Detection of bladder cancer
Provided are methods for detecting bladder cancer in a subject. In some aspects, methylation of one or more of MYO3A, CA10, NKX6-2, SOX11, DBC1, NPTX2, and/or A2BP1 in DNA sediment from a urine sample may be evaluated to detect the presence or absence of a bladder cancer in a human patient.
1. A method of detecting the presence of, or an increased risk of, a bladder cancer in a subject, comprising the steps of:
a) obtaining a biological sample from the subject comprising genomic DNA from the subject's bladder; and
b) testing the genomic DNA using a DNA methylation assay by detecting or measuring the methylation status of at least three genes therein selected from the group of genes consisting of MYO3A, CA10, NKX6-2, SOX11, DBC1, NPTX2;
c) determining the methylation status of the genes tested in step b) in a control sample comprising genomic DNA from normal bladder;
d) comparing the methylation status of the genes tested in step b) to the methylation status of genes tested in step c) to determine whether the methylation status of the one or more of the genes determined in step b) is at least 10% higher than the methylation status determined for the genes tested in step c);
wherein if the methylation status of one or more of the genes tested in step b) is at least 10% higher than that of one or more genes tested in step c), then the subject has, or has an increased risk of having, bladder cancer as compared to subjects that do not exhibit such a methylation status in at least one of the genes so tested.
2. The method of claim 1 , wherein said detecting or measuring comprises detecting or measuring methylation in MYO3A, CA10, and NKX6-2.
3. The method of claim 2 , wherein said detecting or measuring further comprises detecting or measuring methylation in SOX11.
4. The method of claim 2 , wherein said detecting or measuring further comprises detecting or measuring methylation in PENK.
5. The method of claim 1 , wherein said detecting or measuring comprises detecting or measuring methylation in at least four of MYO3A, CA10, NKX6-2, SOX11, DBC1.
6. The method of claim 5 , wherein said detecting or measuring comprises detecting or measuring methylation in MYO3A, CA10, NKX6-2, and DBC1.
7. The method of claim 6 , wherein said detecting further comprises detecting or measuring methylation in SOX11.
8. The method of claim 6 , wherein said detecting further comprises detecting or measuring methylation in PENK.
9. The method of claim 6 , wherein said detecting or measuring comprises detecting or measuring methylation in MYO3A, SOX11, CA10, DBC1, PENK, and NKX6-2.
10. The method of claim 1 , wherein the subject is a mammal.
11. The method of claim 10 , wherein the mammal is a human.
12. The method of claim 1 , wherein the biological sample comprises a urine sample, bladder cells, bladder tissue, or DNA from or derived from urine sediment.
13. The method of claim 12 , wherein the biological sample comprises DNA from or derived from urine sediment.
14. The method of claim 1 , wherein the bladder cancer comprises a papillary tumor.
15. The method of claim 1 , wherein the bladder cancer comprises a non-papillary tumor.
16. The method of claim 1 , wherein the method further comprises a method of measuring the aggressiveness of the bladder cancer.
17. The method of claim 1 , wherein a personalized therapy is administered to the subject.
18. The method of claim 17 , wherein the personalized therapy is a chemotherapeutic, an immunotherapy, a radiotherapy, or a surgery.
19. The method of claim 1 , wherein the method further comprises monitoring the effectiveness of a therapy that is administered to the subject.
20. The method of claim 1 , wherein the detecting or measuring comprises a method selected from the group consisting of methylation specific polymerase chain reaction (PCR-MSP), real-time methylation specific PCR, methylation-sensitive single-strand conformation analysis (MS-SSCA), quantitative methylation specific PCR (QMSP), polymerase chain reaction (PCR) using a methylated DNA-specific binding protein, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), base-specific cleavage/matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF), PCR, real-time PCR, Combined Bisulfite Restriction Analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), a microarray-based method, pyrosequencing, and bisulfite sequencing.
21. The method of claim 20 , wherein the detecting or measuring comprises methylation specific polymerase chain reaction (PCR), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), or bisulfite sequencing.
22. The method of claim 1 , wherein the detecting or measuring comprises reduced representation bisulfite sequencing (RRBS), methyl beads, emulsion, amplification and magnetics (methyl-BEAMing), or fluorescence resonance energy transfer (FRET) technique for detection of DNA methylation.