compounds have phosphorothioate linkages in the wings, except for one phosphodiester linkage at one or both of the extreme 5' and 3' ends of the oligonucleotide.
  • short antisense compounds targeted to SGLT2 have a motif (wing - deoxy gap -wing) selected from 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 2-8-2, 1-9-2, 1-8-1, 3-6-3 or 1-6-1.
  • short antisense compounds targeted to SGLT2 have a motif (wing - deoxy gap - wing) selected from 1-10-1, 1-10-2, 2-8-2, 1-9-2, 1-8-1, 3-6-3 or 1-6-1.
  • short antisense compounds targeted to an SGLT2 nucleic acid and having a mixed backbone are efficiently delivered to the kidney.
  • administration of short antisense compounds targeted to an SGLT2 nucleic acid and having a mixed backbone results in modulation of target gene expression in the kidney.
  • short antisense compounds targeted to an SGLT2 nucleic acid and having a mixed backbone are more potent for reducing SGLT-2 mRNA and have a faster onset compared with a short antisense compound that does not have a mixed back-bone, but is otherwise identical.
  • such increase potency and/or reduced toxicity is in mouse and/or rat.
  • such increase potency and/or reduced toxicity is in a human.
  • ISIS 145733 which comprises uniform phosphorothioate linkages and ISIS 257016 which comprises phosphodiester linkage in the wings and phosphorothioate linkages in the gap, are otherwise identical. Both comprise the sequence GAAGTAGCCACCAACTGTGC (SEQ ID NO. 1572). Both of the oligonucleotides further comprise a gap consisting of ten 2'-deoxynucleotides, flanked on each side by f ⁇ ve-nucleotide "2'-methoxyethyl (2'-MOE) nucleotides. All cytidine residues are 5-methylcytidines.
  • the mixed back-bone compound, ISIS 257016 was about 50 times more potent for reducing SGLT-2 mRNA compared to the non-mixed parent compound, ISIS 145733 (see EXAMPLE 9).
  • ISIS 257016 Pharmacokinetic studies of certain mixed backbone compound ISIS 257016 indicate that in certain embodiments, the compound acts as a prodrug that is metabolized to a 12 nucleobase pharmacophore.
  • ISIS 370717 is a 12 nucleobase antisense oligonucleotide targeted to SGLT-2 comprising the sequence TAGCCACCAACT (SEQ ID NO.
  • ISIS 257016 further comprising a gap consisting of ten 2'-deoxynucleotides, flanked on both sides by one-nucleotide wings.
  • the wings are composed of 2'-methoxyethyl (2'-MOE) nucleotides. All cytidine residues are 5-methylcytidines.
  • short antisense compounds comprising 2' MOE monomers in the wings are efficiently delivered to the kidney and treatment with such compounds results in efficient modulation of target gene expression in the kidney without liver or kidney toxicity. It is further shown herein that in certain embodiments, short antisense compounds are more potent for reducing SGLT-2 mRNA and have a faster onset compared with parent oligonucleotides targeted to SGLT-2 mRNA in mouse and rat. 2' MOE gap shortmers are shown herein to improve potency and bioavailability over parent compounds.
  • ISIS 370717 1-10-1 gapmer was used as a template to make sequence related oligos with varying motifs. Studies evaluating wing, gap and total length variations around the ISIS 370717 12 mer oligonucleotide can be seen in EXAMPLE 12. Certain motifs evaluated included 1- 10-1, 2-8-2, 1-8-1, 3-6-3, and 1-6-1 (see Table 60 in EXAMPLE 12).
  • the compounds were analyzed for their effect on SGLT2 mRNA levels. All the motifs inhibited the expression of SGLT2 in vivo in a dose- 5 dependent manner. The 1-10-1, 2-8-2 and 1-8-1 gapmers were found to be particularly potent. SGLT-2 mRNA was reduced by more than 80% over the controls using these motifs.
  • the invention provides short antisense compounds targeted to an SGLT2 nucleic acid and having a motif selected from: 1-10-1 and 1-10-2 MOE gapmer. (see Table 62 in EXAMPLE 13). Certain such compounds were analyzed for their effect on rat SGLT2 mRNA. Results in 0 Table 63 illustrate that both the 1-10-1 and 1-10-2 MOE gapmers inhibit the expression of SGLT2 in vivo in a dose-dependent manner and over 80% reduction of SGLT-2 mRNA could be achieved.
  • ISIS 388625 the effect of ISIS 388625 on dog SGLT2 mRNA levels was also analyzed. Dog studies illustrate that greater than 80% inhibition of the expression of SGLT2 can be achieved at a 1 mg/kg/wk dose. Even greater inhibition can be achieved at slightly higher doses. Administration of ISIS 388625 in dog was also shown to improved glucose tolerance. Peak plasma glucose levels were 0 decreased by over 50% on average and the subsequent drop in glucose was lessened compared to saline controls in a standard glucose tolerance test (See EXAMPLE 17). Also, in a rat model of diabetes, short antisense compounds were shown to significantly decrease plasma glucose levels and HbAlC over time compared to PBS and control treated animals (See Example 16).
  • short antisense compounds are targeted to an SGLT2 nucleic acid having the sequence of GENBANK® Accession No. NM_003041.1, incorporated herein as SEQ ID NO: 2.
  • a short antisense compound targeted to SEQ ID NO: 3 is at least 90% complementary to SEQ ID NO: 3.
  • a short antisense compound targeted to SEQ ⁇ 5 ID NO: 3 is at least 95% complementary to SEQ ID NO: 3.
  • a short antisense compound targeted to SEQ ID NO: 3 is 100% complementary to SEQ ID NO: 1.
  • a short antisense compound targeted to SEQ ID NO: 3 comprises a nucleotide sequence selected from the nucleotide sequences set forth in Table 4 and 5.
  • nucleotide sequence set forth in each SEQ ID NO set forth in Tables 4 and 5 is independent of any modification to a sugar moiety, a monomelic linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Antisense compounds described by Isis Number (Isis NO.) indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Tables 4 and 5 illustrate examples of short antisense compounds targeted to SEQ DD NO: 3.
  • Table 4 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 3.
  • Table 5 illustrates, short antisense compounds that have one or two mismatches with respect to SEQ ID NO: 3.
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2'-modified sugar.
  • the particular 2'-modif ⁇ ed sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • Table 5 Short antisense compounds targeted to SEQ ID NO: 3 and having 1 or 2 mismatches
  • a target region is nucleotides 85-184 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 85-184 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 85-184 comprises a nucleotide sequence
  • a short antisense compound targeted to nucleotides 85-184 of SEQ ID NO: 3 is selected from Isis No 379684, 405193, 405194, 405195, 405196, 405197, 379685, 405198, 405199, 405200, 405201, 379686, 379711 or 388628.
  • a target region is nucleotides 113-132 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 113-132 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 113-132 comprises a nucleotide sequence selected from SEQ ID NO 215, 216, 217, 218, 219, 221, 222, 223, or 224.
  • a short antisense compound targeted to nucleotides 113-132 of SEQ ID NO: 3 is selected from Isis No 405193, 405194, 405195, 405196, 405197, 379685, 405198, 405199, 405200, or 405201.
  • a target region is nucleotides 207-329 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 207-329 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 207-329 comprises a nucleotide sequence selected from SEQ ID NO 228, 229, 230, 232, 233, 234, 235, 236, 237, 238, 239, 240, or 241.
  • a short antisense compound targeted to nucleotides 207-329 of SEQ ID NO: 3 is
  • »0 selected from Isis No 405202, 405203, 405204, 379687, 405205, 405206, 405207, 405208, 405209, 405210, 405211, 405212, 379688, or 379689.
  • a target region is nucleotides 207-273 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 207-273 of SEQ DD NO: 3.
  • a short antisense compound targeted to nucleotides 207-273 comprises a nucleotide sequence selected from SEQ ID NO 228, 229, 230, 232, 233, 234, 235, 236, 237, 238, or 239.
  • a short antisense compound targeted to nucleotides 207-273 of SEQ ID NO: 3 is selected from Isis No 405202, 405203, 405204, 379687, 405205, 405206, 405207, 405208, 405209, 405210, 405211, or 405212.
  • a target region is nucleotides 207-219 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 207-219 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 207-219 comprises a nucleotide sequence selected from SEQ ID NO 228 or 229.
  • a short antisense compound targeted to nucleotides 207-219 of SEQ ID NO: 3 is selected from Isis NO.. 405202 or 405203.
  • a target region is nucleotides 236-252 of SEQ ID NO: 3.
  • a short antisense compound is .targeted to nucleotides 236-252 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 236-252 comprises a nucleotide sequence selected from SEQ ID NO 230, 232, 233, 234, 235, or 236.
  • a short antisense compound targeted to nucleotides 236-252 of SEQ ID NO: 3 is selected from Isis NO. 405204,
  • a target region is nucleotides 260-273 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 260-273 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 260-273 comprises a nucleotide sequence selected from SEQ ID NO 237, 238, or 239. In certain such embodiments, a short antisense
  • >0 compound targeted to nucleotides 260-273 of SEQ ID NO: 3 is selected from Isis NO. 405210, 405211, or 405212.
  • a target region is nucleotides 435-640 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 435-640 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 435-640 comprises a nucleotide
  • a short antisense compound targeted to nucleotides 435-640 of SEQ ED NO: 3 is selected from Isis NO. 379690, 405248, 379691, 389780, 379692, 382676, 388625, 392170, 392173, 405213, 405214, 405215, 405216, 379693, 405217, 405218, 405219, 405220, 405221, 405222, 405223, 405224, or 379694.
  • a target region is nucleotides 527-540 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 527-540 of SEQ ED NO: 3.
  • a short antisense compound targeted to nucleotides 527-540 comprises a nucleotide sequence selected from SEQ ID NO 245, 246, or 251.
  • a short antisense compound targeted to nucleotides 527-540 of SEQ ED NO: 3 is selected from Isis NO. 389780, 379692,
  • a target region is nucleotides 564-603 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 564-603 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 564-603 comprises a nucleotide sequence selected from SEQ ID NO 252, 253, 254, 256, 257, 258, 259, 260, 261, 262, or 263.
  • a short antisense compound targeted to nucleotides 564-603 of SEQ ID NO: 3 is selected from Isis NO. 405214, 405215, 405216, 379693, 405217, 405218, 405219, 405220, 405221, 405222, 405223, or 405224.
  • a target region is nucleotides 564-579 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 564-579 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 564-579 comprises a nucleotide sequence selected from SEQ ID NO 252, 253, 254, 256, or 257.
  • a short antisense compound targeted to nucleotides 564-579 of SEQ ID NO: 3 is selected from Isis NO. 405214, 405215, 405216, 379693, 405217, or 405218.
  • a target region is nucleotides 587-603 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 587-603 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 587-603 comprises a nucleotide sequence selected from SEQ ID NO 258, 259, 260, 261, 262, or 263.
  • a short antisense compound targeted to nucleotides 587-603 of SEQ ID NO: 3 is selected from Isis NO. 405219, 405220, 405221, 405222, 405223, or 405224.
  • a target region is nucleotides 974-1014 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 974-1014 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 974-1014 comprises a nucleotide sequence selected from SEQ ID NO 267, 268, 269, 270, 271 , 272, or 274.
  • a short antisense compound targeted to nucleotides 974-1014 of SEQ ID NO: 3 is selected from Isis NO. 379696, 405226, 405227, 405228, 405229, 405230, 379697, or 405231.
  • a target region is nucleotides 998-1014 of SEQ ED NO: 3.
  • a short antisense compound is targeted to nucleotides 998-1014 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 998-1014 comprises a nucleotide sequence selected from SEQ ID NO 268, 269, 270, 271, 272, or 274.
  • a short antisense compound targeted to nucleotides 998-1014 of SEQ ID NO: 3 is selected from Isis NO. 405226, 405227, 405228, 405229, 405230, 379697, or 405231.
  • a target region is nucleotides 1091-1170 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 1091-1170 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 1091-1170 comprises a nucleotide sequence selected from SEQ ID NO 275, 276, 277, 278, 279, 280, 281, 283, 284, 285, 286, or 287.
  • a short antisense compound targeted to nucleotides 1091-1170 of SEQ ID NO: 3 is selected from Isis NO. 379698, 405232, 405233, 405234, 405235, 388626, 379699, 382677, 405236, 405237, 405238, 379700, or 405239.
  • a target region is nucleotides 1091-1104 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 1091-1104 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 1091-1104 comprises a nucleotide sequence selected from SEQ ID NO 275, 276, or 277.
  • an short antisense compound targeted to nucleotides 1091-1104 of SEQ ID NO: 3 is selected from Isis NO. 379698, 405232, or 405233.
  • a target region is nucleotides 1130-1144 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 1130-1144 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 1130-1144 comprises a nucleotide sequence selected from SEQ ID NO 278, 279, 280, 281, or 283.
  • a short antisense compound targeted to nucleotides 1130-1144 of SEQ ID NO: 3 is selected from Isis NO. 405234, 405235, 388626, 379699, 382677, or 405236.
  • a target region is nucleotides 1157-1170 of SEQ ID NO: 3.
  • a short antisense compound is targeted to nucleotides 1157-1170 of SEQ ED NO: 3.
  • a short antisense compound targeted to nucleotides 1157-1170 comprises a nucleotide sequence selected from SEQ ID NO 284, 285, or 287.
  • a short antisense compound targeted to nucleotides 1157-1170 of SEQ ID NO: 3 is selected from Isis NO. 405237, 405238, 379700, or 405239.
  • a target region is nucleotides 1542-1556 of SEQ DD NO: 3.
  • a short antisense compound is targeted to nucleotides 1542-1556 of SEQ ID NO: 3.
  • a short antisense compound targeted to nucleotides 1542-1556 comprises a nucleotide sequence selected from SEQ ID NO 289, 290, 291, 292, or 293.
  • a short antisense compound targeted to nucleotides 1542-1556 of SEQ ID NO: 3 is selected from Isis NO. 405240, 405241, 405242, 388629, 379702, or 382678.
  • a target region is nucleotides 1976-1991 of SEQ ED NO: 3.
  • a short antisense compound is targeted to nucleotides 1976-1991 of SEQ ED NO: 3.
  • a short antisense compound targeted to nucleotides 1976-1991 comprises a nucleotide sequence selected from SEQ ED NO 296, 297, 298, 299, or 300.
  • a short antisense compound targeted to nucleotides 1976-1991 of SEQ ED NO: 3 is selected from Isis NO. 405243, 405244, 405245, 405246, or 405247.
  • short antisense compounds targeted to an SGLT2 nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to an SGLT2 nucleic acid are 9 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to an SGLT2 nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds targeted to an SGLT2 nucleic acid are short gapmers.
  • short gapmers targeted to an SGLT2 nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to an SGLT2 nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification. 0
  • the monomers of the wing are BNA's.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'- CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)-O-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to an SGLT2 nucleic acid comprise a gap between the 5' wing and the 3' wing. In certain embodiments the gap comprises five, six, seven, eight,
  • the monomers of the gap are unmodified deoxyribonucleotides. In certain embodiments, the monomers of the gap are unmodified ribonucleotides. In certain embodiments, gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • short antisense compounds targeted to an SGLT2 nucleic acid have uniform monomelic linkages. In certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to an SGLT2 nucleic acid have mixed backbones.
  • short antisense compounds targeted to an SGLT2 nucleic acid are 8
  • short antisense compounds targeted to an SGLT2 nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to an SGLT2 nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to an SGLT2 nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to an SGLT2 nucleic acid are monomers in length. In certain embodiments, short antisense compounds targeted to
  • S 5 an SGLT2 nucleic acid are 13 monomers in length.
  • short antisense compounds targeted to an SGLT2 nucleic acid are 14 monomers in length.
  • short antisense compounds targeted to an SGLT2 nucleic acid are 15 monomers in length.
  • short antisense compounds targeted to an SGLT2 nucleic acid are 16 monomers in length.
  • short antisense compounds targeted to an SGLT2 nucleic acid comprise 9 to 15 monomers.
  • short antisense compounds targeted to an SGLT2 nucleic acid comprise 10 to 15 monomers.
  • short antisense compounds targeted to an SGLT2 nucleic acid comprise 12 to 14 monomers.
  • short antisense compounds targeted to an SGLT2 nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of SGLT2.
  • such methods comprise use of one or more short antisense compound targeted to an SGLT2 nucleic acid, wherein the short antisense compound targeted to an SGLT2 nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to an SGLT2 nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 11 monomers in length.
  • methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 14 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid that is 16 monomers in length.
  • methods of modulating expression of SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of SGLT2 comprise use of a short antisense compound targeted to an SGLT2 nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • LDL-R LDL-receptor
  • apoB apolipoprotein B
  • PCSK9 proprotein convertase subtilisin/kexin type 9
  • ApoB participates in the intracellular assembly and secretion of triglyceride-rich lipoproteins and is a ligand for the LDL-R.
  • PCSK9 is proposed to reduce LDL-R expression levels in the liver. Reduced LDL-R expression results in reduced hepatic uptake of circulating ApoB- containing lipoproteins, which in turn leads to elevated cholesterol.
  • PCSK9 is the gene product or protein of which expression is to be modulated by administration of a short antisense compound.
  • PCSK9 nucleic acid means any nucleic acid encoding PCSK9.
  • a PCSK9nucleic acid includes, without limitation, a DNA sequence encoding PCSK9, an RNA 10 sequence transcribed from DNA encoding PCSK9, and an mRNA sequence encoding PCSK9.
  • PCSK9 mRNA means an mRNA encoding PCSK9.
  • the invention provides methods of modulating the expression of PCSK9 in
  • the invention provides methods of treating an individual comprising administering one or more pharmaceutical compositions of the present invention.
  • the individual has hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing atherosclerosis, coronary heart disease, a history of coronary heart disease, early onset coronary heart disease, one or more risk factors i0 for coronary heart disease, type II diabetes, type II diabetes with dyslipidemia, dyslipidemia, hypertriglyceridemia, hyperlipidemia, hyperfattyacidemia, hepatic steatosis, non-alcoholic steatohepatitis, or non-alcoholic fatty liver disease.
  • the guidelines include obtaining a complete lipoprotein profile, typically after a 9 to 12 hour fast, for determination of LDL-C, total cholesterol, and HDL-C levels.
  • LDL-C levels of 130-159 mg/dL, 160-189 mg/dL, and greater than or equal to 190 mg/dL are considered borderline high, high, and very high, respectively.
  • Total cholesterol levels of 200-239 and greater than or equal to 240 mg/dL are considered borderline high and high, respectively.
  • the individual has been identified as in need of lipid-lowering therapy. In certain such embodiments, the individual has been identified as in need of lipid-lowering therapy according to the guidelines established in 2001 by Adult Treatment Panel III (ATP III) of the National Cholesterol Education Program (NCEP), and updated in 2004 (Grundy et al., Circulation, 2004, 110, 227-239).
  • the individual in need of lipid-lowering therapy has LDL-C above 190 mg/dL.
  • the individual in need of lipid-lowering therapy has LDL-C above 160 mg/dL.
  • the individual in need of lipid-lowering therapy has LDL-C above 130 mg/dL.
  • the individual in need of lipid-lowering therapy has LDL-C above 100 mg/dL.
  • the individual in need of lipid-lowering therapy should maintain LDL-C below 160
  • the individual in need of lipid-lowering therapy should maintain LDL-C below 130 mg/dL. In certain such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C below 100 mg/dL. In certain such embodiments the individual should maintain LDL-C below 70 mg/dL.
  • the invention provides methods for reducing ApoB in an individual.
  • the invention provides methods for reducing ApoB-containing lipoprotein in an individual. In certain embodiments the invention provides methods for reducing LDL-C in an individual. In certain embodiments the invention provides methods for reducing VLDL-C in an individual. In certain embodiments the invention provides methods for reducing IDL-C in an individual. In certain embodiments the invention provides methods for reducing non-HDL-C in an individual. In certain embodiments the i5 invention provides methods for reducing Lp(a) in an individual. In certain embodiments the invention provides methods for reducing serum triglyceride in an individual. In certain embodiments the invention provides methods for reducing liver triglyceride in an individual. In certain embodiments the invention provides methods for reducing Ox-LDL-C in an individual. In certain embodiments the invention provides methods for reducing small LDL particles in an individual. In certain embodiments the invention provides
  • the invention provides methods for reducing small VLDL particles in an individual. In certain embodiments the invention provides methods for reducing phospholipids in an individual. In certain embodiments the invention provides methods for reducing oxidized phospholipids in an individual.
  • the methods provided by the present invention do not lower HDL-C. In certain embodiments, the methods provided by the present invention do not result in accumulation of lipids in
  • a pharmaceutical composition comprising a short antisense compound targeted to a PCSK9 nucleic acid is for use in therapy.
  • the therapy is the reduction of LDL-C, ApoB, VLDL-C, IDL-C, non-HDL-C, Lp(a) , serum triglyceride, liver triglyceride, Ox-LDL-C, small LDL particles, small VLDL, phospholipids, or oxidized phospholipids in an individual.
  • the therapy is the treatment of hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing atherosclerosis, coronary heart disease, a history of coronary heart disease, early onset coronary heart disease, one or more risk factors for coronary heart disease, type II diabetes, type II diabetes with dyslipidemia, dyslipidemia, hypertriglyceridemia, hyperlipidemia, hyperfattyacidemia, hepatic steatosis, non-alcoholic steatohepatitis, or non-alcoholic fatty liver disease.
  • the therapy is the reduction of CHD risk.
  • the therapy is prevention of atherosclerosis.
  • the therapy is the prevention of coronary heart disease.
  • a pharmaceutical composition comprising a short antisense compound targeted to a PCSK9 nucleic acid is used for the preparation of a medicament for reducing LDL-C, ApoB, VLDL-C, IDL-C, non-HDL-C, Lp(a) , serum triglyceride, liver triglyceride, Ox-LDL-C, small LDL particles, small VLDL, phospholipids, or oxidized phospholipids in an individual.
  • pharmaceutical composition comprising a short antisense compound targeted to PCKS9 is used for the preparation of a medicament for reducing coronary heart disease risk.
  • a short antisense compound targeted to a PCSK9 nucleic acid is used for the preparation of a medicament for the treatment of hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing atherosclerosis, coronary heart disease, a history of coronary heart disease, early onset coronary heart disease, one or more risk factors for coronary heart disease, type II diabetes, type II diabetes with dyslipidemia, dyslipidemia, hypertriglyceridemia, hyperlipidemia, hyperfattyacidemia, hepatic steatosis, non-alcoholic steatohepatitis, or non-alcoholic fatty liver disease.
  • one or more pharmaceutical compositions of the present invention are coadministered with one or more other pharmaceutical agents.
  • such one or more other pharmaceutical agents are designed to treat the same disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat a different disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat an undesired effect of one or more pharmaceutical compositions of the present invention.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at the same time. In certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times. In certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared together in a single formulation. In certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared separately.
  • pharmaceutical agents that may be co-administered with a pharmaceutical composition of the present invention include lipid-lowering agents.
  • pharmaceutical agents that may be co-administered with a pharmaceutical composition of the present invention include, but are not limited to atorvastatin, simvastatin, rosuvastatin, and ezetimibe.
  • the lipid-lowering agent is administered prior to administration of a pharmaceutical composition of the present invention.
  • the lipid-lowering agent is administered following administration of a pharmaceutical composition of the present invention.
  • the lipid-lowering agent is administered at the same time as a pharmaceutical composition of the present invention.
  • the dose of a co-administered lipid-lowering agent is the same as the dose that would be administered if the lipid-lowering agent was administered alone. In certain such embodiments the dose of a co-administered lipid-lowering agent is lower than the dose that would be administered if the lipid-lowering agent was administered alone. In certain such embodiments the dose of a co-administered lipid-lowering agent is greater than the dose that would be administered if the lipid-lowering agent was administered alone.
  • a co-administered lipid-lowering agent is a HMG-CoA reductase inhibitor.
  • the HMG-CoA reductase inhibitor is a statin.
  • the statin is selected from atorvastatin, simvastatin, pravastatin, fluvastatin, and rosuvastatin.
  • a co-administered lipid-lowering agent is a cholesterol absorption inhibitor.
  • cholesterol absorption inhibitor is ezetimibe.
  • a co-administered lipid-lowering agent is a co-formulated HMG-CoA reductase inhibitor and cholesterol absorption inhibitor.
  • the co-formulated lipid- lowering agent is ezetimibe/simvastatin.
  • a co-administered lipid-lowering agent is a microsomal triglyceride transfer protein inhibitor (MTP inhibitor).
  • MTP inhibitor microsomal triglyceride transfer protein inhibitor
  • a co-administered lipid-lowering agent is an oligonucleotide targeted to an ApoB nucleic acid.
  • a co-administered pharmaceutical agent is a bile acid sequestrant.
  • the bile acid sequestrant is selected from cholestyramine, colestipol, and colesevelam.
  • a co-administered pharmaceutical agent is a nicotinic acid.
  • the nicotinic acid is selected from immediate release nicotinic acid, extended release nicotinic acid, and sustained release nicotinic acid.
  • a co-administered pharmaceutical agent is a fibric acid.
  • a fibric acid is selected from gemfibrozil, fenofibrate, clofibrate, bezaf ⁇ brate, and ciprofibrate.
  • compositions of the present invention include, but are not limited to, corticosteroids, including but not limited to prednisone; immunoglobulins, including, but not limited to intravenous immunoglobulin (IVIg); analgesics (e.g., acetaminophen); anti-inflammatory agents, including, but not limited to non-steroidal anti-inflammatory drugs (e.g., ibuprofen, COX-I inhibitors, and COX-2, inhibitors); salicylates; antibiotics; antivirals;
  • corticosteroids including but not limited to prednisone
  • immunoglobulins including, but not limited to intravenous immunoglobulin (IVIg)
  • analgesics e.g., acetaminophen
  • anti-inflammatory agents including, but not limited to non-steroidal anti-inflammatory drugs (e.g., ibuprofen, COX-I inhibitors, and COX-2, inhibitors); salicylates; antibiotics; antivirals
  • antifungal agents e.g., biguanides, glucosidase inhibitors, insulins, sulfonylureas, and thiazolidenediones); adrenergic modifiers; diuretics; hormones (e.g., anabolic steroids, androgen, estrogen, calcitonin, progestin, somatostan, and thyroid hormones); immunomodulators; muscle relaxants; antihistamines; osteoporosis agents (e.g., biphosphonates, calcitonin, and estrogens); prostaglandins, antineoplastic agents; psychotherapeutic agents; sedatives; poison oak or poison sumac products; antibodies;
  • antidiabetic agents e.g., biguanides, glucosidase inhibitors, insulins, sulfonylureas, and thiazolidenediones
  • adrenergic modifiers e.g., diuretics
  • hormones e.
  • the pharmaceutical compositions of the present invention may be administered in conjuction with a lipid-lowering therapy.
  • a lipid-lowering therapy is therapeutic lifestyle change.
  • a lipid-lowering therapy is LDL apheresis.
  • short antisense compounds are targeted to a PCSK9 nucleic acid having the sequence of GENBANK® Accession No. NM l 74936.2, incorporated herein as SEQ ID NO: 4.
  • a short antisense compound targeted to SEQ ID NO: 4 is at least 90% complementary to
  • a short antisense compound targeted to SEQ ID NO: 4 is at least 95% complementary to SEQ ID NO: 4. In certain such embodiments, a short antisense compound targeted to SEQ ID NO: 4 is 100% complementary to SEQ ID NO: 4.
  • a short antisense compound targeted to SEQ ID NO: 4 comprises a nucleotide sequence selected from the nucleotide sequences set forth in Table 6 or Table 7. iO The nucleotide sequence set forth in each SEQ ID NO in Tables 6 and 7 is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Short antisense compounds described by Isis Number indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety,
  • Tables 6 and 7 illustrate examples of short antisense compounds targeted to SEQ ID NO: 4.
  • Table 6 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 4.
  • Table 7 illustrates short antisense compounds that have one or two mismatches with respect to SEQ ID NO: 4.
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2'-modified sugar.
  • the particular 2'-modified sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • Table 7 Short antisense compounds targeted to SEQ ID NO: 4 and having 1 or 2 mismatches
  • a target region is nucleotides 695-710 of SEQ ID NO: 4.
  • short antisense compounds targeted to nucleotides 695-710 of SEQ ID NO: 4 comprise a nucleotide sequence selected from SEQ ID NO: 329, 330, or 331.
  • a short antisense compound targeted to nucleotides 695-710 of SEQ ID NO: 4 is selected from Isis NO. 400297,
  • a target region is nucleotides 742-770 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 742-770 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 332 or 333.
  • a short antisense compound targeted to nucleotides 742-770 of SEQ ID NO: 4 is selected from Isis NO. 400300 or 400301.
  • a target region is nucleotides 828-843 of SEQ ED NO: 4.
  • a short antisense compound targeted to nucleotides 828-843 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 334, 335, or 336.
  • a short antisense compound targeted to nucleotides 828-843 of SEQ ID NO: 4 is selected from ISIS No. 400302,
  • a target region is nucleotides 937-1007 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 937-1007 of SEQ ED NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 337, 338, 339, 340, 341, 342, 343, 344, or 345.
  • a short antisense compound targeted to nucleotides 937-1007 of SEQ DD NO: 4 is selected from Isis NO. 400305, 400306, 400307, 400308, 400309, 400310, 400311, 400312, 400313, or 403739.
  • a target region is nucleotides 937-965 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 937-965 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 337 or 338.
  • a short antisense compound targeted to nucleotides 937-965 of SEQ ID NO: 4 is selected from Isis NO. 400305 or 400306.
  • a target region is nucleotides 988-1007 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 988-1007 of SEQ DD NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 339, 340, 341, 342, 343, 344, or 345.
  • a short antisense compound targeted to nucleotides 937-1007 of SEQ ID NO: 4 is selected from Isis NO. 400307, 400308, 400309, 400310, 400311, 400312, 4003313, or 403739.
  • a target region is nucleotides 1057-1160 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1057-1160 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 346, 347, 348, 349, 350, 351, 352, 353, 354, or 355.
  • a short antisense compound targeted to nucleotides 1057-1160 of SEQ ID NO: 4 is selected from ISIS NO. 400314, 400315, 400316, 400317, 400318, 400319, 400320, 400321, 400322, or 400323.
  • a target region is nucleotides 1057-1109 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1057-1109 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 346, 347, 348, 349, 350, 351, 352, 353, or 354.
  • a short antisense compound targeted to nucleotides 1057-1109 of SEQ ID NO: 4 is selected from ISIS NO. 400314, 400315, 400316, 400317, 400318, 400319, 400320, 400321, or 400322.
  • a target region is nucleotides 1057-1091 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1057-1091 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 346, 347, 348, 349, or 350.
  • a short antisense compound targeted to nucleotides 1057-1091 of SEQ ID NO: 4 is selected from ISIS NO.
  • a target region is nucleotides 1093-1109 of SEQ DD NO: 4.
  • a short antisense compound targeted to nucleotides 1093-1109 of SEQ DD NO: 4 comprises a nucleotide sequence selected from SEQ DD NO 351, 352, 353, or 354.
  • a short antisense compound targeted to nucleotides 1057-1109 of SEQ DD NO: 4 is selected from ISIS NO. 400319,
  • a target region is nucleotides 1334-1349 of SEQ DD NO: 4.
  • a short antisense compound targeted to nucleotides 1334-1349 of SEQ DD NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 357, 358, or 359.
  • a short antisense compound targeted to nucleotides 1334-1349 of SEQ ID NO: 4 is selected from ISIS NO 400325, 400326, or 400327.
  • a target region is nucleotides 1453-1469 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1453-1469 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 360, 361, 362, or 363.
  • a short antisense compound targeted to nucleotides 1453-1469 of SEQ ID NO: 4 is selected from ISIS NO 400328,
  • a target region is nucleotides 1569-1591 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1569-1591 of SEQ ID NO: 4 comprises a nucleotide sequence selected.from SEQ ID NO 364, 365, 366, 367, 368, 369, 370, 371, 372, or 373.
  • a short antisense compound targeted to nucleotides 1569-1591 of SEQ ID NO: 4 is selected from ISIS NO 400332, 400333, 400334, 400335, 400336, 400337, 400338, 400339, 400340, or 400341.
  • a target region is nucleotides 1621-1637 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1621-1637 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ DD NO 374, 375, 376, or 377.
  • a short antisense compound targeted to nucleotides 1621-1637 of SEQ ID NO: 4 is selected from ISIS NO 400342, 400343, 400344, or 400345.
  • a target region is nucleotides 1738-1754 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1738-1754 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 378, 379, 380, or 381.
  • a short antisense compound targeted to nucleotides 1738-1754 of SEQ ID NO: 4 is selected from ISIS NO 400346, 400347, 400348, or 400349.
  • a target region is nucleotides 1834-1853 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 1834-1853 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 382, 383, 384, 385, 386, 387, or 388.
  • a short antisense compound targeted to nucleotides 1834-1853 of SEQ ID NO: 4 is selected from ISIS NO 400350, 400351, 400352, 400353, 400354, 400355, or 400356.
  • a target region is nucleotides 2083-2099 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 2083-2099 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 389, 390, 391, or 392.
  • a short antisense compound targeted to nucleotides 2083-2099 of SEQ ID NO: 4 is selected from ISIS NO 400357, 400358, 400359, or 400360.
  • a target region is nucleotides 2316-2338 of SEQ ID NO: 4.
  • a short antisense compound targeted to nucleotides 2316-2338 of SEQ ID NO: 4 comprises a nucleotide sequence selected from SEQ ID NO 393, 394, 395, 396, 397, 398, 399, 400, 401, or 402.
  • a short antisense compound targeted to nucleotides 2316-2338 of SEQ ID NO: 4 is selected from ISIS NO 400361, 400362, 400363, 400364, 400365, 400366, 400367, 400368, 400369, or 5 400370.
  • short antisense compounds targeted to a PCSK9 nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a PCSK9 nucleic acid are 9 to 14 nucleotides in length.
  • short antisense compounds targeted to a PCSK9 nucleic acid are 10 to 14 nucleotides 0 in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds targeted to a PCSK9 nucleic acid are short gapmers.
  • short gapmers targeted to a PCSK9 nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to a PCSK9 nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA' s.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)- O-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to a PCSK9 nucleic acid comprise a gap
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides.
  • the monomers of the gap are unmodified ribonucleotides.
  • gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, i0 RNase H.
  • short antisense compounds targeting a PCSK9 nucleic acid may have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a PCSK9 nucleic acid have a motif (wing - deoxy gap -wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-
  • short antisense compounds targeted to a PCSK9 nucleic acid have uniform monomelic linkages. In certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to a PCSK9 nucleic acid have mixed backbones. In certain embodiments, short antisense compounds targeted to a PCSK9 nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to a PCSK9 nucleic acid are 9 monomers in length.
  • short antisense compounds targeted to a PCSK9 nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to a PCSK9 nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to a PCSK9 nucleic acid are monomers in length. In certain embodiments, short antisense compounds targeted to
  • a PCSK9 nucleic acid are 13 monomers in length.
  • short antisense compounds targeted to a PCSK9 nucleic acid are 14 monomers in length.
  • short antisense compounds targeted to a PCSK9 nucleic acid are 15 monomers in length.
  • short antisense compounds targeted to a PCSK9 nucleic acid are 16 monomers in length.
  • short antisense compounds targeted to a PCSK9 nucleic acid comprise 9 to 15 monomers.
  • short antisense compounds targeted to a PCSK9 nucleic acid comprise 10 to 15 monomers.
  • short antisense compounds targeted to a PCSK9 nucleic acid comprise 12 to 14 monomers.
  • short antisense compounds targeted to a PCSK9 nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of PCSK9.
  • such methods comprise use of one or more short antisense compound targeted to a PCSK9 nucleic acid, wherein the short antisense compound targeted to a PCSK9 nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to a PCSK9 nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 11 monomers in length.
  • methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 14 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid that is 16 monomers in length.
  • methods of modulating expression of PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of PCSK9 comprise use of a short antisense compound targeted to a PCSK9 nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • SODs superoxide dismutases
  • ALS amyotrophic lateral sclerosis
  • ALS amyotrophic lateral sclerosis
  • ALS also known as Lou Gehrig's disease
  • the deleterious effects of various mutations on superoxide dismutase 1 are most likely mediated through a gain of toxic function rather than a loss of superoxide dismutase 1 activity, as the complete absence of superoxide dismutase 1 in mice neither diminishes life nor provokes overt disease (Al-Chalabi and Leigh, Curr. Opin. Neurol, 2000, 13, 397-405; Alisky and Davidson, Hum. Gene Ther., 2000, 11, 2315-2329).
  • SODl means the gene product or protein of which expression is to be modulated by administration of a short antisense compound.
  • SODl nucleic acid means any nucleic acid encoding SODl.
  • a SODl nucleic acid includes, without limitations, a DNA sequence encoding SODl, an RNA sequence transcribed from DNA encoding SODl , and an mRNA sequence encoding SODl .
  • SOD 1 mRNA means an mRNA encoding SOD 1.
  • the invention provides methods for the slowing of disease progression in an individual suffering from familial ALS by administering to such an individual a short antisense compound targeted to an SODl nucleic acid.
  • a short antisense compound targeted to SODl are delivered directly to the cerebrospinal fluid of the individual.
  • methods further comprise increasing survival time of an 5 individual suffering from familial ALS. Slowing of disease progression is indicated by an improvement in one or more indicators of ALS disease progression, including, without limitation, the revised ALS functional rating scale, pulmonary function tests, and muscle strength measurements.
  • one or more pharmaceutical compositions comprising a short antisense compound targeted to an SODl nucleic acid is co-administered with one or more other pharmaceutical agents.
  • such one or more other pharmaceutical agents are designed to treat the same disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat a different disease or
  • such one or more other pharmaceutical agents are designed to treat an undesired effect of one or more pharmaceutical compositions of the present invention.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • compositions of the present invention and one or more other pharmaceutical agents are administered at the same time, hi certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times. In certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared together in a single formulation. In certain embodiments, one or more pharmaceutical compositions
  • a co-administered pharmaceutical agent is a nicotinic acid.
  • the nicotinic acid is selected from immediate release nicotinic acid, extended release nicotinic acid, and sustained release nicotinic acid.
  • a co-administered pharmaceutical agent is a fibric acid.
  • a fibric acid is selected from gemfibrozil, fenofibrate, clofibrate, bezafibrate, and ciprofibrate.
  • compositions comprising a short antisense compound targeted to SODl include, but are not limited to, corticosteroids, including but not limited to prednisone; immunoglobulins, including, but not limited to intravenous immunoglobulin (PVIg); analgesics (e.g., acetaminophen); anti-inflammatory agents, including, but not limited to non-steroidal anti-inflammatory drugs (e.g., ibuprofen, COX-I inhibitors, and COX-2, inhibitors); salicylates; antibiotics; antivirals; antifungal agents; antidiabetic agents (e.g., biguanides, glucosidase inhibitors, insulins, sulfonylureas, and thiazolidenediones); adrenergic modifiers; diuretics; hormones (e.g., anabolic steroids, androgen, estrogen, calcitonin,
  • corticosteroids including but not limited to prednisone
  • short antisense compounds are targeted to a SODl nucleic acid having the sequence of GENBANK® Accession No. NM_X02317.1, incorporated herein as SEQ ID NO: 5.
  • a short antisense compound targeted to SEQ ID NO: 5 is at least 90% complementary to SEQ ID NO: 5.
  • a short antisense compound targeted to SEQ ID NO: 5 is at least 95% complementary to SEQ ID NO: 5.
  • a short antisense compound targeted to SEQ ID NO: 5 is 100% complementary to SEQ ID NO: 5.
  • a short antisense compound targeted to SEQ ID NO: 5 comprises a nucleotide sequence selected from the nucleotide sequences set forth in Table 8 or Table 9.
  • nucleotide sequence set forth in each SEQ ID NO in Tables 8 and 9 is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Short antisense compounds described by Isis Number indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Table 8 illustrates examples of short antisense compounds targeted to SEQ ID NO: 5.
  • Table 8 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 5.
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2'-modified sugar.
  • the particular 2'-modif ⁇ ed sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • short antisense compounds targeting a SODl nucleic acid may have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a SODl nucleic acid have a motif (wing - deoxy gap - wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-8-1, 3-6-3 or 1-6-1, more preferably 1-10-1, 2-10-2, 3-10-3, and 1-9-2.
  • a target region is nucleotides 85-100 of SEQ ID NO: 5.
  • short antisense compounds targeted to nucleotides 85-100 of SEQ ID NO: 5 comprise a nucleotide sequence selected from SEQ ID NO: 406, 407, or 408.
  • a short antisense compound targeted to nucleotides 85-100 of SEQ ID NO: 5 is selected from Isis No. 387541, 387540, or 387539.
  • short antisense compounds targeted to a SODl nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 9 to 14 nucleotides in length.
  • short antisense compounds targeted to a SODl nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds targeted to a SODl nucleic acid are short gapmers.
  • short gapmers targeted to a SODl nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to a SODl nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA's.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)- 0-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to a SODl nucleic acid comprise a gap between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides.
  • the monomers of the gap are unmodified ribonucleotides.
  • gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • short antisense compounds targeted to a SODl nucleic acid have uniform monomelic linkages, hi certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to a SODl nucleic acid have mixed backbones.
  • short antisense compounds targeted to a SODl nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 10 monomers in length, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 11 monomers in length, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid are monomers in length.
  • short antisense compounds targeted to a SODl nucleic acid are 13 monomers in length, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 14 monomers in length. In certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 15 monomers in length, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid are 16 monomers in length, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid comprise 9 to 15 monomers.
  • short antisense compounds targeted to a SODl nucleic acid comprise 10 to 15 monomers, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid comprise 12 to 14 monomers, hi certain embodiments, short antisense compounds targeted to a SODl nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of SODl . In certain embodiments, such methods comprise use of one or more short antisense compound targeted to a SODl nucleic acid, wherein the short antisense compound targeted to a SODl nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e.
  • methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 11 monomers in length.
  • methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 14 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating SODl comprise use of a short antisense compound targeted to a SODl nucleic acid that is 16 monomers in length.
  • methods of modulating expression of SODl comprise use of a short antisense compound targeted to a SODl nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of SODl comprise use of a short antisense compound targeted to a SODl nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of SODl comprise use of a short antisense compound targeted to a SODl nucleic acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of SODl comprise use of a short antisense compound targeted to a SODl nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • CRP also known as C-reactive protein and PTXl
  • PTXl a protein that is highly conserved and considered to be an early indicator of infectious or inflammatory conditions.
  • Plasma CRP levels increase 1, 000-fold in response to infection, ischemia, trauma, burns, and inflammatory conditions.
  • statin therapy lipid-lowering therapy, such as statin therapy, it has been demonstrated that patients having reductions in both LDL-C and CRP have a reduced risk of future coronary events relative to patients experiencing only reductions in LDL-C.
  • CRP means the gene product or protein of which expression is to be modulated by a short antisense compound.
  • CRP nucleic acid means any nucleic acid encoding CRP.
  • a CRP nucleic acid includes, without limitations, a DNA sequence encoding CRP, an RNA sequence transcribed from DNA encoding CRP, and an mRNA sequence encoding CRP.
  • CRP mRNA means an mRNA encoding CRP.
  • the invention provides methods of modulating CRP expression in an individual comprising administering to the individual a short antisense compound targeted to a CRP nucleic 5 acid. In certain embodiments, the invention provides methods of treating an individual comprising administering one or more pharmaceutical compositions comprising a short antisense compound targeted to a CRP nucleic acid. In certain embodiments, the individual has hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing
  • IQ atherosclerosis coronary heart disease, a history of coronary heart disease, early onset coronary heart disease, one or more risk factors for coronary heart disease.
  • the individual has acute coronary syndrome, vascular injury, arterial occlusion, unstable angina, post peripheral vascular disease, post myocardial infarction (MI), thrombosis, deep vein thrombus, end-stage renal disease (ESRD), chronic renal failure, complement activation, congestive heart failure, or systemic vasculitis.
  • MI myocardial infarction
  • thrombosis thrombosis
  • ESRD end-stage renal disease
  • chronic renal failure complement activation
  • congestive heart failure or systemic vasculitis.
  • the individual has acute coronary syndrome, vascular injury, arterial occlusion, unstable angina, post peripheral vascular disease, post myocardial infarction (MI), thrombosis, deep vein thrombus, end-stage renal disease (ESRD), chronic renal failure, complement activation, congestive heart
  • the individual has undergone a procedure selected from elective stent placement, angioplasty, post percutaneous transluminal angioplasty (PTCA), cardiac transplantation, renal dialysis or cardiopulmonary bypass.
  • a procedure selected from elective stent placement, angioplasty, post percutaneous transluminal angioplasty (PTCA), cardiac transplantation, renal dialysis or cardiopulmonary bypass.
  • the individual has an inflammatory disease. In certain such embodiments,
  • the inflammatory disease is selected from inflammatory bowel disease, ulcerative colitis, rheumatoid arthritis, or osteoarthritis.
  • LDL-C levels of 130-159 mg/dL, 160-189 mg/dL, and greater than or equal to 190 mg/dL are considered borderline high, high, and very high, respectively.
  • Total cholesterol levels of 200-239 and greater than or equal to 240 mg/dL are considered borderline high and high, respectively.
  • HDL-C levels of less than 40 mg/dL are considered low.
  • the individual has been identified as in need of lipid-lowering therapy. In certain such embodiments, the individual has been identified as in need of lipid-lowering therapy according to the guidelines established in 2001 by Adult Treatment Panel III (ATP III) of the National Cholesterol Education Program (NCEP), and updated in 2004 (Grundy et al., Circulation, 2004, 110, 227-239).
  • the individual in need of lipid-lowering therapy has LDL-C above 190 mg/dL. In certain 0 such embodiments, the individual in need of lipid-lowering therapy has LDL-C above 160 mg/dL. In certain such embodiments, the individual in need of lipid-lowering therapy has LDL-C above 130 mg/dL.
  • the individual in need of lipid-lowering therapy has LDL-C above 100 mg/dL. In certain such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C below 160 mg/dL. In certain such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C 5 below 130 mg/dL. In certain such embodiments the individual in need of lipid-lowering therapy should maintain LDL-C below 100 mg/dL. In certain such embodiments the individual should maintain LDL-C below 70 mg/dL.
  • the invention provides methods for reducing CRP in an individual.
  • the reduction in CRP is at least 10%, at least 15%, at least 20%, at least 25%, at least
  • the methods provided by the present invention do not lower HDL-C. In certain embodiments, the methods provided by the present invention do not result in accumulation of lipids in the liver. In certain embodiments, the methods provided by the present invention do not cause hepatic
  • the invention provides methods for lowering CRP concentration in a subject while reducing side effects associated with treatment.
  • a side effect is liver toxicity.
  • a side effect is abnormal liver function.
  • a side effect is elevated alanine aminotransferase (ALT).
  • a side effect is elevated i0 aspartate aminotransferase (AST).
  • the invention provides methods for lowering CRP concentration in a subject who is not reaching target LDL-C levels as a result of lipid-lowering therapy.
  • a short antisense compound targeted to a CRP nucleic acid is the only pharmaceutical agent administered to the subject.
  • the subject has not complied with recommended lipid-lowering
  • a pharmaceutical composition of the invention is co-administered with an additional different lipid-lowering therapy.
  • an additional lipid-lowering therapy is LDL-apheresis.
  • an additional lipid-lowering therapy is a statin.
  • an additional lipid-lowering therapy is ezetimibe.
  • the invention provides methods for lowering CRP concentration in a statin- 5 intolerant subject.
  • the subject has creatine kinase concentration increases as a result of statin administration.
  • the subject has liver function abnormalities as a result of statin administration.
  • the subject has muscle aches as a result of statin administration.
  • the subject has central nervous system side effects as a result of statin administration.
  • the subject has not complied with recommended statin 0 administration.
  • the invention provides methods for reducing coronary heart disease risk in a subject. In certain embodiments the invention provides methods for slowing the progression of atherosclerosis in a subject.
  • the invention provides methods for stopping the progression of atherosclerosis in a subject. In certain such embodiments the invention provides methods for 5 reducing the size and/or prevalence of atherosclerotic plaques in a subject. In certain embodiments the methods provided reduce a subject's risk of developing atherosclerosis.
  • the methods provided improve the cardiovascular outcome in a subject.
  • improved cardiovascular outcome is the reduction of the risk of developing coronary heart disease.
  • improved cardiovascular outcome is a reduction in the
  • cardiovascular outcome is evidenced by improved carotid intimal media thickness.
  • improved carotid intimal media thickness is a decrease in thickness.
  • improved carotid intimal media thickness is a prevention
  • a pharmaceutical composition comprising a short antisense compound targeted to a CRP nucleic acid is for use in therapy.
  • the therapy is the reduction of CRP in an individual.
  • the therapy is the treatment of hypercholesterolemia, non- familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia,
  • the therapy is the reduction of CHD risk.
  • the therapy is prevention of atherosclerosis.
  • the therapy is the prevention of coronary heart disease.
  • the therapy is the treatment of acute coronary syndrome, chronic renal failure,
  • the therapy is the treatment of an individual who has undergone a procedure selected from elective stent placement, angioplasty, post percutaneous transluminal angioplasty (PTCA), cardiac transplantation, renal dialysis or cardiopulmonary 5 bypass.
  • the therapy is the treatment of an inflammatory disorder.
  • a pharmaceutical composition comprising a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for reducing CRP in an individual.
  • pharmaceutical composition comprising a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for reducing coronary heart disease risk.
  • a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for the treatment of hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, a risk of developing atherosclerosis, coronary heart disease, a history of coronary heart disease, early onset coronary heart disease, or one or more risk
  • a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for the treatment of acute coronary syndrome, chronic renal failure, vascular injury, arterial occlusion, atherothrombosis, unstable angina, post peripheral vascular disease, post myocardial infarction (MI), thrombosis, deep vein thrombus, end-stage renal disease (ESRD), complement
  • a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for the treatment of an individual who has had a stroke.
  • a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for the treatment in an individual who has undergone a procedure selected from
  • PTCA post percutaneous transluminal angioplasty
  • a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for the treatment of an inflammatory disease. In certain such embodiments, a short antisense compound targeted to a CRP nucleic acid is used for the preparation of a medicament for the
  • one or more pharmaceutical compositions comprising a short antisense compound targeted to a CRP nucleic acid are co-administered with one or more other pharmaceutical agents.
  • the one or more other pharmaceutical agents is a lipid-lowering agent.
  • such one or more other pharmaceutical agents are designed to treat the same disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat a different disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat an undesired effect of one or more pharmaceutical compositions of the present invention.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at the same time.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times.
  • - one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared together in a single formulation.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared separately.
  • pharmaceutical agents that may be co-administered with a pharmaceutical composition comprising a short antisense compound targeted to a CRP nucleic acid include lipid-lowering agents.
  • pharmaceutical agents that may be co-administered with a pharmaceutical composition of the present invention include, but are not limited to atorvastatin, simvastatin, rosuvastatin, and ezetimibe.
  • the lipid-lowering agent is administered prior to administration of a pharmaceutical composition of the present invention.
  • the lipid-lowering agent is administered following administration of a pharmaceutical composition of the present invention.
  • the lipid-lowering agent is administered at the same time as a pharmaceutical composition of the present invention.
  • the dose of a coadministered lipid-lowering agent is the same as the dose that would be administered if the lipid-lowering agent was administered alone. In certain such embodiments the dose of a co-administered lipid-lowering agent is lower than the dose that would be administered if the lipid-lowering agent was administered alone. In certain such embodiments the dose of a co-administered lipid-lowering agent is greater than the dose that would be administered if the lipid-lowering agent was administered alone.
  • a co-administered lipid-lowering agent is a HMG-CoA reductase inhibitor.
  • the HMG-CoA reductase inhibitor is a statin.
  • the statin is selected from atorvastatin, simvastatin, pravastatin, fluvastatin, and rosuvastatin.
  • a co-administered lipid-lowering agent is ISIS 301012.
  • a co-administered lipid-lowering agent is a cholesterol absorption inhibitor. In certain such embodiments, cholesterol absorption inhibitor is ezetimibe.
  • a co-administered lipid-lowering agent is a co-formulated HMG-CoA reductase inhibitor and cholesterol absorption inhibitor.
  • the co-formulated lipid- lowering agent is ezetimibe/simvastatin.
  • a co-administered lipid-lowering agent is a microsomal triglyceride transfer protein inhibitor (MTP inhibitor).
  • MTP inhibitor microsomal triglyceride transfer protein inhibitor
  • a co-administered pharmaceutical agent is a bile acid sequestrant.
  • the bile acid sequestrant is selected from cholestyramine, colestipol, and colesevelam.
  • a co-administered pharmaceutical agent is a nicotinic acid.
  • the nicotinic acid is selected from immediate release nicotinic acid, extended release nicotinic acid, and sustained release nicotinic acid.
  • a co-administered pharmaceutical agent is a fibric acid.
  • a fibric acid is selected from gemfibrozil, fenofibrate, clofibrate, bezaf ⁇ brate, and ciprofibrate.
  • compositions comprising a short antisense compound targeted to a CRP nucleic acid include, but are not limited to, corticosteroids, including but not limited to prednisone; immunoglobulins, including, but not limited to intravenous immunoglobulin (IVIg); analgesics (e.g., acetaminophen); anti-inflammatory agents, including, but not limited to non-steroidal anti-inflammatory drugs (e.g., ibuprofen, COX-I inhibitors, and COX-2, inhibitors); salicylates; antibiotics; antivirals; antifungal agents; antidiabetic agents (e.g., biguanides, glucosidase inhibitors, insulins, sulfonylureas, and thiazolidenediones); adrenergic modifiers; diuretics; hormones (e.g., anabolic steroids, androgen, estrogen,
  • a pharmaceutical composition comprising a short antisense compound targeted to a CRP nucleic acid may be administered in conjuction with a lipid-lowering therapy.
  • a lipid-lowering therapy is therapeutic lifestyle change.
  • a lipid-lowering therapy is LDL apheresis.
  • short antisense compounds are targeted to a CRP nucleic acid having the sequence of GENBANK® Accession No. NM_000567.1, incorporated herein as SEQ ID NO: 6.
  • a short antisense compound targeted to SEQ ID NO: 6 is at least 90% complementary to SEQ ID NO: 6.
  • a short antisense compound targeted to SEQ ID NO: 6 is at least 95% complementary to SEQ ID NO: 6.
  • a short antisense compound targeted to SEQ ID NO: 6 is 100% complementary to SEQ ID NO: 6.
  • a short antisense compound targeted to SEQ ID NO: 6 comprises a nucleotide sequence selected from the nucleotide sequences set forth in Table 9.
  • nucleotide sequence set forth in each SEQ ID NO in Table 9 is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an 5 internucleoside linkage, or a nucleobase.
  • Short antisense compounds described by Isis Number indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Table 9 illustrates examples of short antisense compounds targeted to SEQ ID NO: 6.
  • Table 9 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 6.
  • the column labeled 0 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2 '-modified sugar.
  • the particular 2'-modif ⁇ ed sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside 5 linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • short antisense compounds targeting a CRP nucleic acid may have any one
  • short antisense compounds targeting a CRP nucleic acid have a motif (wing - deoxy gap - wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-8-1, 3-6-3 or 1-6-1, more preferably 1-10-1, 2-10-2, 3-10-3, and 1-9-2.
  • motif wing - deoxy gap - wing
  • a target region is nucleotides 1305-1320 of NM 000567.1.
  • short antisense compounds targeted to nucleotides 1305-1320 of NM_000567.1 comprise a
  • a short antisense compound targeted to nucleotides 263-278 of NM_000567.1 is selected from Isis NO. 353484 or 353485.
  • a target region is nucleotides 1257-1272 of NM_000567.1.
  • a short antisense compound targeted to nucleotides 1257-1272 of NM_000567.1 comprises a nucleotide sequence selected from SEQ ID NO 1257 or 1258.
  • a short antisense compound targeted to nucleotides 428-483 of NMJ)00567.1 is selected from Isis NO. 353506 or 353507.
  • short antisense compounds targeted to a CRP nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 9 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds targeted to a CRP nucleic acid are short gapmers.
  • short gapmers targeted to a CRP nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to a CRP nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA's.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)-O- 2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to a CRP nucleic acid comprise a gap between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides.
  • the monomers of the gap are unmodified ribonucleotides.
  • gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • short antisense compounds targeted to a CRP nucleic acid have uniform monomelic linkages. In certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid have mixed backbones.
  • short antisense compounds targeted to a CRP nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 13 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 14 monomers in length.
  • short antisense compounds targeted to a CRP nucleic acid are 15 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid are 16 monomers in length. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid comprise 9 to 15 monomers. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid comprise 10 to 15 monomers. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid comprise 12 to 14 monomers. In certain embodiments, short antisense compounds targeted to a CRP nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of CRP.
  • such methods comprise use of one or more short antisense compound targeted to a CRP nucleic acid, wherein the short antisense compound targeted to a CRP nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to a CRP nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 11 monomers in length.
  • methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 14 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating CRP comprise use of a short antisense compound targeted to a CRP nucleic acid that is 16 monomers in length.
  • methods of modulating expression of CRP comprise use of a short antisense compound targeted to a CRP nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of CRP comprise use of a short antisense compound targeted to a CRP nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of CRP comprise use of a short antisense compound targeted to a CRP nucleic acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of CRP comprise use of a short antisense compound targeted to a CRP nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • GCCR Glucocorticoid Receptor
  • Glucocorticoids were among the first steroid hormones to be identified and are responsible for a multitude of physiological functions, including the stimulation of gluconeogenesis, decreased glucose uptake and utilization in peripheral tissues, increased glycogen deposition, suppression of immune and inflammatory responses, inhibition of cytokine synthesis and acceleration of various developmental events. Glucocorticoids are also especially important for combating stress. Stress-induced elevation of glucocorticoid synthesis and release leads to, among other responses, increased ventricular workload, inhibition of inflammatory mediators, inhibition of cytokine synthesis and increased glucose production (Karin, Cell, 1998, 93, 487-490).
  • glucocorticoid receptor a ubiquitously expressed cytoplasmic member of the nuclear hormone superfamily of receptors.
  • Human glucocorticoid receptor is also known as nuclear receptor subfamily 3, group C, member 1 ; NR3C1; GCCR; GCR; GRL; Glucocorticoid receptor, lymphocyte.
  • the gene is located on human chromosome 5ql l-ql3 and consists of 9 exons (Encio and Detera-Wadleigh, J Biol Chem, 1991, 266, 7182- 7188; Gehring et al., Proc Natl Acad Sd U S A, 1985, 82, 3751-3755).
  • human glucocorticoid receptor mRNA a 5.5 kb human glucocorticoid receptor ⁇ cDNA containing exons 1-8 and exon 9 ⁇ ; a 4.3 kb human glucocorticoid receptor ⁇ cDNA containing exons 1-8 and exon 9 ⁇ ; and a 7.0 kb human glucocorticoid receptor ⁇ cDNA containing exons 1-8 and the entire exon 9, which includes exon 9 ⁇ , exon 9 ⁇ and the 'J region', which is flanked by exons 9 ⁇ and 9 ⁇ (Hollenberg et al., Nature, 1985, 318, 635- 641; Oakley et al., J Biol Chem, 1996, 271, 9550-9559).
  • Human glucocorticoid receptor ⁇ is the predominant isoform of the receptor and the one that exhibits steroid binding activity (Hollenberg et al., Nature, 1985, 318, 635-641). Additionally, through usage of three different promoters three different exon 1 variants can be transcribed, and alternative splicing of one exon 1 variant can result in three different versions of this exon. Thus, human glucocorticoid receptor mRNA may contain 5 different versions of exon 1 (Breslin et al., MoI Endocrinol, 2001, 15, 1381-1395).
  • ⁇ and ⁇ isoforms of human glucocorticoid receptor mRNA Examination of the expression patterns of the ⁇ and ⁇ isoforms of human glucocorticoid receptor mRNA reveals that the ⁇ isoform is more abundantly expressed. Both isoforms are expressed in similar tissues and cell types, including lung, kidney, heart, liver, skeletal muscle, macrophages, neutrophils and peripheral blood mononuclear cells. Only human glucocorticoid receptor ⁇ is expressed in colon.
  • the ⁇ isoform is undetectable, suggesting that under physiological conditions, the default splicing pathway is the one that produces the ⁇ isoform (Pujols et al., Am J Physiol Cell Physiol, 2002, 283, C1324-1331).
  • the ⁇ isoform of glucocorticoid receptor binds neither a glucocorticoid agonist nor an antagonist.
  • the ⁇ isoform is localized primarily in the nucleus in transfected cells, independent of hormone stimulation.
  • the glucocorticoid receptor ⁇ inhibits the hormone-induced, glucocorticoid receptor ⁇ -mediated stimulation of gene expression, suggesting that the ⁇ isoform functions as an inhibitor of glucocorticoid receptor ⁇ activity (Oakley et al., J Biol Chem, 1996, 271, 9550-9559).
  • the human glucocorticoid receptor described herein is defined as the ubiquitous product(s) of the gene located on chromosome 5q 11 -ql 3.
  • glucocorticoid receptor antagonists have been measured in animal models designed to assess anxiety, learning and memory. Reduced expression of glucocorticoid receptor in rats long- term intracerebroventricularly infused with antisense oligodeoxynucleotides targeting glucocorticoid receptor mRNA did not interfere with spatial navigation in the Morris water maze test (Engelmann et al., Eur J Pharmacol, 1998, 361, 17-26).
  • Glucocorticoids are frequently used for their immunosuppressive, anti-inflammatory effects in the treatment of diseases such as allergies, athsma, rheumatoid arthritis, ADDS, systemic lupus erythematosus and degenerative osteoarthritis.
  • Negative regulation of gene expression such as that caused by the interaction of glucocorticoid receptor with NF-kB, is proposed to be at least partly responsible for the anti-inflammatory action of glucocorticoids in vivo.
  • Interleukin-6, tumor necrosis factor ⁇ and interleukin-1 are the three cytokines that account for most of the hypothalamic-pituitary-adrenal (HPA) axis stimulation during the stress of inflammation.
  • HPA hypothalamic-pituitary-adrenal
  • HPA axis and the systemic sympathetic and adrenomedullary system are the peripheral components of the stress system, responsible for maintaining basal and stress-related homeostasis.
  • Glucocorticoids the end products of the HPA axis, inhibit the production of all three inflammatory cytokines and also inhibit their effects on target tissues, with the exception of interleukin-6, which acts synergistically with glucocorticoids to stimulate the production of acute-phase reactants.
  • Glucocorticoid treatment decreases the activity of the HPA axis (Chrousos, N Engl J Med, 1995, 332, 1351-1362).
  • glucocorticoid receptor gene A total of 15 missense, three nonsense, three frameshift, one splice site, and two alternative spliced mutations, as well as 16 polymorphisms, have been reported in the NR3C1 gene in association with glucocorticoid resistance (Bray and Cotton, Hum Mutat, 2003, 21, 557-568). Additional studies in humans have suggested a positive association between, metabolic syndrome incidence and progression, with alleles at the glucocorticoid receptor (GR) gene (Rosmond, Obes Res, 2002, 10, 1078-1086).
  • GR glucocorticoid receptor
  • glucocorticoid receptor ⁇ Increased expression of glucocorticoid receptor ⁇ is also observed in a significantly high number of glucocorticoid-insensitive asthmatics. Additionally, cytokine-induced abnormalities in the DNA binding capacity of the glucocorticoid receptor were found in peripheral blood mononuclear cells from glucocorticoid-insensitive patients transfection, and HepG2 cells with the glucocorticoid receptor ⁇ gene resulted in a significant reduction of glucocorticoid receptor ⁇ DNA- binding capacity (Leung et al., J Exp Med, 1997, 186, 1567-1574).
  • glucocorticoid receptor ⁇ does not alter the affinity of glucocorticoid receptor oc for hormonal ligands, but rather its ability to bind to the GRE (Bamberger et al., J Clin Invest, 1995, 95, 2435- 2441). Taken together, these results illustrate that glucocorticoid receptor ⁇ , through competition with glucocorticoid receptor ⁇ for GRE target sites, may function as a physiologically and pathophysiologically relevant endogenous inhibitor of glucocorticoid action.
  • glucocorticoid agonists increase hepatic glucose production by activating the glucocorticoid receptor, which subsequently leads to increased expression of the gluconeogenic enzymes phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase.
  • PPCK phosphoenolpyruvate carboxykinase
  • glucose-6-phosphatase Through gluconeogenesis, glucose is formed through non-hexose precursors, such as lactate, pyruvate and alanine (Link, Curr Opin Investig Drugs, 2003, 4, 421-429).
  • Steroidal glucocorticoid receptor antagonists such as RU 486 have been tested in rodent models of diabetes.
  • mice deficient in the leptin receptor gene are genetically obese, diabetic and hyperinsulinemic.
  • Treatment of hyperglycemic db/db mice with RU 486 decreased blood glucose levels by approximately 49%, without affecting plasma insulin levels. Additionally, RU 486 treatment reduced the expression of glucocorticoid receptor responsive genes PEPCK, glucose-6- phosphatase, glucose transporter type 2 and tyrosine aminotransferase in db/db mice as compared to untreated animals (Friedman et al., J Biol Chem, 1997, 272, 31475-31481).
  • RU 486 also ameliorates diabetes in the ob/ob mouse model of diabetes, obesity and hyperinsulinemia, through a reduction in serum insulin and blood glucose levels (Gettys et al., Int J Obes Relat Metab Disord, 1997, 21, 865-873).
  • glucocorticoid receptor antagonists include activation of the HPA axis (Link, Curr Opin Investig Drugs, 2003, 4, 421-429). Increased HPA axis activity is associated with suppression of immune- related inflammatory action, which can increase susceptibility to infectious agents and neoplasms.
  • Conditions associated with suppression of immune-mediated inflammation through defects in the HPA axis, or its target tissues include Cushing's syndrome, chronic stress, chronic alcoholism and melancholic depression (Chrousos, N Engl J Med, 1995, 332, 1351-1362).
  • Steroidal glucocorticoid receptor antagonists have been conjugated to bile acids for the purpose of targeting them to the liver (Apelqvist et al., 2000).
  • Currently, there are no known therapeutic agents that target the glucocorticoid receptor without undesired peripheral effects (Link, Curr Opin Investig Drugs, 2003, 4, 421-429). Consequently, there remains a long felt need for agents capable of effectively inhibiting hepatic glucocorticoid receptor.
  • Glucocorticoid receptor is the gene product or protein of which expression is to be modulated by administration of a short antisense compound. Glucocorticoid receptor is generally referred to as GCCR.
  • GCCR nucleic acid means any nucleic acid encoding GCCR.
  • a GCCR nucleic acid includes, without limitation, a DNA sequence encoding GCCR, an RNA sequence transcribed from DNA encoding GCCR, and an mRNA sequence encoding GCCR.
  • GCCR mRNA means an mRNA encoding GCCR.
  • Antisense technology is an effective means of reducing the expression of specific gene products and therefore is useful in a number of therapeutic, diagnostic and research applications for the modulation of glucocorticoid receptor expression.
  • liver is one of the tissues in which the highest concentrations of antisense oligonucleotides are found following administration (Geary et al., Curr. Opin. Investig. Drugs, 2001, 2, 562-573). Therefore, in such embodiments, antisense technology represents an attractive method for the liver-specific inhibition of glucocorticoid receptor.
  • short antisense compounds targeted to a nucleic acid encoding glucocorticoid receptor are preferentially distributed to the liver.
  • short antisense compounds have increased potency in the liver when compared to a longer parent compound.
  • target RNA is predominantly expressed in the liver.
  • a subject, suspected of having a disease or disorder which can be treated by modulating the expression of GCCR is treated by administering one or more short antisense compound.
  • the methods comprise the step of administering to an animal a therapeutically effective amount of a short antisense compound.
  • Certain short antisense compounds inhibit the activity of GCCR and/ or inhibit expression of GCCR.
  • the activity or expression of GCCR in a subject is inhibited by at least 10%, by at least 20%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at least 99%, or by 100%.
  • the activity or expression of GCCR in a subject is inhibited by at least 30%.
  • the activity or expression of GCCR in a subject is inhibited by at least 50% or more.
  • GCCR reduced expression of GCCR
  • cells contained within such fluids, tissues or organs being analyzed comprise nucleic acids encoding GCCR and/or they contain the GCCR protein itself.
  • short antisense compounds are be utilized in pharmaceutical compositions by adding to them an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier.
  • short antisense compounds targeting a GCCR nucleic acid have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a GCCR nucleic acid have a motif (wing - deoxy gap - wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-8-1, 3-6-3 or 1-6-1, .
  • short antisense compounds targeting a GCCR nucleic acid have a motif (wing - deoxy gap -wing) selected from 1-10-1, 2-10-2, 3-10-3, and 1-9-2. .
  • short antisense compounds targeting a GCCR nucleic acid have a motif (wing - deoxy gap -wing) selected from 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 2-8-2, 1-8-1, 3-6-3 or 1-6-1, more preferably 2-10-2 and 2-8-2.
  • motif wing - deoxy gap -wing
  • provided herein are methods of treating an individual by administering one or more short antisense compound targeted to a GCCR nucleic acid or a pharmaceutical composition comprising such compound. Further provided are methods of treating a subject having a disease or conditions associated with GCCR activity by administering a short antisense compound targeted to a GCCR nucleic acid.
  • diseases and conditions associated with GCCR include but are not limited to, obesity, Metabolic syndrome X, Cushing's Syndrome, Addison's disease, inflammatory diseases such as asthma, rhinitis and arthritis, allergy, autoimmune disease, immunodeficiency, anorexia, cachexia, bone loss or bone frailty, and wound healing.
  • Metabolic syndrome, metabolic syndrome X or simply Syndrome X refers to a cluster of risk factors that include obesity, dyslipidemia, particularly high blood triglycerides, glucose intolerance, high blood sugar and high blood pressure.
  • short antisense compounds targeted to GCCR are used for amelioration of hyperglycemia induced by systemic steroid therapy.
  • antisense technology provides a means of inhibiting the expression of the glucocorticoid receptor ⁇ isoform, demonstrated to be overexpressed in patients refractory to glucocorticoid treatment.
  • the invention provides short antisense compounds targeted to a nucleic acid encoding GCGR, and which modulate the expression of glucocorticoid receptor.
  • Pharmaceutical and other compositions comprising the compounds of the invention are also provided. Further provided are methods of screening for modulators of glucocorticoid receptor and methods of modulating the expression of glucocorticoid receptor in cells, tissues or animals comprising contacting said cells, tissues or animals with one or more of the compounds or compositions of the invention. Methods of treating an animal, particularly a human, suspected of having or being prone to a disease or condition associated with expression of glucocorticoid receptor are also set forth herein. Such methods comprise administering a therapeutically or prophylactically effective amount of one or more of the compounds or compositions of the invention to the person in need of treatment.
  • short antisense compounds are targeted to a GCCR nucleic acid having the sequence of nucleotides 1 to 106000 of GENBANK® Accession No. ACO 12634, incorporated herein as SEQ ID NO: 8.
  • a short antisense compound targeted to SEQ ID NO: 8 is at least 90% complementary to SEQ ID NO: 8.
  • a short antisense compound targeted to SEQ ID NO: 8 is at least 95% complementary to SEQ ID NO: 8.
  • a short antisense compound targeted to SEQ ID NO: 8 is 100% complementary to SEQ ID NO: 8.
  • a short antisense compound targeted to SEQ ID NO: 8 includes a nucleotide sequence selected from the nucleotide sequences set forth in Tables 10 and 11.
  • nucleotide sequence set forth in each SEQ ID NO in Tables 10 and 11 is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Short antisense compounds described by Isis Number indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds targeted to a GCCR nucleic acid comprise a gapmer motif. In certain embodiments, a short antisense compound targeted to a GCCR nucleic acid comprises a 2-10-2 gapmer motif.
  • Tables 10 and 11 illustrate examples of short antisense compounds targeted to SEQ DD NO: 8.
  • Table 10 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 8.
  • Table 11 illustrates short antisense compounds that have one or two mismatches with respect to SEQ ID NO: 8.
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2'-modified sugar.
  • the particular 2'-modif ⁇ ed sugar is also indicated in.the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • Table 11 Short antisense compounds targeted to SEQ ID NO: 8 and having 1 or 2 mismatches
  • a target region is nucleotides 88142-88269 of SEQ ID NO: 8.
  • a short antisense compound is targeted to nucleotides 88142-88269 of SEQ ID NO: 8.
  • a short antisense compound targeted to nucleotides 88142-88269 comprises a nucleotide sequence selected from SEQ ID NO 413, 414, 415, 416, 417, or 418.
  • an antisense compound targeted to nucleotides 88142-88269 of SEQ ID NO: 8 is selected from Isis NO. 371644, 371645, 371649, 371651, 371652, or 371653.
  • a target region is nucleotides 88142-88169 of SEQ ID NO: 8.
  • a short antisense compound is targeted to nucleotides 88142-88169 of SEQ ID NO: 8.
  • a short antisense compound targeted to nucleotides 88142-88169 comprises a nucleotide sequence selected from SEQ ID NO 413 or 414.
  • an antisense compound targeted to nucleotides 88142-88169 of SEQ ID NO: 8 is selected from Isis NO. 371644 or 371645.
  • a target region is nucleotides 88242-88269 of SEQ ID NO: 8.
  • a short antisense compound is targeted to nucleotides 88242-88269 of SEQ ID NO: 8.
  • a short antisense compound targeted to nucleotides 88242-88269 comprises a nucleotide sequence selected from SEQ ID NO 416, 417, or 418.
  • an antisense compound targeted to nucleotides 88242-88269 of SEQ DD NO: 8 is selected from Isis NO. 371651, 371652, or 371653.
  • a target region is nucleotides 92037-92155 of SEQ ID NO: 8.
  • a short antisense compound is targeted to nucleotides 92037-92155 of SEQ ID NO: 8.
  • a short antisense compound targeted to nucleotides 92037-92155 comprises a nucleotide sequence selected from SEQ ID NO 419, 420, 421, or 422.
  • an antisense compound targeted to nucleotides 92037-92155 of SEQ UD NO: 8 is selected from Isis NO. 371665, 371669, 371671, or 171673.
  • a target region is nucleotides 92114-92155 of SEQ ID NO: 8.
  • a short antisense compound is targeted to nucleotides 921 14-92155 of SEQ ID NO: 8.
  • a short antisense compound targeted to nucleotides 921 14-92155 comprises a nucleotide sequence selected from SEQ ID NO 421 or 422.
  • an antisense compound targeted to nucleotides 92114-92155 of SEQ ID NO: 8 is selected from Isis NO. 371671 or 171673.
  • short antisense compounds targeted to a GCCR nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 9 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are short gapmers.
  • short gapmers targeted to a GCCR nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to a GCCR nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA' s.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)- O-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to a GCCR nucleic acid comprise a gap between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides.
  • the monomers of the gap are unmodified ribonucleotides.
  • gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • short antisense compounds targeted to a GCCR nucleic acid have uniform monomeric linkages. In certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid have mixed backbones.
  • short antisense compounds targeted to a GCCR nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 13 monomers in length.
  • short antisense compounds targeted to a GCCR nucleic acid are 14 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 15 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid are 16 monomers in length. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid comprise 9 to 15 monomers. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid comprise 10 to 15 monomers. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid comprise 12 to 14 monomers. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of GCCR.
  • such methods comprise use of one or more short antisense compound targeted to a GCCR nucleic acid, wherein the short antisense compound targeted to a GCCR nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to a GCCR nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 11 monomers in length.
  • methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 14 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid that is 16 monomers in length.
  • methods of modulating expression of GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of GCCR comprise use of a short antisense compound targeted to a GCCR nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • Glucagon Receptor The maintenance of normal glycemia is a carefully regulated metabolic event.
  • Glucagon the 29- amino acid peptide responsible for maintaining blood glucose levels in the postabsorbative state, increases glucose release from the liver by activating hepatic glycogenolysis, gluconeogenesis, stimulating lipolysis in adipose tissue, and stimulating insulin secretion.
  • insulin reverses the glucagon-mediated enhancement of glycogenolysis and gluconeogenesis.
  • insulin is either not available or not fully effective. While treatment for diabetes has traditionally focused on increasing insulin levels, antagonism of glucagon function has been considered as an alternative therapy.
  • glucagon exerts its physiological effects by signaling through the glucagon receptor
  • the glucagon receptor has been proposed as a potential therapeutic target for diabetes (Madsen et al., Curr. Pharm. Des., 1999, 5, 683-691).
  • Glucagon receptor is belongs to the superfamily of G-protein-coupled receptors having seven transmembrane domains. It is also a member of the smaller sub-family of homologous receptors which bind peptides that are structurally similar to glucagon.
  • the gene encoding human glucagon receptor was cloned in 1994 and analysis of the genomic sequence revealed multiple introns and an 82% identity to the rat glucagon receptor gene (Lok et al., Gene, 1994, 140, 203-209.; MacNeil et al., Biochem. Biophys. Res. Commun., 1994, 198, 328-334).
  • rat glucagon receptor gene Cloning of the rat glucagon receptor gene also led to the description of multiple alternative splice variants (Maget et al., FEBS Lett., 1994, 351, 271-275).
  • the human glucagon receptor gene is localized to chromosome 17q25 (Menzel et al., Genomics, 1994, 20, 327-328).
  • a missense mutation of GIy to Ser at codon 40 in the glucagon receptor gene leads to a 3-fold lower affinity for glucagon (Fujisawa et al., Diabetologia, 1995, 38, 983-985) and this mutation has been linked to several disease states, including non-insulin-dependent diabetes mellitus (Fujisawa et al., Diabetologia, 1995, 38, 983-985), hypertension (Chambers and Morris, Nat. Genet., 1996, 12, 122), and central adiposity (Siani et al., Obes. Res., 2001, 9, 722-726).
  • Glucagon receptor is the gene product or protein of which expression is to be modulated by administration of a short antisense compound. Glucagon receptor is generally referred to as GCGR but may also be referred to as GR, GGR, MGC 138246, MGC93090.
  • GCGR nucleic acid means any nucleic acid encoding GCGR.
  • a GCGR nucleic acid includes, without limitation, a GCGR sequence encoding GCGR, an RNA sequence transcribed from DNA encoding GCGR, and an mRNA sequence encoding GCGR.
  • GCGR mRNA means an mRNA encoding a GCGR protein.
  • Antisense technology is an effective means for reducing glucagon receptor (GCGR) expression and has proven to be uniquely useful in a number of therapeutic, diagnostic, and research applications.
  • the present invention provides short antisense compounds targeted to a nucleic acid encoding glucagon receptor, and which modulate the expression of glucagon receptor.
  • short antisense compounds capable of inhibiting GCGR expression.
  • methods of treating an individual comprising administering one or more pharmaceutical compositions comprising a short antisense compound targeted to a GCGR nucleic acid.
  • short antisense compounds targeted to a GCGR nucleic acid inhibit GCGR expression
  • methods of treating a subject having a disease or condition associated with GCGR activity by administering one or more pharmaceutical compositions comprising a short antisense compound targeted to a GCGR nucleic acid.
  • methods of treating a subject having high blood glucose, hyperglycemia, prediabetes, diabetes, Type 2 diabetes, metabolic syndrome, obesity and/or insulin resistance are also contemplated herein.
  • pharmaceutical composition comprising one or more short antisense compounds targeted to GCGR and optionally a pharmaceutically acceptable carrier, diluent, enhancer or excipient.
  • Certain compounds of the invention can also be used in the manufacture of a medicament for the treatment of diseases and disorders related to glucagon effects mediated by GCGR.
  • Certain embodiments of the present invention include methods of reducing the expression of GCGR in tissues or cells comprising contacting said cells or tissues with a short antisense compound targeted to a nucleic acid encoding GCGR or pharmaceutical composition comprising such a short antisense compound.
  • the invention provides methods of decreasing blood glucose levels, blood triglyceride levels, or blood cholesterol levels in a subject comprising administering to the subject a short antisense compound or a pharmaceutical composition. Blood levels may be plasma levels or serum levels.
  • methods of improving insulin sensitivity methods of increasing GLP-I levels and methods of inhibiting hepatic glucose output in an animal comprising administering to said animal an antisense oligonucleotide or a pharmaceutical composition of the invention.
  • An improvement in insulin sensitivity may be indicated by a reduction in circulating insulin levels.
  • the invention provides methods of treating a subject having a disease or condition associated with glucagon activity via GCGR comprising administering to the subject a therapeutically or prophylactically effective amount of a short antisense compound or a pharmaceutical composition.
  • disease or condition may be a metabolic disease or condition.
  • the metabolic disease or condition is diabetes, hyperglycemia, hyperlipidemia, metabolic syndrome X, obesity, primary hyperglucagonemia, insulin deficiency, or insulin resistance.
  • the diabetes is Type 2 diabetes.
  • the obesity is diet-induced.
  • hyperlipidemia is associated with elevated blood lipid levels. Lipids include cholesterol and triglycerides.
  • the condition is liver steatosis.
  • the steatosis is steatohepatitis or non-alcoholic steatohepatitis.
  • the invention provides methods of preventing or delaying the onset of elevated blood glucose levels in an animal as well as methods of preserving beta-cell function in an animal using the oligomeric compounds delineated herein.
  • Certain short antisense compounds targeted to GCGR can be used to modulate the expression of GCGR in a subject in need thereof, such as an animal, including, but not limited to, a human
  • such methods comprise the step of administering to said animal an effective amount of a short antisense compound that reduces expression of GCGR RNA.
  • short antisense compounds effectively reduce the levels or function of GCGR RNA. Because reduction in GCGR mRNA levels can lead to alteration in GCGR protein products of expression as well, such resultant alterations can also be measured.
  • Certain antisense compounds that effectively reduce the levels or function of GCGR RNA or protein products of expression is considered an active antisense compound.
  • short antisense compounds reduce the expression of GCGR causing a reduction of RNA by at least 10%, by at least 20%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at least 99%, or by 100%.
  • methods of screening for modulators of glucagon receptor and methods of modulating the expression of glucagon receptor in cells, tissues or animals comprising contacting said cells, tissues or animals with one or more short antisense compounds targeted to GCGR or with compositions comprising such compounds.
  • Methods of treating an animal, particularly a human, suspected of having or being prone to a disease or condition associated with expression of glucagon receptor are also set forth herein. Certain such methods comprise administering a therapeutically or prophylactically effective amount of one or more of the compounds or compositions of the invention to the person in need of treatment.
  • the reduction of the expression of glucagon receptor may be measured, for example, in blood, plasma, serum, adipose tissue, liver or any other body fluid, tissue or organ of the animal.
  • the cells contained within said fluids, tissues or organs being analyzed contain a nucleic acid molecule encoding glucagon receptor protein and/or the glucagon receptor protein itself.
  • Pharmaceutical and other compositions comprising short antisense compounds are also provided.
  • short antisense compounds targeted to a nucleic acid encoding GCGR are utilized in pharmaceutical compositions by adding an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier.
  • the short antisense compounds targeting a GCGR nucleic acid may have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a GCGR nucleic acid have a motif (wing - deoxy gap -wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-8-1, 3-6-3 or 1-6-1.
  • short antisense compounds targeting a GCGR nucleic acid have a motif (wing - deoxy gap -wing) selected from 1-12-1, 2-10-2, 3-10-3, 3-8-3, 1-1-10-2.
  • short antisense compounds are targeted to a GCGR nucleic acid having the sequence GENBANK® Accession No. NM_000160.1, incorporated herein as SEQ ID NO: 9.
  • a short antisense compound targeted to SEQ ID NO: 9 is at least 90% complementary to SEQ ID NO: 9.
  • a short antisense compound targeted to SEQ ID NO: 9 is at least 95% complementary to SEQ ID NO: 9.
  • a short antisense compound targeted to SEQ ID NO: 9 is 100% complementary to SEQ ID NO: 9.
  • a short antisense compound targeted to SEQ ID NO: 9 includes a nucleotide sequence selected from the nucleotide sequences set forth in Tables 12 and 13.
  • the nucleotide sequences set forth in each SEQ ID NO in Tables 12 and 13 are independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds defined by a SEQ ID NO may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Short antisense compounds described by Isis Number indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds targeted to a GCCR nucleic acid comprise a gapmer motif. In certain embodiments, a short antisense compound targeted to a GCCR nucleic acid comprises a 3-10-3 gapmer motif. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid comprise a gapmer motif. In certain embodiments, a short antisense compound targeted to a GCCR nucleic acid comprises a 3-8-3 gapmer motif. In certain embodiments, short antisense compounds targeted to a GCCR nucleic acid comprise a gapmer motif. In certain embodiments, a short antisense compound targeted to a GCCR nucleic acid comprises a 2-10-2 gapmer motif.
  • Tables 12 and 13 illustrate examples of short antisense compounds targeted to SEQ ID NO: 9.
  • Table 12 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 9.
  • Table 13 illustrates short antisense compounds that have one or two mismatches with respect to SEQ ID NO: 9.
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2 '-modified sugar.
  • the particular 2'-modif ⁇ ed sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5-methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • Table 13 Short antisense compounds targeted to SEQ ID NO: 1 and having 1 or 2 mismatches
  • a target region is nucleotides 378-391 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 378-391 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 378-391 comprises a nucleotide sequence selected from SEQ ID NO 486 or 487.
  • a short antisense compound targeted to nucleotides 378-391 of SEQ ID NO: 9 is selected from Isis No 338463 or 338534.
  • a target region is nucleotides 499-521 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 499-521 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 499-521 comprises a nucleotide sequence selected from SEQ ED NO 488, 489, 490, 491, 492, 493, 494, 495, 496, or 497.
  • a short antisense compound targeted to nucleotides 499-521 of SEQ ED NO: 9 is selected from Isis No 327130, 327131, 327132, 327133, 327134, 327135, 327136, 327137, 327138, or 327139.
  • a target region is nucleotides 531-553 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 531-553 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 531-553 comprises a nucleotide sequence selected from SEQ ID NO 498, 499, 500, 501, 502, 503, 504, 505, 506, or 507.
  • a short antisense compound targeted to nucleotides 531-553 of SEQ ID NO: 9 is selected from Isis No 327140, 327141, 327142, 327143, 327144, 327145, 327146, 327147, 327148, or 327149.
  • a target region is nucleotides 545-567 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 545-567 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 545-567 comprises a nucleotide sequence selected from SEQ ID NO 508, 509, 510, 511, 512, 513, 514, 515, 516, or 517.
  • a short antisense compound targeted to nucleotides 545-567 of SEQ ID NO: 9 is selected from Isis No 327150, 327151, 327152, 327153, 327154, 327155, 327156, 327157, 327158, or 327159.
  • a target region is nucleotides 531-567 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 531-567 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 531-567 comprises a nucleotide sequence selected from SEQ ID NO 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, or 517.
  • a short antisense compound targeted to nucleotides 531-567 of SEQ ID NO: 9 is selected from Isis No 327140, 327141, 327142, 327143, 327144, 327145, 327146, 327147, 327148, 327149, 327150, 327151 , 327152, 327153, 327154, 327155, 327156, 327157, 327158, or 327159.
  • a target region is nucleotides 684-714 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 684-714 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 684-714 comprises a nucleotide sequence selected from SEQ ID NO 518, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, or 536.
  • a short antisense compound targeted to nucleotides 684- 714 of SEQ ID NO: 9 is selected from Isis No 345897, 327160, 327161, 327162, 327163, 327164, 327165, 327166, 327167, 327168, 327169, 327170, 327171, 327172, 327173, 327174, 327175, 327176, or 327177.
  • a target region is nucleotides 869-891 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 869-891 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 869-891 comprises a nucleotide sequence selected from SEQ ID NO 537, 538, 539, 540, 541 , 542, 543, 544, 545, or 546.
  • a short antisense compound targeted to nucleotides 869-891 of SEQ ID NO: 9 is selected from Isis No 327178, 327179, 327180, 327181, 327182, 327183, 327184, 327185, 327186, or 327187.
  • a target region is nucleotides 955-977 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 955-977 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 955-977 comprises a nucleotide sequence selected from SEQ ID NO 547, 548, 549, 550, 551, 552, 553, 554, 555, or 556.
  • a short antisense compound targeted to nucleotides 955-977 of SEQ ID NO: 9 is selected from 5 Isis No 327188, 327189, 327190, 327191, 327192, 327193, 327194, 327195, 327196, or 327197.
  • a target region is nucleotides 1019-1041 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 1019-1041 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 1019-1041 comprises a nucleotide sequence selected from SEQ ID NO 557, 558, 559, 560, 561, 562, 563, 564, 565, or 566.
  • a short antisense compound targeted to nucleotides 1019-1041 of SEQ ID NO: 9 is selected from Isis No 327198, 327199, 327200, 327201, 327202, 327203, 327204, 327205, 327206, or 327207.
  • a target region is nucleotides 1160-1175 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 1160-1175 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 1160-1175 comprises a nucleotide
  • a short antisense compound targeted to nucleotides 1160-1175 of SEQ ID NO: 9 is selected from Isis No 338491 or 338562.
  • a target region is nucleotides 1307-1377 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 1307-1377 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 1307-1377 comprises a nucleotide
  • a short antisense compound targeted to nucleotides 1307-1377 of SEQ ID NO: 9 is selected from Isis No 338498, 338569, 338499, 338570, or 385067.
  • a target region is nucleotides 1307-1414 of SEQ ID NO: 9.
  • a short antisense compound is targeted to nucleotides 1307-1414 of SEQ ID NO: 9.
  • a short antisense compound targeted to nucleotides 1307-1414 comprises a nucleotide sequence selected from SEQ ID NO 569, 570, 571, 572, 573, or 574.
  • a short antisense compound targeted to nucleotides 1307-1414 of SEQ ID NO: 9 is selected from Isis No 338498, 338569, 338499, 338570, 385067, or 338573.
  • short antisense compounds targeted to a GCGR nucleic acid are 8 to 16,
  • short antisense compounds targeted to a GCGR nucleic acid are 9 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides.
  • short antisense compounds targeted to a GCGR nucleic acid are short
  • short gapmers targeted to a GCGR nucleic acid comprise at least one high affinity modification in one or more wings of the compound.
  • short antisense compounds targeted to a GCGR nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA's.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-CH 2 -O-2') BNA , Ethyleneoxy (4'-(CH 2 ) 2 -O-2') BNA , Aminooxy (4'-CH 2 -O-N(R)-2') BNA and Oxyamino (4'-CH 2 -N(R)- 0-2') BNA.
  • the monomers of a wing are 2'MOE nucleotides.
  • short antisense compounds targeted to a GCGR nucleic acid comprise a gap between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides.
  • the monomers of the gap are unmodified ribonucleotides.
  • gap modifications (if any) gap result in an antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • short antisense compounds targeted to a GCGR nucleic acid have uniform monomelic linkages. In certain such embodiments, those linkages are all phosphorothioate linkages. In certain embodiments, the linkages are all phosphodiester linkages. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid have mixed backbones.
  • short antisense compounds targeted to a GCGR nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 13 monomers in length.
  • short antisense compounds targeted to a GCGR nucleic acid are 14 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 15 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid are 16 monomers in length. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid comprise 9 to 15 monomers. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid comprise 10 to 15 monomers. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid comprise 12 to 14 monomers. In certain embodiments, short antisense compounds targeted to a GCGR nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of GCGR.
  • such methods comprise use of one or more short antisense compound targeted to a 5 GCGR nucleic acid, wherein the short antisense compound targeted to a GCGR nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to a GCGR nucleic acid is from about 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 8 monomers in length. In certain embodiments, methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 10 monomers in length. In certain embodiments,
  • methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 11 monomers in length. In certain embodiments, methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating GCGR
  • £0 comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 14 monomers in length.
  • methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 15 monomers in length.
  • methods of modulating GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid that is 16 monomers in length.
  • methods of modulating expression of GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid comprising 9 to 15 monomers. In certain embodiments, methods of modulating expression of GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid comprising 10 to 15 monomers. In certain embodiments, methods of modulating expression of GCGR comprise use of a short antisense compound targeted to a GCGR nucleic i0 acid comprising 12 to 14 monomers. In certain embodiments, methods of modulating expression of GCGR comprise use of a short antisense compound targeted to a GCGR nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • Diacylglycerol transferase 2 (also known as DGAT2, diacylglycerol O-transferase 2, acyl- CoA:diacylglycerol acyltransferase 2)
  • Diacylglycerol transferase 2 has been shown to be implicated in the absorption process of triglycerides (also called triacylglycerols) from food.
  • the absorption of triglycerides from food is a very efficient process which occurs by a series of steps wherein the dietary triacylglycerols are hydrolyzed in the intestinal lumen and then resynthesized within 5 enterocytes.
  • the resynthesis of triacylglycerols can occur via the monoacylglycerol pathwaywhich commences with monoacylglycerol acyltransferase (MGAT) catalyzing the synthesis of diacylglycerol from monoacylglycerol and fatty acyl-CoA.
  • MGAT monoacylglycerol acyltransferase
  • diacylglycerols are provided by the glycerol-phosphate pathway which describes the coupling of two molecules of fatty acyl-CoA to glycerol-3- phosphate. In either case, diacylglycerol is then acylated with another molecule of fatty acyl-CoA in a
  • diacylglycerol acyltransferase The reaction catalyzed by diacylglycerol acyltransferase is the final and only committed step in triglyceride synthesis. As such, diacylglycerol acyltransferase is involved in intestinal fat absorption, lipoprotein assembly, regulating plasma triglyceride concentrations, and fat storage in adipocytes. The first
  • diacylglycerol transferase 2 also known as DGAT2, diacylglycerol O-transferase 2, acyl-CoA:diacylglycerol acyltransferase 2
  • DGAT2 diacylglycerol O-transferase 2
  • acyl-CoA acyl-CoA:diacylglycerol acyltransferase 2
  • Enzymatic assays indicate that this recently identified protein does possess diacylglycerol transferase activity that utilizes a broad range of long chain fatty acyl-CoA substrates
  • Diacylglycerol transferase 2 is a member of a family of genes whose sequences are unrelated to diacylglycerol transferase 1. In addition to differing in sequence compared to diacylglycerol transferase 1, in vitro assays illustrate that diacylglycerol transferase 2 has higher activity at lower concentrations of magnesium chloride and oleoyl-CoA (Cases et al., J. Biol. Chem., 2001, 276, 38870-38876). The predicted
  • diacylglycerol transferase 2 contains at least one putative transmembrane domain, three potential N-linked glycosylation sites, six potential protein kinase C phosphorylation consensus sites, as well as sequences in common with a putative glycerol phosphorylation site found in acyltransferase enzymes (Cases et al., J. Biol. Chem., 2001, 276, 38870-38876).
  • the International Radiation Hybrid Mapping Consortium has mapped human diacylglycerol transferase 2 to chromosome 1 Iql3.3.
  • diacylglycerol transferase 2 is expressed in all 5 segments of the small intestine in mice, with higher expression in the proximal intestine and lower expression in the distal intestine (Cases et al., J. Biol. Chem., 2001, 276, 38870-38876).
  • Diacylglycerol transferase activity exhibits distinct patterns during postnatal development of the rat liver. As there is no correlation between the mRNA expression and activity patterns, post-translational modifications may participate in the regulation of diacylglycerol transferase 2 activity during rat development
  • Diacylglycerol transferase 2 mRNA is preferentially upregulated by insulin treatment, as shown by in vitro assays measuring the diacylglycerol activity from the membrane fraction of cultured mouse adipocytes (Meegalla et al., Biochem. Biophys. Res. Commun., 2002, 298, 317-323). In fasting mice, diacylglycerol transferase 2 expression is greatly reduced, and dramatically increases upon refeeding. The expression
  • mice harboring a disruption in the diacylglycerol acyltransferase 1 gene provide evidence that diacylglycerol acyltransferase 2 contributes to triglyceride synthesis.
  • Levels of diacylglycerol transferase 2 mRNA expression are similar in intestinal segments from both wild type and diacylglycerol transferase 1- deficient mice (Buhman et al., J. Biol. Chem., 2002, 277, 25474-25479).
  • magnesium chloride to distinguish between diacylglycerol transferase 1 and 2 activity, Buhman, et al. observed that, in
  • diacylglycerol transferase activity is reduced to 50% in the proximal intestine and to 10-15% in the distal intestine (Buhman et al., J. Biol. Chem., 2002, 277, 25474- 25479).
  • diacylglycerol transferase 2 mRNA levels are not up-regulated the liver or adipose tissues of diacylglycerol transferase 1 -deficient mice, even after weeks of high-fat diet (Cases et al., J. Biol.
  • Diacylglycerol acyltransferase 1 knockout mice exhibit interesting phenotypes in that they are lean, resistant to diet-induce obesity, have decreased levels of tissue triglycerides and increased sensitivity to insulin and leptin (Chen et al., J. Clin. Invest, 2002, 109, 1049-1055; Smith et al., Nat. Genet., 2000, 25, 87-
  • diacylglycerol transferase 2 also participates in triglyceride synthesis, interfering with diacylglycerol transferase 2 may similarly lead to reduced body fat content.
  • DGAT2 means the gene product or protein of which expression is to be modulated by 15 administration of a short antisense compound.
  • DGAT2 nucleic acid means any nucleic acid encoding DGAT2.
  • a DGAT2 nucleic acid includes, without limitation, a DNA sequence encoding DGAT2, an RNA sequence transcribed from DNA encoding DGAT2, and an mRNA sequence encoding DGAT2.
  • DGAT2 mRNA means an mRNA encoding DGAT2. >0
  • Antisense technology is an effective means for reducing DGAT2 expression and has proven to be uniquely useful in a number of therapeutic, diagnostic, and research applications.
  • the present invention provides compounds targeted to nucleic acid encoding DGAT2, which
  • .5 modulate the expression of DGAT2.
  • short antisense compounds capable of effectively inhibiting DGAT2 expression.
  • a subject, suspected of having a disease or associated with DGAT2 is treated by administering one or more short antisense compounds targeted to a nucleic acid encoding DGAT2.
  • methods comprise the step of administering to an animal a
  • short antisense compounds effectively inhibit the activity of DGAT2 or inhibit the expression of DGAT2.
  • the activity or expression of DGAT2 in a subject is inhibited by at least 10%, by at least 20%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least
  • the activity or expression of DGAT2 in a subject is inhibited by about 30%. More preferably, the activity or expression of DGAT2 in a subject is inhibited by 50% or more.
  • the reduction of the expression of DGAT2 may be measured, for example, in blood, plasma, serum, adipose tissue, liver or any other body fluid, tissue or organ of the animal.
  • the cells contained within said fluids, tissues or organs being analyzed contain a nucleic acid molecule encoding DGAT2 and/or the DGAT2 protein itself.
  • compositions comprising the compounds of the invention are also provided.
  • short antisense compounds targeted to a DGAT2 nucleic acid can be utilized in pharmaceutical compositions by adding an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier.
  • Certain short antisense compounds targeting DGAT2 may have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a DGAT2 nucleic acid have a motif (wing - deoxy gap —wing) selected from 1-12-1, 1-1-10-2, 2-10-1-1, 3-10-3, 2-10-3, 2-10-2, 1-10-1,1-10-2, 3-8-3, 2-8-2, 1-8-1, 3-6-3 or 1-6-1.
  • short antisense compounds targeting a DGAT2 nucleic acid have a motif (wing - deoxy gap -wing) selected from 1-10-1, 2-10-2 and 3-10-3.
  • DGAT2 nucleic acid Provided herein are methods of treating an individual by administering one or more short antisense compound targeted to a DGAT2 nucleic acid or a pharmaceutical composition comprising such compound. Further provided are methods of treating a subject having a disease or conditions associated with DGAT2 activity by administering a short antisense compound targeted to a DGAT2 nucleic acid.
  • Diseases and conditions associated with DGAT2 include, but are not limited to, cardiovascular disorders, obesity, diabetes, cholesterolemia, and liver steatosis.
  • short antisense compounds are targeted to a DGAT2 nucleic acid having the sequence of GENBANK® Accession No. NM 032564.2, incorporated herein as SEQ ID NO: 10.
  • a short antisense compound targeted to SEQ ID NO: 10 is at least 90% complementary to SEQ ID NO: 10.
  • a short antisense compound targeted to SEQ ID NO: 10 is at least 95% complementary to SEQ ID NO: 10.
  • a short antisense compound targeted to SEQ ID NO: 10 is 100% complementary to SEQ DD NO: 10.
  • a short antisense compound targeted to SEQ ID NO: 10 includes a nucleotide sequence selected from the nucleotide sequences set forth in Tables 14 and 15.
  • Each nucleotide sequence set forth in each Tables 14 and 15 is independent of any modification to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • short antisense compounds comprising a nucleotide sequence as set forth in Tables 14 and 15 may comprise, independently, one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Antisense compounds described by Isis Number (Isis NO.) indicate a combination of nucleobase sequence and one or more modifications to a sugar moiety, an internucleoside linkage, or a nucleobase.
  • Tables 14 and 15 illustrate examples of short antisense compounds targeted to SEQ ID NO: 10.
  • Table 14 illustrates short antisense compounds that are 100% complementary to SEQ ID NO: 10.
  • Table 15 illustrates short antisense compounds that have one or two mismatches with respect to SEQ ID NO: 10.
  • the column labeled 'gapmer motif indicates the wing-gap-wing motif of each short antisense compounds.
  • the gap segment comprises 2'-deoxynucleotides and each nucleotide of each wing segment comprises a 2'- modified sugar.
  • the particular 2 '-modified sugar is also indicated in the 'gapmer motif column.
  • '2-10-2 MOE' means a 2-10-2 gapmer motif, where a gap segment of ten 2'-deoxynucleotides is flanked by wing segments of two nucleotides, where the nucleotides of the wing segments are 2'-MOE nucleotides. Internucleoside linkages are phosphorothioate.
  • the short antisense compounds comprise 5- methylcytidine in place of unmodified cytosine, unless "unmodified cytosine" is listed in the gapmer motif column, in which case the indicated cytosines are unmodified cytosines.
  • "5-mC in gap only” indicates that the gap segment has 5-methylcytosines, while the wing segments have unmodified cytosines.
  • Table 15 Short antisense compounds targeted to SEQ ID NO: 10 and having 1 or 2 mismatches
  • a target region is nucleotides 231-267 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 231-267 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 231-267 comprises a nucleotide sequence selected from SEQ ID NO 681, 682, 683, 684, 685, 686, or 687.
  • a short antisense compound targeted to nucleotides 231-267 of SEQ ID NO: 10 is selected from Isis No 372556, 372557, 382601, 372480, 372481, 372558, or 372559.
  • a target region is nucleotides 249-267 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 249-267 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 249-267 comprises a nucleotide sequence selected from SEQ ID NO 683, 684, 685, 686, or 687.
  • a short antisense compound targeted to nucleotides 249-267 of SEQ ID NO: 10 is selected from Isis No 382601, 5 372480, 372481, 372558, or 372559.
  • a target region is nucleotides 331-493 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 331-493 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 331-493 comprises a nucleotide sequence selected from SEQ ID NO 688, 689, 690, 691, 692, 693, or 694.
  • a 0 short antisense compound targeted to nucleotides 331-493 of SEQ ID NO: 10 is selected from Isis No
  • a target region is nucleotides 331-427 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 331-427 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 331-427 comprises a nucleotide 5 sequence selected from SEQ ID NO 688, 689, 690, 691, 692, or 693.
  • a short antisense compound targeted to nucleotides 331-427 of SEQ ID NO: 10 is selected from Isis No 382603,
  • a target region is nucleotides 392-408 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 392-408 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 392-408 comprises a nucleotide sequence selected from SEQ ID NO 690, 691, or 692.
  • a short antisense compound targeted to nucleotides 392-408 of SEQ ID NO: 10 is selected from Isis No 372485, 372563, or 382605.
  • a target region is nucleotides 651-707 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 651-707 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 651-707 comprises a nucleotide sequence selected from SEQ ID NO 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, or 728.
  • a short antisense compound targeted to nucleotides 651-707 of SEQ ID NO: 10 is
  • a target region is nucleotides 724-745 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 724-745 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 724-745 comprises a nucleotide sequence selected from SEQ ID NO 729, 730, 731, 732, or 733.
  • a short antisense compound targeted to nucleotides 724-745 of SEQ ID NO: 10 is selected from Isis No 382609, 372514, 372592, 372515, or 372593.
  • a target region is nucleotides 651-745 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 651-745 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 651-745 comprises a nucleotide sequence selected from SEQ ID NO 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, or 733.
  • a short antisense compound targeted to nucleotides 651-745 0 of SEQ ID NO: 10 is selected from Isis No 372497, 372498, 372575, 372576, 382607, 372499, 372577, 372500, 372578, 372501, 372579, 372502, 372580, 372503, 372581, 372504, 372582, 372505, 372506, 372583, 372584, 372507, 372585, 382608, 372508, 372586, 372509, 372587, 372510, 372588, 372511, 372512, 372589, 372590, 382609, 372514, 372592, 372515, or 372593.
  • a target region is nucleotides 851-922 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 851-922 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 851-922 comprises a nucleotide sequence selected from SEQ ID NO 734, 735, 736, or 737.
  • a short antisense compound targeted to nucleotides 851-922 of SEQ ID NO: 10 is selected from Isis No 382610, 382611, 382602, or 382612.
  • a target region is nucleotides 851-879 of SEQ DD NO: 10.
  • a short antisense compound is targeted to nucleotides 851-879 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 851-879 comprises a nucleotide sequence selected from SEQ ID NO 734, 735, or 736.
  • a short antisense compound targeted to nucleotides 851-879 of SEQ ID NO: 10 is selected from Isis No 382610, 382611, or
  • a target region is nucleotides 965-1007 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 965-1007 of SEQ DD NO: 10.
  • a short antisense compound targeted to nucleotides 965-1007 comprises a nucleotide sequence selected from SEQ DD NO 738, 739, 740, 741, 742, 743, 744, or 745. In certain such embodiments,
  • a short antisense compound targeted to nucleotides 965-1007 of SEQ DD NO: 10 is selected from Isis No 372524, 372602, 382613, 382614, 372525, 372603, 372526, or 372604.
  • a target region is nucleotides 965-979 of SEQ DD NO: 10.
  • a short antisense compound is targeted to nucleotides 965-979 of SEQ DD NO: 10.
  • a short antisense compound targeted to nucleotides 965-979 comprises a nucleotide
  • a short antisense compound targeted to nucleotides 965-979 of SEQ ID NO: 10 is selected from Isis No 372524, 372602, or 382613.
  • a target region is nucleotides 987-1007 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 987-1007 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 987-1007 comprises a nucleotide sequence selected from SEQ ID NO 741, 742, 743, 744, or 745.
  • a short antisense compound targeted to nucleotides 987-1007 of SEQ ID NO: 10 is selected from Isis No 382614, 372525, 372603, 372526, or 372604.
  • a target region is nucleotides 1106-1132 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 1106-1132 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 1106-1132 comprises a nucleotide sequence selected from SEQ ID NO 746, 747, 748, 749, 750, 751, 752, 753, or 754.
  • a short antisense compound targeted to nucleotides 1106-1132 of SEQ ID NO: 10 is selected from Isis No 372530, 372608, 372531, 372609, 372532, 372610, 372533, 382615, or 372611.
  • a target region is nucleotides 1199-1233 of SEQ ID NO: 10.
  • a short antisense compound is targeted to nucleotides 1199-1233 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 1199-1233 comprises a nucleotide sequence selected from SEQ ID NO 755, 756, 757, 758, 759, 760, 761, 762, or 763.
  • a short antisense compound targeted to nucleotides 1199-1233 of SEQ ID NO: 10 is selected
  • a target region is nucleotides 1293-1394 of SEQ ED NO: 10.
  • a short antisense compound is targeted to nucleotides 1293-1394 of SEQ DD NO: 10.
  • a short antisense compound targeted to nucleotides 1293-1394 comprises a nucleotide sequence selected from SEQ ID NO 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, or 777.
  • a short antisense compound targeted to nucleotides 1293-1394 of SEQ ED NO: 10 is selected from Isis No 372540, 372618, 382617, 372541, 372619, 372542, 372620, 372543, 372621, 372544, 372622, 382618, 382619, or 382620.
  • a target region is nucleotides 1293-1336 of SEQ ED NO: 10.
  • a short antisense compound is targeted to nucleotides 1293-1336 of SEQ ED NO: 10.
  • a short antisense compound targeted to nucleotides 1293-1336 comprises a nucleotide sequence selected from SEQ ED NO 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, or 776.
  • a short antisense compound targeted to nucleotides 1293-1336 of SEQ ED NO: 10 is selected from Isis No 372540, 372618, 382617, 372541, 372619, 372542, 372620, 372543, 372621, 372544, 372622, 382618, or 382619.
  • a target region is nucleotides 1293-1324 of SEQ ED NO: 10.
  • a short antisense compound is targeted to nucleotides 1293-1324 of SEQ ID NO: 10.
  • a short antisense compound targeted to nucleotides 1293-1324 comprises a nucleotide sequence selected from SEQ ID NO 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, or 775.
  • a short antisense compound targeted to nucleotides 1293-1324 of SEQ ID NO: 10 is 5 selected from Isis No 372540, 372618, 382617, 372541, 372619, 372542, 372620, 372543, 372621, 372544, 372622, or 382618.
  • short antisense compounds targeted to a DGAT2 nucleic acid are 8 to 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 nucleotides in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid are 9 to 14 nucleotides in length.
  • short antisense compounds targeted to a DGAT2 nucleic acid are 10 to 14 nucleotides in length. In certain embodiments, such short antisense compounds are short antisense oligonucleotides .
  • short antisense compounds targeted to a DGAT2 nucleic acid are short gapmers.
  • short gapmers targeted to a DGAT2 nucleic acid comprise at least
  • short antisense compounds targeted to a DGAT2 nucleic acid comprise 1 to 3 high-affinity modifications in each wing.
  • the nucleosides or nucleotides of the wing comprise a 2' modification.
  • the monomers of the wing are BNA' s.
  • the monomers of the wing are selected from ⁇ -L-Methyleneoxy (4'-CH 2 -O-2') BNA , ⁇ -D-Methyleneoxy (4'-
  • the monomers of a substituent at the 2' position selected from allyl, amino, azido, thio, O-allyl, 0-Ci-C 10 alkyl, -OCF 3 , O-(CH 2 ) 2 -O-CH 3 , T- O(CH 2 ) 2 SCH 3
  • .5 wing are 2'MOE nucleotides.
  • short antisense compounds targeted to a DGAT2 nucleic acid comprise a gap between the 5' wing and the 3' wing.
  • the gap comprises five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen monomers.
  • the monomers of the gap are unmodified deoxyribonucleotides. In certain embodiments, the monomers of the gap are unmodified
  • gap modifications result in a short antisense compound that, when bound to its target nucleic acid, supports cleavage by an RNase, including, but not limited to, RNase H.
  • short antisense compounds targeted to a DGAT2 nucleic acid have uniform monomelic linkages. In certain such embodiments, those linkages are all phosphorothioate linkages.
  • the linkages are all phosphodiester linkages.
  • short antisense compounds targeted to a DGAT2 nucleic acid have mixed backbones.
  • short antisense compounds targeted to a DGAT2 nucleic acid are 8 monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid are 9 monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic 5 acid are 10 monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid are 11 monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid are monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid are 13 monomers in length.
  • short antisense compounds targeted to a DGAT2 nucleic acid are 14 monomers in length. In certain embodiments, short antisense 0 compounds targeted to a DGAT2 nucleic acid are 15 monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid are 16 monomers in length. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid comprise 9 to 15 monomers. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid comprise 10 to 15 monomers. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid comprise 12 to 14 5 monomers. In certain embodiments, short antisense compounds targeted to a DGAT2 nucleic acid comprise 12 to 14 nucleotides or nucleosides.
  • the invention provides methods of modulating expression of DGAT2.
  • such methods comprise use of one or more short antisense compound targeted to a DGAT2 nucleic acid, wherein the short antisense compound targeted to a DGAT2 nucleic acid is from about 0 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • the short antisense compound targeted to a DGAT2 nucleic acid is from about 0 8 to about 16, preferably 9 to 15, more preferably 9 to 14, more preferably 10 to 14 monomers (i.e. from about 8 to about 16 linked monomers).
  • methods of modulating DGAT2 comprise use of a short antisense compound
  • methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 9 monomers in length. In certain embodiments, methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 10 monomers in length. In certain embodiments, methods of modulating DGAT2 comprise use of a short antisense compound targeted to a
  • methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 12 monomers in length. In certain embodiments, methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 13 monomers in length. In certain embodiments, methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 14
  • methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 15 monomers in length. In certain embodiments, methods of modulating DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid that is 16 monomers in length.
  • methods of modulating expression of DGAT2 comprise use of a short
  • methods of modulating expression of DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid comprising 10 to 15 monomers.
  • methods of modulating expression of DGAT2 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid comprising 12 to 14 monomers.
  • methods of modulating expression of DGAT2 0 comprise use of a short antisense compound targeted to a DGAT2 nucleic acid comprising 12 or 14 nucleotides or nucleosides.
  • PTPlB (also known as protein phosphatase IB and PTPNl) is an endoplasmic reticulum (ER)-
  • PTPlB An essential regulatory role in signaling mediated by the insulin receptor has been established for PTPlB.
  • PTPlB interacts with and dephosphorylates the activated insulin receptor both in vitro and in intact cells resulting in the downregulation of the signaling pathway (Goldstein et al. , MoI. Cell.
  • Diabetes and obesity are interrelated. Most of the ingredients listed above.
  • Syndrome X or metabolic syndrome is a new term for a cluster of conditions, that, when occurring together, may indicate a predisposition to diabetes and cardiovascular disease. These symptoms, including high blood pressure, high triglycerides, decreased HDL and obesity, tend to appear together in some individuals.
  • PTPlB is believed to be a therapeutic target for a range of metabolic conditions, including diabetes, obesity and metabolic syndrome.
  • inhibitors of PTPlB may also be useful in slowing, preventing, delaying or ameliorating the sequelae of diabetes, which include retinopathy, neuropathy, cardiovascular complications and nephropathy.
  • PTPlB which is differentially regulated during the cell cycle (Schievella et al, Cell. Growth Differ., 1993, 4, 239-246), is expressed in insulin sensitive tissues as two different isoforms that arise from alternate splicing of the pre-mRNA (Shifrin and Neel, J. Biol. Chem., 1993, 268, 25376-25384).
  • the ratio of the alternatively spliced products is affected by growth factors, such as insulin, and differs in various tissues examined (Sell and Reese, MoI. Genet. Metab., 1999, 66, 189-192).
  • the levels of the variants correlated with the plasma insulin concentration and percentage body fat. These variants may therefore be used as a biomarker for patients with chronic hyperinsulinemia or type 2 diabetes.
  • Protein tyrosine phosphatase IB is the gene product or protein of which expression is to be modulated by administration of a short antisense compound. Protein tyrosine phosphatase IB is generally referred to as PTPlB but may also be referred to as protein tyrosine phosphatase; PTPNl; RKPTP; protein tyrosine phosphatase, non-receptor type 1.
  • PTPlB nucleic acid means any nucleic acid encoding PTPlB.
  • a PTPlB nucleic acid includes, without limitation, a DNA sequence encoding PTPlB, an RNA sequence transcribed from DNA encoding PTPlB, and an mRNA sequence encoding PTPlB.
  • PTPlB mRNA means an mRNA encoding a PTPlB protein.
  • Antisense technology is an effective means for reducing PTPlB expression and has proven to be uniquely useful in a number of therapeutic, diagnostic, and research applications.
  • the present invention provides compounds targeted to a nucleic acid encoding PTPlB, which modulate the expression of PTPlB. Further provided herein are short antisense compounds capable of effectively inhibiting PTPlB expression.
  • a subject, suspected of having a disease or disorder which can be treated by modulating the expression of PTPlB is treated by administering one or more short antisense compounds targeted to a nucleic acid encoding PTPlB.
  • the methods comprise the step of administering to an animal a therapeutically effective amount of a short antisense compound.
  • the short antisense compounds of the present invention effectively inhibit the activity of PTPlB or inhibit the expression of PTPlB.
  • the activity or expression of PTPlB in a subject is inhibited by at least 10%, by at least 20%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at least 99%, or by 100%.
  • activity or expression of PTPlB in a subject is inhibited by about 30%.
  • the activity or expression of PTPlB in a subject is inhibited by 50% or more.
  • the reduction of the expression of PTPlB may be measured, for example, in blood, plasma, serum, 5 adipose tissue, liver or any other body fluid, tissue or organ of the animal.
  • the cells contained within said fluids, tissues or organs being analyzed contain a nucleic acid molecule encoding PTPlB and/or the PTPlB protein itself.
  • compositions comprising the compounds of the invention are also provided.
  • short antisense compounds targeted to a PTPlB nucleic acid are utilized in 10 pharmaceutical compositions by adding an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier.
  • the short antisense compounds targeting PTPlB may have any one or more properties or characteristics of the short antisense compounds generally described herein.
  • short antisense compounds targeting a PTPlB nucleic acid have a motif (wing - deoxy gap -wing) selected from
  • methods of treating an individual by administering one or more short antisense compound targeted to a PTPlB nucleic acid or a pharmaceutical composition comprising such compound are provided herein. Further provided are methods of treating a subject having a disease or
  • -0 conditions associated with PTPlB activity by administering a short antisense compound targeted to a PTPlB nucleic acid.
  • Diseases and conditions associated with PTPlB include but are not limited to high blood glucose or hyperglycemia, prediabetes, diabetes, Type 2 diabetes, metabolic syndrome, obesity and insulin resistance. Therefore, provided herein are methods of treating to high blood glucose or hyperglycemia, prediabetes, diabetes, Type 2 diabetes, metabolic syndrome, obesity and insulin resistance by administering a
  • the present invention provides compositions and methods for decreasing blood glucose levels in a subject or for preventing or delaying the onset of a rise in blood glucose levels in a subject, by administering to the subject a short antisense inhibitor of PTPlB expression.
  • the present invention provides compositions and methods for improving 50 insulin sensitivity in a subject or for preventing or delaying the onset of insulin resistance in a subject, by administering to the subject a short antisense inhibitor of PTPlB expression.
  • the present invention provides compositions and methods for treating a metabolic condition in a subject or for preventing or delaying the onset of a metabolic condition in a subject, by administering to the subject a short antisense compound targeted to a PTPlB nucleic acid.
  • 55 condition may be any metabolic condition associated with PTPlB expression, including but not limited to diabetes and obesity. Also provided are methods of reducing adiposity. Also provided is a method of treating obesity wherein metabolic rate is increased.
  • the subject has Type 2 diabetes.
  • the subject exhibits elevated HbAIc levels
  • HbAIc levels are at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10% or at least about 11%.
  • HbAi 0 levels are reduced to about 7% or below about 7%.
  • the subject exhibits an elevated body mass index In certain embodiments, the elevated body mass index is greater than 25 kg/m2.
  • the subject exhibits hyperglycemia or elevated blood glucose levels.
  • the blood glucose levels are fasting blood glucose levels.
  • the elevated fasting blood glucose levels are at least 130 mg/dL.
  • the subject exhibits hyperglycemia prior to the start of treatment or exhibits fasting blood glucose levels above about 130 mg/dL, baseline HbAi 0 levels of at least about 7%, or body mass index of greater than 25 kg/m 2 or any combination thereof.
  • a method of reducing one or more such levels by administering a short antisense compound targeted to a PTPlB nucleic acid is provided.
  • Fasting glucose may be fasting blood glucose, fasting serum glucose, or fasting plasma glucose.
  • fasting plasma glucose levels are reduced by at least about 25 mg/dL or by at least about 10 mg/dL.
  • said subject does not achieve normal glucose levels on a therapeutic regimen of a glucose- lowering agent such as insulin, sulfonylurea, or metformin.
  • the invention provides methods of altering lipid levels. Certain such methods reduce cholesterol, LDL and/or VLDL levels or any combination thereof in a subject by administering to the subject a short antisense compound targeted to a PTPlB nucleic acid. In certain embodiments HDL levels in a subject are increased by administering to the subject a short antisense compound targeted to a PTPlB nucleic acid. In certain embodiments, LDL:HDL ratio and/or total cholesterol:HDL ratio in a subject is reduced by administering to the subject a short antisense compound targeted to a PTPlB nucleic acid.
  • lipid profile in a subject is improved by increasing HDL, lowering LDL, lowering VLDL, lowering triglycerides, lowering apolipoprotein B levels, or lowering total cholesterol levels, or a combination thereof, by administering to the subject a short antisense compound targeted to a PTPlB nucleic acid .
  • the subject is an animal, including a human.
  • one or more pharmaceutical compositions comprising a short antisense compound targeted to a PTPlB nucleic acid are co-administered with one or more other pharmaceutical agents.
  • such one or more other pharmaceutical agents are designed to treat the same disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat a different disease or condition as the one or more pharmaceutical compositions of the present invention.
  • such one or more other pharmaceutical agents are designed to treat an undesired effect of one or more pharmaceutical compositions of the present invention.
  • one or more pharmaceutical compositions of the present invention are co-administered with another pharmaceutical agent to treat an undesired effect of that other pharmaceutical agent.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at the same time.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared together in a single formulation.
  • one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared separately.
  • the glucose-lowering agent is a PPAR agonist (gamma, dual, or pan), a dipeptidyl peptidase (IV) inhibitor, a GLP-I analog, insulin or an insulin analog, an insulin secretagogue, a SGLT2 inhibitor, a human amylin analog, a biguanide, an alpha- glucosidase inhibitor, a meglitinide, a thiazolidinedione, or a sulfonylurea.
  • the glucose-lowering therapeutic is a GLP-I analog. In some embodiments, the GLP-I analog is exendin-4 or liraglutide. In other embodiments, the glucose-lowering therapeutic is a sulfonylurea. In some embodiments, the sulfonylurea is acetohexamide, chlorpropamide, tolbutamide, tolazamide, glimepiride, a glipizide, a glyburide, or a gliclazide.
  • the glucose lowering drug is a biguanide.
  • the biguanide is metformin, and in some embodiments, blood glucose levels are decreased without increased lactic acidosis as compared to the lactic acidosis observed after treatment with metformin alone.
  • the glucose lowering drug is a meglitinide.
  • the meglitinide is nateglinide or repaglinide.

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