Measuring a level of a 5-hydroxymethylcytosine in a sample from a subject having a cancer or suspected of having cancer

• US 10,041,938 B2
• Filed: 02/23/2017
• Issued: 08/07/2018
• Est. Priority Date: 09/26/2008
• Status: Active Grant

• Current Assignee: Children's Medical Center Corporation, United States Department Of Health And Human Services (Government of the United States of America)
• Original Assignee: Children's Medical Center Corporation, United States Department Of Health And Human Services (Government of the United States of America)
• Inventors: Rao, Anjana, Tahiliani, Mamta, Koh, Kian Peng, Agarwal, Suneet, Iyer, Aravind
• Primary Examiner(s): Dauner, Joseph G.
• Application Number:
  US15/440,826
• Publication Number:
  US 20180120304A1
• Time in Patent Office: 530 Days
• Field of Search: None
• CPC Class Codes: C12N 2501/70 Enzymes
• CPC Class Codes: C12N 2501/71 Oxidoreductases (EC 1.)
• CPC Class Codes: C12N 2501/724 Glycosyltransferases (EC 2.4.)
• CPC Class Codes: C12N 9/0071 acting on paired donors with incorporation of molecular oxygen (1.14)
• CPC Class Codes: C12N 9/1007 Methyltransferases (general) (2.1.1.)
• CPC Class Codes: C12Q 1/26 involving oxidoreductase
• 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 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/531 Glycosylase
• CPC Class Codes: C12Q 2522/10 Nucleic acid binding proteins
• CPC Class Codes: C12Q 2537/164 Methylation detection other then bisulfite or methylation sensitive restriction endonucleases
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: G01N 2500/00 Screening for compounds of potential therapeutic value
• CPC Class Codes: G01N 33/5011 for testing antineoplastic activity
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Abstract

Provided herein are methods and kits for measuring a level of a 5-hydroxymethylcytosine in a nucleotide sequence from a subject, wherein the subject is a subject having a cancer or suspected of having cancer.

Claims

1. A method comprising:

a) measuring a level of a 5-hydroxymethylcytosine in a nucleotide sequence from a subject, wherein the subject is a subject having a cancer or suspected of having cancer; and

b) comparing the level of the 5-hydroxymethylcytosine in the nucleotide sequence from the subject to a level of a 5-hydroxymethylcytosine in a control sample.

2. The method of claim 1, wherein the measuring comprises contacting a glucose or glucose derivative donor substrate to the 5-hydroxymethylcytosine in the nucleotide sequence.

3. The method of claim 2, wherein the glucose or glucose derivative donor substrate comprises a label or a tag.

4. The method of claim 2, wherein the glucose derivative donor substrate comprises uridine diphosphate glucose (UDPG).

5. The method of claim 1, wherein the measuring comprises contacting an agent to the 5 hydroxymethylcytosine in the nucleotide sequence, wherein the agent comprises an antibody, an antigen-binding portion thereof, an intrabody, or a protein.

6. The method of claim 5, wherein the agent selectively binds to the 5-hydroxymethylcytosine in the nucleotide sequence.

7. The method of claim 5, wherein the agent is engineered to increase its binding affinity or selectivity for 5-hydroxymethylcytosine.

8. The method of claim 5, wherein the agent comprises a label or a tag.

9. The method of claim 1, wherein the measuring comprises imaging analysis or mass spectrometry.

10. The method of claim 1, wherein the measuring comprises a thin-layer chromatography, a blotting assay or a linked enzyme mediated substrate conversion.

11. The method of claim 1, wherein the nucleotide sequence is obtained from a tissue sample of the subject.

12. The method of claim 11, wherein the tissue sample comprises bone marrow.

13. The method of claim 11, wherein the tissue sample comprises a diseased tissue sample.

14. The method of claim 1, wherein the control sample is a normal control sample, and wherein a difference between the level of 5-hydroxymethylcytosine in the nucleotide sequence and the level of 5-hydroxymethylcytosine in the normal control sample is indicative of the subject having the cancer.

15. The method of claim 1, wherein a difference between the level of 5-hydroxymethylcytosine in the nucleotide sequence and the level of 5-hydroxymethylcytosine in the control sample provides a likelihood of the subject having the cancer.

16. The method of claim 1, wherein the control sample comprises a diseased tissue or a diseased cell, and wherein the level of 5-hydroxymethylcytosine in the nucleotide sequence that is similar to the level of 5-hydroxymethylcytosine in the control sample is indicative of the subject having the cancer.

17. The method of claim 1, wherein the level of the 5-hydroxymethylcytosine in the nucleotide sequence from the subject is higher than the level of the 5-hydroxymethylcytosine in the control sample.

18. The method of claim 1, wherein the level of the 5-hydroxymethylcytosine in the nucleotide sequence from the subject is lower than the level of the 5-hydroxymethylcytosine in the control sample.

19. The method of claim 1, further comprising treating the subject.