Antisense composition and method for treating cancer

• US 20050261249A1
• Filed: 03/10/2005
• Published: 11/24/2005
• Est. Priority Date: 03/12/2004
• Status: Active Grant

• Current Assignee: Avi Biopharma, Inc.
• Original Assignee: Avi Biopharma, Inc.
• Inventors: Iversen, Patrick L., Bestwick, Richard K., Roy, Hemant K.
• Granted Patent: US 7,402,574 B2
• Time in Patent Office: Days
• US Class Current: 514/81
• CPC Class Codes: A01K 2217/075 inducing loss of function, i.e. knock out
• CPC Class Codes: A01K 2227/105 Murine
• CPC Class Codes: A01K 2267/0331 Animal model for proliferative diseases
• CPC Class Codes: A01K 67/0276 Knock-out vertebrates
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: 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
• CPC Class Codes: C12N 15/8509 for producing genetically modified animals, e.g. transgenic
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/3145 with the nitrogen in 3' or 5'-position
• CPC Class Codes: C12N 2310/3233 Morpholino-type ring

Abstract

A method and composition for of treating cancer, and in particular, for arresting the progression of a solid or primary cancer to a more invasive, metastatic state, are disclosed. The composition includes a substantially uncharged antisense compound (i) having a nuclease-resistant backbone, (ii) capable of uptake by target cancer cells in the subject, (iii) containing between 10-40 nucleotide bases, and (iv) having a base sequence effective to hybridize to a region of processed or preprocessed human SNAIL RNA transcript. The compound, when administered to the subject, is effective to form within target cancer cells in the subject, a base-paired heteroduplex structure composed of human SNAIL RNA transcript and the oligonucleotide compound, where this structure is characterized by a Tm of dissociation of at least 45° C. The compound is administered in an amount sufficient to inhibit SNAIL expression in target cancer cells, thereby to inhibit the progression of the patient'"'"'s cancer to a more invasive, metastatic state. Also disclosed are methods for preventing the transdifferentiation of peritoneal mesothelial cells and failure of ultrafiltration in a patient undergoing peritoneal dialysis, by including the compound in the patient dialysis fluid.

Claims

1. A method of treating cancer in a subject, comprising

(a) administering to the subject a therapeutically effective dose of a substantially uncharged antisense compound (i) having a nuclease-resistant backbone, (ii) capable of uptake by target cancer cells in the subject, (iii) containing between 10-40 nucleotide bases, and (iv) having a base sequence effective to hybridize to a region of processed or preprocessed human SNAIL RNA transcript, identified, in its preprocessed form, by SEQ ID NO:

21, and

(b) by said administering, forming within target cancer cells in the subject, a base-paired heteroduplex structure composed of human SNAIL RNA transcript and the oligonucleotide compound, where

(1) said structure is characterized by a Tm of dissociation of at least 45°

C., and

(2) the amount of compound administered is sufficient to inhibit SNAIL expression in target cancer cells, thereby to inhibit the progression of the patient'"'"'s cancer to a more invasive, metastatic state.

2. The method of claim 1, wherein the compound administered is composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5′

exocyclic carbon of an adjacent subunit.

3. The method of claim 2, wherein the morpholino subunits in the compound administered are joined by phosphorodiamidate linkages, in accordance with the structure:

4. The method of claim 1, wherein the compound administered as a conjugate of the compound and an arginine-rich polypeptide effective to promote uptake of the compound into target cells.

5. The method of claim 4, wherein the arginine rich peptide has one of the sequences identified as SEQ ID NOS:

22-24. (R9F2C, R5F2R4C, (RAhxR)₄).

6. The method of claim 4, arginine-rich peptide is covalently coupled at its C terminus to the 3′

end of the antisense compound.

7. The method of claim 1, wherein the compound administered is effective to target the start site of the processed SNAIL transcript, and has a base sequence that is complementary to a target region containing at least 12 contiguous bases in a processed human SNAIL transcript, and which includes at least 6 contiguous bases of the sequence selected from the group consisting of:

SEQ ID NOS;

1-6.

8. The method of claim 7, wherein the compound administered includes a base sequence selected from the group consisting of SEQ ID NOS:

11-16.

9. The method of claim 1, wherein the compound administered is effective to target a splice site of preprocessed human SNAIL transcript, and has a base sequence that is complementary to a target region containing at least 12 contiguous bases in a preprocessed human SNAIL transcript, and which includes at least 6 contiguous bases of the sequence selected from the group consisting of:

SEQ ID NOS;

7-10.

10. The method of claim 9, wherein the antisense compound that is administered includes a base sequence selected from the group consisting of:

SEQ ID NOS;

17-20.

11. The method of claim 1, which further includes administering a non-oliogomeric chemotherapeutic compound to the subject.

12. The method of claim 11, wherein said administering is carried out for a selected period of at least 1-3 weeks.

13. An antisense composition comprising

a substantially uncharged antisense compound (i) having a nuclease-resistant backbone, (ii) capable of uptake by target cancer cells in the subject, (iii) containing between 10-40 nucleotide-bases, and (iv) having and a base sequence effective to hybridize to a region of processed or preprocessed human SNAIL RNA transcript, identified, in its preprocessed form, by SEQ ID NO:

21, where

the compound is effective to form a base-paired heteroduplex structure composed of human SNAIL RNA transcript and the oligonucleotide compound, and characterized by a Tm of dissociation of at least 45°

C.

14. The composition of claim 13, wherein the compound is composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5′

exocyclic carbon of an adjacent subunit.

15. The composition of claim 14, wherein the morpholino subunits in the compound are joined by phosphorodiamidate linkages, in accordance with the structure:

16. The composition of claim 15, which is a conjugate of the compound and an arginine-rich polypeptide effective to promote uptake of the compound into target cells.

17. The composition of claim 16, wherein the arginine rich peptide has one of the sequences identified as SEQ ID NOS:

22-24. (R9F2C, R5F2R4C, (RAhxR)₄).

18. The composition of claim 15, wherein arginine-rich peptide is covalently coupled at its C terminus to the 3′

end of the compound.

19. The composition of claim 13, wherein the compound is effective to target the start site of the processed SNAIL transcript, and has a base sequence that is complementary to a target region containing at least 12 contiguous bases in a processed human SNAIL transcript, and which includes at least 6 contiguous bases of the sequence selected from the group consisting of:

SEQ ID NOS;

1-6.

20. The composition of claim 19, wherein the compound includes a base sequence selected from the group consisting of SEQ ID NOS:

11-16.

21. The composition of claim 13, wherein the compound is effective to target a splice site of preprocessed human SNAIL transcript, and has a base sequence that is complementary to a target region containing at least 12 contiguous bases in a preprocessed human SNAIL transcript, and which includes at least 6 contiguous bases of the sequence selected from the group consisting of:

SEQ ID NOS;

7-10.

22. The composition of claim 21, wherein the antisense compound that is administered includes a base sequence selected from the group consisting of:

SEQ ID NOS;

17-20.

23. The composition of claim 13 for use in inhibiting the progression of a cancer to an invasive, which further includes a pharmaceutically acceptable vehicle for administering the compound to the patient.

24. The composition of claim 13, for use in preventing the transdifferentiation of peritoneal mesothelial cells and failure of ultrafiltration in patients undergoing peritoneal dialysis, wherein said composition includes a sterile vehicle suitable for addition of the compound to dialysis fluid.

25. A method for inhibiting or preventing the transdifferentiation of peritoneal mesothelial cells and failure of ultrafiltration in a patient undergoing peritoneal dialysis, comprising

(a) adding to the dialysis fluid of the patient, during a peritoneal dialysis procedure, a sterile solution of a substantially uncharged antisense compound (i) having a nuclease-resistant backbone, (ii) capable of uptake by target cancer cells in the subject, (iii) containing between 10-40 nucleotide bases, and (iv) having and a base sequence effective to hybridize to a region of processed or preprocessed human SNAIL RNA transcript, identified, in its preprocessed form, by SEQ ID NO:

21, and

(b) by said adding, forming within target mesothelial cells in the patient, a base-paired heteroduplex structure composed of human SNAIL RNA transcript and the oligonucleotide compound, where

(1) said structure is characterized by a Tm of dissociation of at least 45°

C., and

(2) the amount of compound added is sufficient to inhibit SNAIL expression in target mesothelial cells, thereby to inhibit or prevent the transdifferentiation of peritoneal mesothelial cells in the patient.

26. The method of claim 25, wherein said adding is carried out each time the patient undergoes a peritioneal dialysis procedure.