Biomarkers of cancer metastasis

Abstract

There is provided a panel of biomarkers of tumour metastasis comprising any two of carbonic anhydrase-9 (CAIX), vascular endothelial growth factor C (VEGF-C), ephrin A5 (EFNA5), eph receptor B2 (EPHB2), transforming growth factor beta 3 (TGF-β3), pyruvate dehydrogenase kinase isoenzyme-3 (PDK3), carbonic anhydrase-12 (CAXII), keratin 14 (KRT14), hypoxia inducible factor 1 alpha subunit (HIF-1α), or tenascin C (TNC). CAIX, VEGF-C, EFNA5, EPHB2, TGF-β3 or PDK3 may be indicators of moderate metastatic potential, while CAXII, KRT14, HIF-1α, or TNC may be indicators of high metastatic potential. There is also provided a method of determining risk of tumour metastasis using the aforementioned biomarkers is also provided. The biomarkers may be used in diagnosis, prognosis, treatment selection, or to test putative therapeutics. The biomarkers may be used to assess malignancies or cancers having hypoxic regions, such as breast cancer.

1 . A panel for detecting biomarkers of tumour metastasis, wherein said biomarkers comprise at least two of:
 carbonic anhydrase-9 (CAIX),   vascular endothelial growth factor C (VEGF-C),   ephrin A5 (EFNA5),   eph receptor B2 (EPHB2),   transforming growth factor beta 3 (TGF-β3),   pyruvate dehydrogenase kinase isoenzyme-3 (PDK3),   carbonic anhydrase-12 (CAXII),   keratin 14 (KRT14),   hypoxia inducible factor 1 alpha subunit (HIF-1α), or   tenascin C (TNC).   
     
     
         2 . The panel of  claim 1 , wherein said biomarkers comprise:
 at least one of CAIX, VEGF-C, EFNA5, EPHB2, TGF-β3, or PDK3; and   at least one of CAXII, KRT14, HIF-1α or TNC.   
     
     
         3 . The panel of  claim 2 , wherein said biomarkers comprise CAIX and CAXII. 
     
     
         4 . The panel of  claim 3 , wherein said biomarkers comprise CAIX, CAXII, VEGF-C, EFNA5, EPHB2, TNC, TGF-β3, PDK3, KRT14, and HIF-1α. 
     
     
         5 . The panel of  claim 1  for detecting cancer, determining risk of metastasis, determining tumour grade, determining tumour sub-type, selecting optimized treatment, predicting the treatment response, measuring treatment response, predicting clinical outcome, predicting likelihood of recurrence, as targets enabling the development of new therapeutic agents for treatment of breast cancer, or for screening for candidate therapeutic agents. 
     
     
         6 . The panel of  claim 1 , wherein said tumour is a human breast cancer tumour. 
     
     
         7 . A method of determining tumour metastatic potential comprising:
 measuring expression levels in a tumour tissue sample of at least two indicators of metastatic potential which are each independently:
 carbonic anhydrase-9 (CAIX), 
 vascular endothelial growth factor C (VEGF-C), 
 ephrin A5 (EFNA5), 
 eph receptor B2 (EPHB2), 
 transforming growth factor beta 3 (TGF-β3), 
 pyruvate dehydrogenase kinase isoenzyme-3 (PDK3), 
 carbonic anhydrase-12 (CAXII), 
 keratin 14 (KRT14), 
 hypoxia inducible factor 1 alpha subunit (HIF-1α), or 
 tenascin C (TNC); and 
   comparing said expression levels to a control to determine metastatic potential.   
     
     
         8 . The method of  claim 7 , wherein said at least two indicators of metastatic potential comprise CAIX and CAXII. 
     
     
         9 . The method of  claim 7 , wherein said step of measuring expression levels comprises measuring protein or mRNA expression levels. 
     
     
         10 . The method of  claim 7 , wherein said tumour tissue sample is from a human breast cancer tumour. 
     
     
         11 . The method of  claim 7 , wherein said control comprises a control sample having low or no metastatic potential and wherein, when said expression levels are elevated relative to said control, said tumour is determined to have metastatic potential. 
     
     
         12 . The method of  claim 7  comprising wherein said step of measuring comprises measuring expression levels of at least one indicator of moderate metastatic potential which is CAIX, VEGF-C, EFNA5, EPHB2, TGF-β3, or PDK3, and at least one indicator of high metastatic potential which is CAXII, KRT14, HIF-1α, or TNC;
 and further comprising determining:
 (a) low metastatic potential if expression levels of said at least one indicator of moderate metastatic potential and said at least one indicator of high metastatic potential are both less than or substantially equal to said control, 
 (b) moderate metastatic potential if said expression levels of said at least one indicator of moderate metastatic potential are elevated compared to said control, and said expression levels of said at least one indicator of high metastatic potential are less than or equal to said control, or 
 (c) high metastatic potential if said expression levels of said at least one indicator of moderate metastatic potential and said at least one indicator of high metastatic potential are elevated compared to said control. 
   
     
     
         13 . The method of  claim 12 , wherein said at least one indicator of moderate metastatic potential is CAIX and said at least one indicator of high metastatic potential is CAXII. 
     
     
         14 . The method of  claim 12 , wherein expression levels of CAIX, CAXII, VEGF-C, EFNA5, EPHB2, TNC, TGF-β3, PDK3, KRT14, and HIF-1α are measured. 
     
     
         15 . The method of  claim 12 , wherein
 (a) high metastatic potential is determined if said expression levels are substantially similar to 4T1 cells;   (b) moderate metastatic potential is determined if said expression levels are substantially similar to 66cl4 cells; or   (c) low metastatic potential is determined if said expression levels are substantially similar to 67NR cells.   
     
     
         16 . The method of  claim 12 , wherein moderate metastatic potential is indicative of local metastasis, site-specific metastasis, organic-specific metastasis, or tissue-specific metastasis. 
     
     
         17 . The method of  claim 12 , wherein high metastatic potential is indicative of multiple or distant metastases. 
     
     
         18 . The method of  claim 12 , wherein said control is from a sample having low or no metastatic potential. 
     
     
         19 . The method of  claim 12 , wherein said control is from 67NR cells or normal mammary gland. 
     
     
         20 . A method of selecting a cancer treatment comprising:
 carrying out the method of  claim 7 ; and   selecting an aggressive treatment regime if said tumour is determined to have metastatic potential.   
     
     
         21 . The method of  claim 20 , wherein said step of measuring comprises measuring expression levels of at least one indicator of moderate metastatic potential which is CAIX, VEGF-C, EFNA5, EPHB2, TGF-β3, or PDK3, and of at least one indicator of high metastatic potential which is CAXII, KRT14, HIF-1α, or TNC;
 and further comprising:   (a) selecting a non-aggressive treatment if expression levels of said at least one indicator of moderate metastatic potential and said at least one indicator of high metastatic potential are less than or substantially equal to said control,   (b) selecting a moderately aggressive treatment regime if said expression levels of said at least one indicator of moderate metastatic potential are elevated compared to said control, and said expression levels of said at least one indicator of high metastatic potential are less than or equal to said control, or   (c) selecting a highly aggressive treatment regime if said expression levels of said at least one indicator of moderate metastatic potential and said at least one indicator of high metastatic potential are elevated compared to said control.   
     
     
         22 . The method of  claim 21 , wherein said highly aggressive treatment regime or said moderately aggressive treatment regime comprises an inhibitor of said at least one indicator of moderate metastatic potential or of said at least one indicator of high metastatic potential. 
     
     
         23 . The method of  claim 22 , wherein said highly aggressive treatment regime or said moderately aggressive treatment regime comprises an inhibitor of CAIX or CAXII. 
     
     
         24 . A kit comprising the panel of  claim 1  and instructions for use. 
     
     
         25 . The kit of  claim 24  comprising antibodies, antigen-binding polypeptides, or complementary nucleic acids of said biomarkers. 
     
     
         26 . A method of identifying or validating a putative cancer therapeutic comprising:
 measuring expression levels of the panel of  claim 1  in a sample from malignant cells;   exposing said malignant cells to said putative cancer therapeutic; and   identifying or validating a putative cancer therapeutic if said expression levels are reduced following exposure.