Methods and compositions for detecting colon cancers
View Patent ↗This application describes methods and compositions for detecting and treating HLTF-associated neoplasia. Differential methylation of the HLTF nucleotide sequences has been observed in HLTF-associated neoplasia such as colon neoplasia.
1. A method for detecting differential methylation patterns in an HLTF nucleotide sequence, comprising:
a) obtaining a sample from a patient;
b) assaying said sample for the presence of methylation within the nucleotide sequence as set forth in SEQ ID NO: 2;
c) obtaining a sample from a healthy subject;
d) assaying for the presence of methylation in the nucleotide sequence as set forth in SEQ ID NO: 2; and
e) comparing the methylation patterns in the sample from the patient to the methylation patterns in the sample from the healthy subject.
2. A method for detecting colon or gastro-intestinal neoplasia, comprising:
a) obtaining a sample from a patient; and
b) assaying said sample for the presence of methylation within the nucleotide sequence as set forth in SEQ ID NO: 2;
wherein methylation of said nucleotide sequence is indicative of colon or nastro-intestinal neoplasia.
3. The method of any one of claims 1 or 2 , wherein the sample is a bodily fluid selected from the group consisting of blood, serum, plasma, a blood-derived fraction, stool, urine, and a colonic effluent.
4. The method of claim 3 , wherein the bodily fluid is obtained from a subject suspected of having or is known to have colon or gastro-intestinal neoplasia.
5. The method of claim 2 , wherein said method is for detecting colon neoplasia.
6. The method of any of claims 1 or 2 , wherein the assay is methylation-specific PCR.
7. The method of claim 6 , comprising:
a) treating DNA fiom the sample with a compound that converts non-methylated cytosine bases in the DNA to a different base;
b) amplifying a region of the compound converted HLTF nucleotide sequence with a forward primer and a reverse primer; and
c) analyzing the methylation patterns of said HLTF nucleotide sequences.
8. The method of claim 6 , comprising:
a) treating DNA from the sample with a compound that converts non-methylated cytosine bases in the DNA to a different base;
b) amplifying a region of the compound converted HLTF nucleotide sequence with a forward primer and a reverse primer; and
c) detecting the presence and/or amount of the amplified product.
9. The method of claim 6 , wherein the compound used to treat DNA is a bisulfite compound.
10. The method of any of claims 1 or 2 , wherein the assay comprises digesting DNA from the sample with a methylation-specific restriction enzyme.
11. The method of claim 10 , wherein said methylation-specific restriction enzyme is selected from HpaII, SmaI, SacII, EagI, MspI, BstUI, and BssHII.
12. A method for detecting colon or gastro-intestinal neoplasia in a subject, comprising detecting the level of a HLTF protein set forth in SEQ ID NO: 1 or a nucleic acid which encodes SEQ ID NO: 1 in a sample from the subject, wherein decreased level of the HLTF protein or nucleic acid relative to a control sample is indicative of colon or gastro-intestinal neoplasia.
13. The method of claim 12 , wherein the sample is a bodily fluid selected from the group consisting of blood, serum, plasma, a blood-derived fraction, stool, urine, and a colonic effluent.
14. The method of claim 13 , wherein the bodily fluid is from a subject suspected of having or known to have colon or gastro-intestinal neoplasia.
15. The method of claim 12 , wherein said method is for detecting colon neoplasia.