Methods and compositions involving microRNA

• US 7,919,245 B2
• Filed: 08/11/2007
• Issued: 04/05/2011
• Est. Priority Date: 05/28/2004
• Status: Expired due to Fees

• Current Assignee: Asuragen, Inc.
• Original Assignee: Asuragen, Inc.
• Inventors: Keiger, Kerri, Brown, David, Labourier, Emmanuel, Shingara, Jaclyn, Shelton, Jeffrey
• Primary Examiner(s): Chong; Kimberly
• Application Number:
  US11/837,495
• Publication Number:
  US 20080026951A1
• Time in Patent Office: 1,333 Days
• Field of Search: None
• US Class Current: 435/5
• 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/3517 Marker; Tag
• CPC Class Codes: C12N 2310/3519 Fusion with another nucleic acid
• CPC Class Codes: C12N 2320/10 in screening processes
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2525/207 siRNA, miRNA
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2600/158 Expression markers
• 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

The present invention concerns methods and compositions for isolating, enriching, and/or labeling miRNA molecules and for preparing and using arrays or other detection techniques for miRNA analysis. Moreover, the present invention concerns methods and compositions for generating miRNA profiles and employing such profiles for therapeutic, diagnostic, and prognostic applications.

Claims

1. A method for identifying a patient as having a marker correlated with lung cancer based on an increase in miR-21 expression comprising:

a) analyzing miR-21 expression in a lung sample from a patient suspected of having lung cancer; and

,

b) identifying the patient as i) having a marker correlated with lung cancer if an increase in miR-21 expression compared to a noncancerous lung sample is detected in the lung sample or ii) as not having a marker correlated with lung cancer if the increase fails to be detected.

2. The method of claim 1, wherein analyzing the lung sample from the patient comprises generating an miRNA profile from the patient'"'"'s lung sample comprising:

(a) labeling the miRNA isolated from the patient'"'"'s lung sample;

(b) hybridizing the miRNA to an miRNA array; and

,

(c) determining miRNA hybridization to the array.

3. The method of claim 1, further comprising analyzing the sample for a decrease in let-7, miR-30a-AS, miR-95, miR-125a, miR-126, miR-331, or miR-342 or for an increase in miR-200b or miR-205 compared to a noncancerous lung sample.

6. The method of claim 2, further comprising treating the patient for lung cancer after the patient is identified as having a marker correlated with lung cancer.

4. A method for identifying a patient as having a marker correlated with lung cancer based on an increase in miR-21 expression comprising:

a) obtaining from a patient a lung sample, wherein the patient is suspected of having lung cancer; and

,

b) identifying the patient, based on a determination of the lung sample, as i) having a marker correlated with lung cancer if there is an increase in miR-21 expression in the sample compared to a noncancerous lung sample or ii) as not having a marker correlated with lung cancer if the increase fails to be detected.

5. The method of claim 4, wherein the determination of the lung sample from the patient comprises generating an miRNA profile from the sample comprising:

(a) labeling the miRNA isolated from the patient'"'"'s lung sample;

(b) hybridizing the miRNA to an miRNA array; and

,

(c) determining miRNA hybridization to the array.

7. A method for identifying a patient as having a marker correlated with lung cancer based on an increase in miR-21 expression comprising:

a) analyzing miR-21 expression in a lung sample from a patient suspected of having lung cancer; and

,

b) identifying the patient as having a marker correlated with lung cancer if an increase in miR-21 expression of at least 50% in the patient'"'"'s lung sample compared to a noncancerous lung sample is determined;

or identifying the patient as not having a marker correlated with lung cancer if the increase is not determined.

8. The method of claim 7, wherein analyzing the patient'"'"'s lung sample comprises generating an miRNA profile from the patient'"'"'s lung sample comprising:

(a) labeling the miRNA isolated from the patient'"'"'s lung sample;

(b) hybridizing the miRNA to an miRNA array; and

,

(c) determining miRNA hybridization to the array.

9. The method of claim 7, further comprising analyzing the sample for a decrease in let-7, miR-30a-AS, miR-95, miR-125a, miR-126, miR-331, or miR-342 and/or an increase in miR-200b or miR-205 compared to a noncancerous lung sample.

10. A method for identifying a patient as having lung cancer cells based on an increase in miR-21 expression comprising:

a) obtaining a lung sample from a patient suspected of having lung cancer; and

,

b) identifying the patient as having lung cancer cells if an increase in miR-21 expression in the patient'"'"'s lung sample compared to a noncancerous lung sample is determined or identifying the patient as not having a marker for lung cancer if the increase is not determined.

11. The method of claim 10, further comprising analyzing the patient'"'"'s lung sample for an increase in miR-21 expression compared to a noncancerous lung sample.

12. The method of claim 11, wherein analyzing the lung sample from the patient comprises generating an miRNA profile from the patient'"'"'s lung sample comprising:

(a) labeling the miRNA isolated from the patient'"'"'s lung sample;

(b) hybridizing the miRNA to an miRNA array; and

,

(c) determining miRNA hybridization to the array.

13. The method of claim 10, wherein an increase in miR-21 is determined based on the generation of an miRNA profile.