Methods and compositions for detecting gastrointestinal and other cancers
This application describes methods and compositions for detecting and treating vimentin-associated neoplasia. Differential methylation of the vimentin nucleotide sequences has been observed in vimentin-associated neoplasia such as neoplasia of the upper or lower gastrointestinal tract, pancreas, and/or bladder.
1. A method for determining vimentin methylation in a human subject, comprising assaying a vimentin nucleic acid in a sample obtained from a subject for the presence or absence of methylation within a sequence that is at least 95% identical to any one of SEQ ID NOs: 2 and 40-45 or a fragment thereof, wherein said fragment is 15, 20, 25, 50, 100, or 150 base pairs in length; wherein the sample was obtained from a subject suspected of having or that is known to have an esophageal neoplasia.
2. The method of claim 1 , wherein the sample is obtained from an esophageal brushing.
3. The method of claim 1 , wherein the esophageal neoplasia is Barrett's esophagus or Barrett's esophagus with high grade dysplasia.
4. The method of claim 1 , wherein said esophageal neoplasia is adenocarcinoma of the esophagus.
5. The method of claim 1 , wherein the assay comprises methylation-specific PCR.
6. The method of claim 5 , 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 vimentin nucleotide sequence with a forward primer and a reverse primer; and c) analyzing the methylation patterns of said vimentin nucleotide sequences.
7. The method of claim 5 , 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 vimentin nucleotide sequence with a forward primer and a reverse primer; and c) detecting the presence and/or amount of the amplified product.
8. The method of claim 5 , wherein the compound used to treat DNA is a bisulfite compound.
9. The method of claim 1 , wherein the assay comprises using a methylation-specific restriction enzyme.
10. The method of claim 9 , wherein said methylation-specific restriction enzyme is selected from HpaII, SmaI, SacII, EagI, MspI, BstUI, and BssHII.
11. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 2 or a fragment thereof.
12. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 40 or a fragment thereof.
13. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 41 or a fragment thereof.
14. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 42 or a fragment thereof.
15. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 43 or a fragment thereof.
16. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 44 or a fragment thereof.
17. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is at least 95% identical to SEQ ID NO: 45 or a fragment thereof.
18. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 2 or a fragment thereof.
19. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 40 or a fragment thereof.
20. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 41 or a fragment thereof.
21. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 42 or a fragment thereof.
22. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 43 or a fragment thereof.
23. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 44 or a fragment thereof.
24. The method of claim 1 , wherein the presence or absence of methylation is assayed within a nucleotide sequence that is SEQ ID NO: 45 or a fragment thereof.