Neoplasia diagnostic compositions and methods of use
AssigneeThe Johns Hopkins University
InventorDavid Sidransky
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Abstract
The invention generally features compositions and methods for the diagnosis and monitoring of a neoplasia (e.g., a prostatic neoplasia) in a subject, as well as methods of treatment selection.
Claims41
A method for detecting a neoplasia in a biologic sample, the method comprising quantifying the promoter methylation of at least two promoters in the sample, wherein one of the promoters is pi-class glutathione S-transferase (GSTP1) and the second promoter is selected from the group consisting of O6-methylguanine DNA methyltransferase (MGMT), p14/ARF, p16/INK4a, RAS-associated domain family 1A (RASSFIA), adenomatous polyposis coli (APC), tissue inhibitor of metalloproteinase-3 (TIMP3), S100A2, cellular retinoid binding protein 1 (CRBP1), and retinoic acid receptor β2 (RARβ2), wherein an increased quantity of promoter methylation relative to a reference indicates the presence of a neoplasia in the sample.
3-4. (canceled)
A method of determining the clinical aggressiveness of a neoplasia in a biologic sample, the method comprising quantifying the level of GSTP1 or APC promoter methylation in the sample, wherein an increased level of promoter methylation relative to a reference indicates an increased clinical aggressiveness of the neoplasia.
A method of determining the stage of a neoplasia in a biologic sample, the method comprising quantifying the level of promoter methylation in the sample of at least one promoter selected from the group consisting of GSTP1, APC, RASSF1A, and RARβ2, wherein an increased level of promoter methylation in the sample relative to a reference indicates an increased stage of neoplasia.
8-9. (canceled)
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19-36. (canceled)
A method of determining the prognosis of a subject diagnosed as having a neoplasia, the method comprising quantifying the level of promoter methylation in a sample derived from the subject, wherein at least one promoter is selected from the group consisting of GSTP1, APC, RASSF1A, CRBP1, and RARβ2, and wherein an altered level of promoter methylation relative to a reference indicates the prognosis of the subject.
40-43. (canceled)
A method of monitoring a subject diagnosed as having a neoplasia, the method comprising quantifying the level of promoter methylation in a sample derived from the subject, wherein at least one promoter is selected from the group consisting of GSTP1, APC, RASSF1A, CRBP1, and RARβ2, and wherein an altered level of promoter methylation relative to the level of methylation in a reference indicates an altered severity of neoplasia in the subject.
46-50. (canceled)
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54-57. (canceled)
A method of selecting a treatment for a subject diagnosed as having a neoplasia, the method comprising:
- (a) quantifying the level of promoter methylation in a biologic sample from the subject relative to a reference, wherein the level of promoter methylation is indicative of a treatment;
- and
- (b) selecting a treatment.
A method of selecting a treatment for a subject diagnosed as having prostate cancer, the method comprising:
- (a) quantifying the level of promoter methylation of a promoter selected from the group consisting of GSTP1, APC, RASSF1A, CRBP1, and RARβ2 in a subject sample;
- and
- (b) selecting a treatment for the subject, wherein the treatment is selected from the group consisting of surveillance, surgery, hormone therapy, chemotherapy, and radiotherapy.
A method for determining the methylation profile of a prostate cancer, the method comprising quantifying the level of promoter methylation at two or more promoters selected from the group consisting of GSTP1, APC, RASSF1A, CRBP1, and RARβ2 in a biologic sample, wherein the level of promoter methylation relative to a reference determines the methylation profile of the prostatic neoplasia.
A kit for the analysis of promoter methylation, the kit comprising at least one primer capable of distinguishing between methylated and unmethylated promoter sequences, wherein the promoter sequences are selected from the group consisting of GSTP1, APC, RASSF1A, CRBP1, and RARβ2, and directions for using the primer for the analysis of promoter methylation.
64-68. (canceled)
A microarray comprising at least two nucleic acid molecules, or fragments thereof, bound to a solid support, wherein the two nucleic acid molecules are selected from the group consisting of GSTP1, MGMT, p14/ARF, p16/INK4a, APC, RASSF1A, TIMP3, S100A, CRBP1, and RARβ2.
A primer having a nucleic acid sequence selected from the group consisting of:
- (SEQ ID NO:[[1]]12)
- 5′- TGG TTT CGA TTT TTT GAT TTC G -3′.
- (SEQ ID NO:[[2]]13)
- 5′- TCA AAA TTC TTT TTA CAA CAA CGC C -3′,
- (SEQ ID NO:[[4]]15)
- 5′- CTG GGA ATC CAG CTG TCG CCG CCC CGC A -3′,
- (SEQ ID NO:[[5]]16)
- 5′- GCG CAT CAT AGC CAT CAG CAA CAA A -3′,
- (SEQ ID NO:[[7]]18)
- 5′-CGA GAA CGC GAG CGA TTC -3′,
- (SEQ ID NO:[[8]]19)
- 5′-CAA ACT TAG TCG ACG AAT CCA ACC -3′,
- (SEQ ID NO:[[10]]21)
- 5′-TGG TGA TGG AGG AGG TTT AGT AAG T -3′
- (SEQ ID NO:[[11]]22)
- 5′- AAC CAA TAA AAC CTA CTC CTC CCT TAA -3′.
A probe having a nucleic acid sequence selected from the group consisting of:
- (SEQ ID NO:[[3]]14)
- 5′- CGA CCG AAC GCG ATA ACT TAG TCC -3′-TAMRA,
- (SEQ ID NO:[[6]]17)
- 5′- GAC CCG AAA ATA AAC GCC CTC CGA AAA CA -3′,
- (SEQ ID NO:[[9]]20)
- 5′-TCG GAA CGT ATT CGG AAG GTT TTT TGT AAG TAT
- TT -3′,
- (SEQ ID NO:[[12]]23)
- 5′-ACC ACC ACC CAA CAC ACA ATA ACA AAC ACA-3′.
A collection of primer sets, each of said primer sets comprising at least two primers that bind to a promoter selected from the group consisting of GSTP1, MGMT, p14/ARF, p16/INK4a, APC, RASSF1A, TIMP3, S100A, CRBP1, and RARβ2, said collection comprising at least two primer sets.
Dependencies are inferred from the claim text.