Micrornas and uses thereof

• US 20070050146A1
• Filed: 05/16/2005
• Published: 03/01/2007
• Est. Priority Date: 05/14/2004
• Status: Active Grant

• Current Assignee: Rosetta Genomics Limited (Rosetta Genomics)
• Original Assignee: Rosetta Genomics Limited (Rosetta Genomics)
• Inventors: Bentwich, Itzhak, Avniel, Amir, Aharonov, Ranit, Karov, Yael
• Granted Patent: US 7,709,616 B2
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/141 MicroRNAs, miRNAs
• CPC Class Codes: C12N 2310/531 Stem-loop; Hairpin
• CPC Class Codes: C12N 2320/10 in screening processes
• CPC Class Codes: C12N 2320/11 for the determination of target sites, i.e. of active nucleic acids
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2330/10 naturally occurring
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/178 miRNA, siRNA or ncRNA
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Described herein are novel polynucleotides associated with prostate and lung cancer. The polynucleotides are miRNAs and miRNA precursors. Related methods and compositions that can be used for diagnosis, prognosis, and treatment of those medical conditions are disclosed. Also described herein are methods that can be used to identify modulators of prostate and lung cancer.

Claims

1. An isolated nucleic acid comprising a sequence selected from the group consisting of:

(a) the sequence of a hairpin referred to in Table 1;

(b) the sequence of sequence identifiers 6757248-6894882 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572;

(c) the sequence of sequence identifiers 1-6318 or 18728-18960 of the Sequence Listing of U.S. Provisional Patent Application No. 60/655,094;

(d) the sequence of a miRNA referred to in Table 1;

(e) the sequence of sequence identifiers 1-117750 or 6894883-10068177 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572;

(f) the sequence of sequence identifiers 6319-18727 or 18961-19401 of the Sequence Listing of U.S. Provisional Patent Application No. 60/655,094;

(g) the sequence of a target gene binding site referred to in Table 4;

(h) the sequence of sequence identifiers 117751-6757247 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572;

(i) complement of (a)-(h);

(j) nucleotide sequence comprising at least 12 contiguous nucleotides at least 60% identical to (a)-(h);

wherein the nucleic acid is from 5-250 nucleotides in length.

2. A probe comprising the nucleic acid of claim 1.

3. The probe of claim 2 wherein the nucleic acid comprises at least 8-22 contiguous nucleotides complementary to a miRNA referred to in Table 2 as differentially expressed in prostate cancer or lung cancer.

4. A plurality of probes of claim 3.

5. The plurality of probes of claim 4 comprising at least one probe complementary to each miRNA referred to in Table 2 as differentially expressed in prostate cancer.

6. The plurality of probes of claim 4 comprising at least one probe complementary to each miRNA referred to in Table 2 as differentially expressed in lung cancer.

7. A composition comprising the plurality of probes of claim 3.

8. A biochip comprising a solid substrate, said substrate comprising a plurality of probes of claim 3, wherein each probe is attached to the substrate at a spatially defined address.

9. The biochip of claim 8 wherein the probes are complementary to a miRNA referred to in Table 2 as differentially expressed in prostate cancer.

10. The biochip of claim 8 wherein the probes are complementary to a miRNA referred to in Table 2 as differentially expressed in lung cancer.

17. A method of treating a patient with a disorder set forth on Table 6 comprising administering to a patient in need thereof a composition comprising the nucleic acid of claim 1.

11. A method for detecting differential expression of a miRNA comprising:

(a) providing a biological sample; and

(b) measuring the level of a nucleic acid at least 70% identical to (i) a sequence of a miRNA referred to in Table 1, (ii) the sequence of sequence identifiers 1-117750 or 6894883-10068177 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572, (iii) the sequence of sequence identifiers 6319-18727 or 18961-19401 of the Sequence Listing of U.S. Provisional Patent Application No. 60/655,094, or (iv) a variant of (i)-(iii),

wherein a difference in the level of the nucleic acid compared to a control is indicative of differential expression.

12. A method for identifying a compound that modulates expression of a miRNA:

(a) providing a cell that is capable of expressing a nucleic acid at least 70% identical to (i) a sequence of a miRNA referred to in Table 1, (ii) the sequence of sequence identifiers 1-117750 or 6894883-10068177 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572, (iii) the sequence of sequence identifiers 6319-18727 or 18961-19401 of the Sequence Listing of U.S. Provisional Patent Application No. 60/655,094, or (iv) a variant of (i)-(iii);

(b) contacting the cell with a candidate modulator; and

(c) measuring the level of expression of the nucleic acid,

wherein a difference in the level of the nucleic acid compared to a control identifies the compound as a modulator of expression of the miRNA.

14. The method of claim 12 wherein expression is inhibited in vitro or in vivo.

13. A method of inhibiting expression of a target gene in a cell comprising introducing a nucleic acid into the cell in an amount sufficient to inhibit expression of the target gene, wherein the target gene comprises a (i) binding site substantially identical to a binding site referred to in Table 4, (ii) sequence of sequence identifiers 117751-6757247 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572, or (iii) a variant of (i) or (ii);

and wherein the nucleic acid comprises a sequence (a) of SEQ ID NOS;

1-760616, (b) sequence of sequence identifiers 1-117750 and 6757248-10068177 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572, (c) a sequence set forth on the Sequence Listing of U.S. Provisional Patent Application No. 60/655,094, or (d) a variant of (a)-(c).

15. A method of increasing expression of a target gene in a cell comprising introducing a nucleic acid into the cell in an amount sufficient to increase expression of the target gene, wherein the target gene comprises a (i) binding site substantially identical to a binding site referred to in Table 4, (ii) sequence of sequence identifiers 117751-6757247 of the Sequence Listing of U.S. patent application Ser. No. 10/709,572, or (iii) a variant of (i) or (ii);

wherein the nucleic acid comprises a sequence substantially complementary to a sequence (a) of SEQ ID NOS;

1-760616, (b) set forth on the Sequence Listing of U.S. patent application Ser. No. 10/709,572, (c) a sequence set forth on the Sequence Listing of U.S. Provisional Patent Application No. 60/655,094, or (d) a variant of (a)-(c).

16. The method of claim 15 wherein expression is inhibited in vitro or in vivo.