# US 2014/0155464 A1 · Treatment of tristetraproline (ttp) related diseases by inhibition of natural antisense transcript to ttp

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- Number: US 2014/0155464 A1
- Document ID: US20140155464A1
- Status: Published application
- Kind: A1
- Application number: 14/140,305
- Filed: 2013-12-24
- Published: 2014-06-05
- Earliest claimed: 2009-05-06
- Assignees: CuRNA, Inc.
- Applicants: CuRNA, Inc.
- Inventors: JOSEPH COLLARD; OLGA KHORKOVA SHERMAN
- Web page: https://patentgrep.com/patent/US20140155464A1

## CPC

- C12N 15/113: Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)}
- A61K 31/713: Double-stranded nucleic acids or oligonucleotides
- A61P 1/00: Drugs for disorders of the alimentary tract or the digestive system
- A61P 1/04: for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
- A61P 3/00: Drugs for disorders of the metabolism (of the blood or the extracellular fluid A61P7/00)
- A61P 3/04: Anorexiants; Antiobesity agents
- A61P 7/00: Drugs for disorders of the blood or the extracellular fluid
- A61P 9/00: Drugs for disorders of the cardiovascular system
- A61P 9/04: Inotropic agents, i.e. stimulants of cardiac contraction; Drugs for heart failure
- A61P 9/10: for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
- A61P 19/02: for joint disorders, e.g. arthritis, arthrosis
- A61P 21/00: Drugs for disorders of the muscular or neuromuscular system
- A61P 29/00: Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
- A61P 31/18: for HIV
- A61P 35/00: Antineoplastic agents
- A61P 37/02: Immunomodulators
- C12Q 1/6876: Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12N 2310/11: Antisense
- C12N 2310/313: Phosphorodithioates
- C12N 2310/314: Phosphoramidates
- C12N 2310/315: Phosphorothioates
- C12N 2310/321: 2'-O-R Modification
- C12N 2310/322: 2'-R Modification
- C12N 2310/3231: having an additional ring, e.g. LNA, ENA
- Y10T 436/143333: Saccharide [e.g., DNA, etc.]
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

## Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Tristetraproline (TTP), in particular, by targeting natural antisense polynucleotides of Tristetraproline (TTP). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of TTP.

## Claims

### Claim 1

A method of modulating a function of and/or the expression of a Tristetraproline (TTP) polynucleotide in patient cells or tissues in vivo or in vitro comprising:
contacting said cells or tissues with at least one antisense oligonucleotide 5 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 50% sequence identity to a reverse complement of a polynucleotide comprising 5 to 30 consecutive nucleotides within nucleotides 1 to 970 of SEQ ID NO: 3, 1 to 1117 of SEQ ID NO: 4 and 1 to 297 of SEQ ID NO: 5 (FIG. 3); thereby modulating a function of and/or the expression of the Tristetraproline (TTP) polynucleotide in patient cells or tissues in vivo or in vitro.

### Claim 2

A method of modulating a function of and/or the expression of a Tristetraproline (TTP) polynucleotide in patient cells or tissues in vivo or in vitro comprising:
contacting said cells or tissues with at least one antisense oligonucleotide 5 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 50% sequence identity to a reverse complement of a natural antisense of a Tristetraproline (TTP) polynucleotide; thereby modulating a function of and/or the expression of the Tristetraproline (TTP) polynucleotide in patient cells or tissues in vivo or in vitro.

### Claim 3

A method of modulating a function of and/or the expression of a Tristetraproline (TTP) polynucleotide in patient cells or tissues in vivo or in vitro comprising:
contacting said cells or tissues with at least one antisense oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to an antisense oligonucleotide to the Tristetraproline (TTP) polynucleotide: thereby modulating a function of and/or the expression of the Tristetraproline (TTP) polynucleotide in patient cells or tissues in vive or in vitro.

### Claim 4

A method of modulating a function of and/or the expression of a Tristetraproline (TTP) polynucleotide in patient cells or tissues in vivo or in vitro comprising:
contacting said cells or tissues with at least one antisense oligonucleotide that targets a region of a natural antisense oligonucleotide of the Tristetraproline (TTP) polynucleotide; thereby modulating a function of and/or the expression of the Tristetraproline (TTP) polynucleotide in patient cells or tissues in vim or in vitro.

### Claim 5 (depends on 4)

The method of claim 4, wherein a function of and/or the expression of the Tristetraproline (TTP) is increased in vivo or in vitro with respect to a control.

### Claim 6 (depends on 4)

The method of claim 4, wherein the at least one antisense oligonucleotide targets a natural antisense sequence of a Tristetraproline (TTP) polynucleotide.

### Claim 7 (depends on 4)

The method of claim 4, wherein the at least one antisense oligonucleotide targets a nucleic acid sequence comprising coding and/or non-coding nucleic acid sequences of a Tristetraproline (TTP) polynucleotide.

### Claim 8 (depends on 4)

The method of claim 4, wherein the at least one antisense oligonucleotide targets overlapping and/or non-overlapping sequences of a Tristetraproline (TTP) polynucleotide.

### Claim 9 (depends on 4)

The method of claim 4, wherein the at least one antisense oligonucleotide comprises one or more modifications selected from: at least one modified sugar moiety, at least one modified internucleoside linkage, at least one modified nucleotide, and combinations thereof.

### Claim 10 (depends on 9)

The method of claim 9, wherein the one or more modifications comprise at least one modified sugar moiety selected from: a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxy modified sugar moiety, a 2′-O-alkyl modified sugar moiety, a bicyclic sugar moiety, and combinations thereof.

### Claim 11 (depends on 9)

The method of claim 9, wherein the one or more modifications comprise at least one modified internucleoside linkage selected from: a phosphorothioate, 2′-Omethoxyethyl (MOE), 2′-fluoro, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.

### Claim 12 (depends on 9)

The method of claim 9, wherein the one or more modifications comprise at least one modified nucleotide selected from: a peptide nucleic acid (PNA), a locked nucleic acid (LNA), an arabino-nucleic acid (FANA), an analogue, a derivative, and combinations thereof.

### Claim 13 (depends on 1)

The method of claim 1, wherein the at least one oligonucleotide comprises at least one oligonucleotide sequences set forth as SEQ ID NOS: 6 to 10.

### Claim 14

A method of modulating a function of and/or the expression of a Tristetraproline (TTP) gene in mammalian cells or tissues in vivo or in vitro comprising:
contacting said cells or tissues with at least one short interfering RNA (siRNA) oligonucleotide 5 to 30 nucleotides in length, said at least one siRNA oligonucleotide being specific for an antisense polynucleotide of a Tristetraproline (TTP) polynucleotide, wherein said at least one siRNA oligonucleotide has at least 50% sequence identity to a complementary sequence of at least about five consecutive nucleic acids of the antisense and/or sense nucleic acid molecule of the Tristetraproline (TTP) polynucleotide; and, modulating a function of and/or the expression of Tristetraproline (TTP) in mammalian cells or tissues in vive or in vitro.

### Claim 15 (depends on 14)

The method of claim 14, wherein said oligonucleotide has at least 80% sequence identity to a sequence of at least about five consecutive nucleic acids that is complementary to the antisense and/or sense nucleic acid molecule of the Tristetraproline (TTP) polynucleotide.

### Claim 16

A method of modulating a function of and/or the expression of Tristetraproline (TTP) in mammalian cells or tissues in vivo or in vitro comprising:
contacting said cells or tissues with at least one antisense oligonucleotide of about 5 to 30 nucleotides in length specific for noncoding and/or coding sequences of a sense and/or natural antisense strand of a Tristetraproline (TTP) polynucleotide wherein said at least one antisense oligonucleotide has at least 50% sequence identity to at least one nucleic acid sequence set forth as SEQ ID NOS: 1, 3, 4 and 5; and, modulating the function and/or expression of the Tristetraproline (TTP) in mammalian cells or tissues in vivo or in vitro.

### Claim 17

A synthetic, modified oligonucleotide comprising at least one modification wherein the at least one modification is selected from: at least one modified sugar moiety; at least one modified internucleotide linkage; at least one modified nucleotide, and combinations thereof; wherein said oligonucleotide is an antisense compound which hybridizes to and modulates the function and/or expression of a Tristetraproline (TTP) gene in vivo or in vitro as compared to a normal control.

### Claim 18 (depends on 17)

The oligonucleotide of claim 17, wherein the at least one modification comprises an internucleotide linkage selected from the group consisting of: phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.

### Claim 19 (depends on 17)

The oligonucleotide of claim 17, wherein said oligonucleotide comprises at least one phosphorothioate internucleotide linkage.

### Claim 20 (depends on 17)

The oligonucleotide of claim 17, wherein said oligonucleotide comprises a backbone of phosphorothioate internucleotide linkages.

### Claim 21 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide comprises at least one modified nucleotide, said modified nucleotide selected from: a peptide nucleic acid, a locked nucleic acid (LNA), analogue, derivative, and a combination thereof.

### Claim 22 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified nucleotides selected from: phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and a combination thereof.

### Claim 23 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified nucleotides selected from: peptide nucleic acids, locked nucleic acids (LNA), analogues, derivatives, and a combination thereof.

### Claim 24 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide comprises at least one modified sugar moiety selected from: a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxy modified sugar moiety, a 2′-O-alkyl modified sugar moiety, a bicyclic sugar moiety, and a combination thereof.

### Claim 25 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified sugar moieties selected from: a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxy modified sugar moiety, a 2′-O-alkyl modified sugar moiety, a bicyclic sugar moiety, and a combination thereof.

### Claim 26 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide is of at least about 5 to 30 nucleotides in length and hybridizes to an antisense and/or sense strand of a Tristetraproline (TTP) polynucleotide wherein said oligonucleotide has at least about 20% sequence identity to a complementary sequence of at least about five consecutive nucleic acids of the antisense and/or sense coding and/or noncoding nucleic acid sequences of the Tristetraproline (TTP) polynucleotide.

### Claim 27 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide has at least about 80% sequence identity to a complementary sequence of at least about five consecutive nucleic acids of the antisense and/or sense coding and/or noncoding nucleic acid sequence of the Tristetraproline (TTP) polynucleotide.

### Claim 28 (depends on 17)

The oligonucleotide of claim 17, wherein said oligonucleotide hybridizes to and modulates expression and/or function of at least one Tristetraproline (TTP) polynucleotide in vivo or in vitro, as compared to a normal control.

### Claim 29 (depends on 17)

The oligonucleotide of claim 17, wherein the oligonucleotide comprises the sequences set forth as SEQ ID NOS: 6 to 10.

### Claim 30

A composition comprising one or more oligonucleotides specific for one or more Tristetraproline (TTP) polynucleotides, said polynucleotides comprising antisense sequences, complementary sequences, alleles, homologs, isoforms, variants, derivatives, mutants, fragments, or combinations thereof.

### Claim 31 (depends on 30)

The composition of claim 30, wherein the oligonucleotides have at least about 40% sequence identity as compared to any one of the nucleotide sequences set forth as SEQ ID NOS: 6 to 10.

### Claim 32 (depends on 30)

The composition of claim 30, wherein the oligonucleotides comprise nucleotide sequences set forth as SEQ ID NOS: 6 to 10.

### Claim 33 (depends on 32)

The composition of claim 32, wherein the oligonucleotides set forth as SEQ ID NOS: 6 to 10 comprise one or more modifications or substitutions.

### Claim 34 (depends on 33)

The composition of claim 33, wherein the one or more modifications are selected from: phosphorothioate, methylphosphonate, peptide nucleic acid, locked nucleic acid (LNA) molecules, and combinations thereof.

### Claim 35

A method of preventing or treating a disease associated with at least one Tristetraproline (TTP) polynucleotide and/or at least one encoded product thereof, comprising:
administering to a patient a therapeutically effective dose of at least one antisense oligonucleotide that binds to a natural antisense sequence of said at least one Tristetraproline (TTP) polynucleotide and modulates expression of said at least one Tristetraproline (TTP) polynucleotide; thereby preventing or treating the disease associated with the at least one Tristetraproline (TTP) polynucleotide and/or at least one encoded product thereof.

### Claim 36 (depends on 35)

The method of claim 35, wherein a disease associated with the at least one Tristetraproline (TTP) polynucleotide is selected from: tristetraprolin-deficiency syndrome, a cardiovascular disease or disorder, a cardiac injury (e.g., cardiac injury selected from the group of hemodynamic overloading, myocardial reperfusion injury, hypertrophic cardiomyopathy, end-stage congestive heart failure and an ischemic condition or a consequence thereof like myocardial infarction and unstable angina etc.), arthritis, an inflammation, joint and skin inflammation, AIDS, inflammatory bowel disease, Crohn's disease, ulcerative colitis, cancer, obesity, metabolic syndrome, obesity-associated metabolic complications, an autoimmune disease or disorder, cachexia, myeloid hyperplasia, skeletal muscle injury.

### Claim 37

A method of identifying and selecting at least one oligonucleotide for in vivo administration comprising:
selecting a target polynucleotide associated with a disease state; identifying at least one oligonucleotide comprising at least five consecutive nucleotides which are complementary to the selected target polynucleotide or to a polynucleotide that is antisense to the selected target polynucleotide; measuring the thermal melting point of a hybrid of an antisense oligonucleotide and the target polynucleotide or the polynucleotide that is antisense to the selected target polynucleotide under stringent hybridization conditions; and selecting at least one oligonucleotide for in vivo administration based on the information obtained.