Carbonic anhydrase IX-related markers and use thereof

1. A method for treating cancer in a human patient, comprising:

(A) isolating a cancer sample from a human patient,

(B) performing an assay to detect the presence of cancer stem cells in the cancer sample, comprising:

(a) measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of at least six markers in the cancer sample, wherein the at least six markers are:

(1) a cancer stem cell marker that is CAIX,

(2) a mesenchymal marker that is smooth muscle actin,

(3) an epithelial marker that is E-cadherin,

(4) a stemness marker that is Notch 1,

(5) an mTORC1 marker that is mTOR, and

(6) a chemokine marker that is Granulocyte-Colony Stimulating Factor (G-CSF);

(b) comparing the level of each of the at least six markers measured in step (a) with a reference level for each of the at least six markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample;

(c) identifying the cancer sample as containing cancer stem cells if based on the comparing of step (b), an increase in the levels of the cancer stem cell marker, the mesenchymal marker, the stemness marker, the mTORC1 marker, and the chemokine marker and a decrease in the level of the epithelial marker are detected in the cancer sample; and

(B) administering to the human patient an effective amount of a carbonic anhydrase IX (CAIX) inhibitor.

2. The method of claim 1 , wherein the CAIX inhibitor is one of the compounds having the following structures:

and

3. The method of claim 1 , further comprising administering an effective amount of an antiangiogenic agent or a chemotherapeutic agent to the patient.

4. The method of claim 3 , wherein the chemotherapeutic agent is taxane.

5. The method of claim 1 , wherein step (a) comprises measuring the protein modification level(s) of one or more of the at least six markers.

6. The method of claim 1 , wherein step (a) comprises measuring the gene transcription level(s) of one or more of the at least six markers.

7. The method of claim 1 , wherein step (a) comprises measuring the protein expression level(s) of one or more of the at least six markers.

8. The method of claim 7 , wherein step (a) comprises measuring the level of the chemokine marker secreted by the cells of the cancer sample.

9. The method of claim 5 , wherein step (a) comprises measuring the phosphorylation level of one or more of the at least six markers.

10. The method of claim 1 , wherein the cancer stem cells are breast cancer stem cells, brain cancer stem cells, colon cancer stem cells, ovarian cancer stem cells, pancreas cancer stem cells, prostate cancer stem cells, melanoma stem cells, or multiple myeloma stem cells.

11. The method of claim 1 , wherein the sample is from a cancer patient after a prior cancer treatment.

12. The method of claim 1 , wherein step (a) further comprises measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of one or more of additional cancer stem cell markers selected from Epithelial Cell Adhesion Molecule (EpCAM), Aldehyde dehydrogenase 1 family member A3 (ALDH1A3), CD44, and CD133, and

step (b) further comprises comparing the level of each of the one or more of additional cancer stem cell markers measured in step (a) with a reference level for each of the one or more additional cancer stem cell markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.

13. The method of claim 12 , wherein the additional cancer stem cell markers are selected from Epithelial Cell Adhesion Molecule (EpCAM), CD44, and CD133.

14. The method of claim 1 , wherein step (a) further comprises measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of one or more of additional mesenchymal markers selected from zinc finger protein SNA1 (Snail)-1, Snail-2, Wingless-Type MMTV Integration Site Family Member 5B (Wnt5B), Goosecoid, Zinc Finger E-box Binding Homeobox 2 (Zeb2), Forkhead Box Protein C2 (FoxC2), vimentin, and p23, and

step (b) further comprises comparing the level of each of the one or more of additional mesenchymal markers measured in step (a) with a reference level for each of the one or more additional mesenchymal markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.

15. The method of claim 14 , wherein the additional mesenchymal markers are selected from zinc finger protein SNA1 (Snail)-1, Snail-2, and vimentin.

16. The method of claim 1 , wherein step (a) further comprises measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of one or more of additional epithelial markers selected from cytokeratin and Desmoplakin, and

step (b) further comprises comparing the level of each of the one or more of additional epithelial markers measured in step (a) with a reference level for each of the one or more additional epithelial markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.

17. The method of claim 16 , wherein the one or more of additional epithelial markers is cytokeratin.

18. The method of claim 1 , wherein step (a) further comprises measuring the gene transcription level, the protein expression level, the protein modification level, or a combination thereof of an additional stemness marker that is Jagged 1, and

step (b) further comprises comparing the level of the additional stemness marker measured in step (a) with a reference level for the additional stemness marker measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.

19. The method of claim 1 , wherein step (a) further comprises measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of one or more of additional mTORC1 markers selected from Regulatory-Associated Protein of mTOR (Raptor), elf4E-Binding Protein 1 (4EBP1), and Tuberous Sclerosis Complex 2 (TSC2), and

step (b) further comprises comparing the level of each of the one or more of additional mTORC1 markers measured in step (a) with a reference level for each of the one or more additional mTORC1 markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.

20. The method of claim 19 , wherein the one or more of additional mTORC1 markers are selected from Raptor and 4EBP1.

21. The method of claim 1 , wherein step (a) further comprises measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of one or more of additional chemokine markers selected from Activation Normal T Expressed and Secreted (RANTES), Phosphatidylinositol-Glycan Biosyntheses Class F Protein (PIGF), C-X-C Motif Chemokine 3 (CXCR3), and C-X-C Motif Chemokine 10 (CXCL10), and

step (b) further comprises comparing the level of each of the one or more of additional chemokine markers measured in step (a) with a reference level for each of the one or more additional chemokine markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.

22. The method of claim 21 , wherein the additional chemokine markers are selected from Activation Normal T Expressed and Secreted (RANTES), Phosphatidylinositol-Glycan Biosyntheses Class F Protein (PIGF), and C-X-C Motif Chemokine 10 (CXCL10).

23. The method claim 1 , wherein step (a) further comprises measuring gene transcription level(s), protein expression level(s), protein modification level(s), or a combination thereof of:

one or more additional cancer stem cell markers selected from Epithelial Cell Adhesion Molecule (EpCAM), CD44, and CD133,

one or more additional mesenchymal markers selected from zinc finger protein SNA1 (Snail)-1, Snail-2, and vimentin,

an additional epithelial marker that is cytokeratin,

an additional stemness marker that is Jagged-1,

one or more additional mTORC1 markers selected from Raptor and 4EBP1, and

one or more additional chemokine markers selected from Activation Normal T Expressed and Secreted (RANTES), Phosphatidylinositol-Glycan Biosyntheses Class F Protein (PIGF), and C-X-C Motif Chemokine 10 (CXCL10); and

step (b) further comprises comparing the level of each of the one or more of additional chemokine markers, the one or more additional mesenchymal markers, the additional epithelial marker, the additional stemness marker, the one or more additional mTORC1 markers, and the one or more additional chemokine markers measured in step (a) with a reference level for each of the one or more additional chemokine markers, the one or more additional mesenchymal markers, the additional epithelial marker, the additional stemness marker, the one or more additional mTORC1 markers, and the one or more additional chemokine markers measured in normal or non-tumorigenic cancer cells from the same tissue origin as the cancer sample.