Methods for diagnosing colon cancer using MicroRNAs

• US 8,658,362 B2
• Filed: 02/28/2012
• Issued: 02/25/2014
• Est. Priority Date: 01/05/2006
• Status: Active Grant

• Current Assignee: Ohio State University
• Original Assignee: Ohio State University
• Inventors: Croce, Carlo M., Calin, George A., Volinia, Stefano
• Primary Examiner(s): AEDER, SEAN E
• Application Number:
  US13/406,615
• Publication Number:
  US 20120214694A1
• Time in Patent Office: 728 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: A61K 31/7105 Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
• 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 2310/113 targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/141 MicroRNAs, miRNAs
• CPC Class Codes: C12N 2320/11 for the determination of target sites, i.e. of active nucleic acids
• CPC Class Codes: C12N 2320/12 in functional genomics, i.e. for the determination of gene function
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2330/10 naturally occurring
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/178 miRNA, siRNA or ncRNA

Abstract

The present invention provides novel methods and compositions for the diagnosis and treatment of solid cancers. The invention also provides methods of identifying inhibitors of tumorigenesis.

Claims

1. A method of diagnosing whether a subject has, or is at risk for developing, colon cancer, comprising:

extracting a test sample from a subject having, or suspected of having, colon cancer, wherein the sample is extracted from colon tissue;

measuring, by hybridization assay, the level of at least one miR gene product of miR-24-1 in the test sample;

comparing the level of at least one miR-24-1 gene product in the test sample to a control level of at least one corresponding miR gene product;

correlating an increase in the test sample level of miR-24-1 gene product compared to the level of miR-24-1 gene product in the control sample with a subject having, or being at risk for developing, colon cancer; and

diagnosing the subject as having, or being at risk for developing, colon cancer, if the level of the at least one miR gene product in the test sample from the subject is greater than the control level of the corresponding miR gene product;

wherein an increase in the level of miR-24-1 gene product in the test sample, relative to the control level of the at least one corresponding miR gene product, is indicative of the subject having, or being at risk for developing, colon cancer.

2. A method of claim 1, which further comprises:

comparing the level of at least one additional miR gene product in the test sample from the subject to a control level of the miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of;

miR-21;

miR-17-5p;

miR-191;

miR-29b-2;

miR-223;

miR-128b;

miR-199a-1;

miR-24-2;

miR-146;

miR-155;

miR-181b-1;

miR-20a;

miR-107;

miR-32;

miR-92-2;

miR-214;

miR-30c;

miR-25;

miR-221; and

miR-106a.

3. A method of claim 1, which further comprises:

comparing the level of at least one additional miR gene product in the test sample from the subject to a control level of the miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

4. A method of claim 1, which further comprises:

comparing the level of at least two additional miR gene products in the test sample from the subject to a control level of the corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

5. A method of claim 1, which further comprises:

comparing the level of at least three additional miR gene products in the test sample from the subject to a control level of the corresponding miR gene products, wherein the at least three additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

6. A method of claim 1, which further comprises:

comparing the level of at least four additional miR gene products in the test sample from the subject to a control level of the corresponding miR gene products, wherein the at least four additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

7. A method of claim 1, which further comprises:

comparing the level of at least five additional miR gene products in the test sample from the subject to a control level of the corresponding miR gene products, wherein the at least five additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

15. A method of claim 1, further comprising communicating a result of the diagnosing to at least one person.

8. A method of diagnosing whether a subject has, or is at risk for developing, colon cancer, comprising:

obtaining a test sample from a subject having, or suspected of having, colon cancer, wherein the test sample comprises colon tissue;

reverse transcribing at least one miR gene product of miR-24-1 from the test sample to provide at least one corresponding miR gene product target oligonucleotides;

hybridizing target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides that include at least one corresponding to miR-24-1 miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample;

comparing the signal of the at least one miR gene product of miR-24-1 in the test sample hybridization profile to the signal of a corresponding miR-24-1 miRNA in a control hybridization profile;

correlating an increase in the signal of the at least miR-24-1 in the test sample hybridization profile compared to the signal of the corresponding miR-24-1 in the control hybridization profile with a subject having, or being at risk for developing, colon cancer; and

diagnosing the subject as having, or being at risk for developing, colon cancer, if the level of miR gene product of miR-24-1 in the test sample hybridization profile is greater than the level of miR gene product of miR-24-1 in the control hybridization profile;

wherein an increase in the level of miR-24-1 gene product in the test sample, relative to the control level of miR-24-1 gene product, is indicative of the subject having, or being at risk for developing, colon cancer.

9. A method of claim 8, which further comprises:

comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to a control hybridization profile of the miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of;

miR-21;

miR-17-5p;

miR-191;

miR-29b-2;

miR-223;

miR-128b;

miR-199a-1;

miR-24-2;

miR-146;

miR-155;

miR-181b-1;

miR-20a;

miR-107;

miR-32;

miR-92-2;

miR-214;

miR-30c;

miR-25;

miR-221; and

miR-106a.

10. A method of claim 8, which further comprises:

comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to a control hybridization profile of the corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

11. A method of claim 8, which further comprises:

comparing a hybridization profile of at least two additional miR gene products in the test sample from the subject to a control hybridization profile of the corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

12. A method of claim 8, which further comprises:

comparing a hybridization profile of at least three additional miR gene products in the test sample from the subject to a control hybridization profile of the corresponding miR gene products, wherein the at least three additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

13. A method of claim 8, which further comprises:

comparing a hybridization profile of at least four additional miR gene products in the test sample from the subject to a control hybridization profile of the corresponding miR gene products, wherein the at least four additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.

14. A method of claim 8, which further comprises:

comparing a hybridization profile of at least five additional miR gene products in the test sample from the subject to a control hybridization profile of the corresponding miR gene products, wherein the at least five additional miR gene products are selected from the group consisting of;

miR-29b-2;

miR-20a;

miR-10a;

miR-32;

miR-203;

miR-106a;

miR-17-5p;

miR-30c;

miR-223;

miR-126;

miR-128b;

miR-21;

miR-24-2;

miR-99b prec;

miR-155;

miR-213;

miR-150;

miR-107;

miR-191;

miR-221; and

miR-9-3.