Cancer markers and methods of use thereof

Abstract

The present disclosure relates to methods and compositions which can modulate the globoseries glycosphingolipid synthesis. Particularly, the present disclosure is directed to glycoenzyme inhibitor compound and compositions and methods of use thereof that can modulate the synthesis of globoseries glycosphingolipid SSEA-3/SSEA-4/GloboH in the biosynthetic pathway; particularly, the glycoenzyme inhibitors target the alpha-4GalT; beta-4GalNAcT-I; or beta-3GalT-V enzymes in the globoseries synthetic pathway. Additionally, the present disclosure is also directed to vaccines, antibodies, and/or immunogenic conjugate compositions targeting the SSEA-3/SSEA-4/GLOBO H associated epitopes (natural and modified) which elicit antibodies and/or binding fragment production useful for modulating the globoseries glycosphingolipid synthesis. Moreover, the present disclosure is also directed to the method of using the compositions described herein for the treatment or detection of hyperproliferative diseases and/or conditions. Furthermore, the instant disclosure also relates to cancer stem cell biomarkers for diagnostic and therapeutic uses.

What is claimed is: 
     
         1 .- 8 . (canceled) 
     
     
         9 . A method for detecting a cancer comprising cancer stem cells from a patient, the method comprising:
 a) obtaining a biological sample from the patient;   b) labeling cancer stem cells in the biological sample by contacting the biological sample with one or more labeled binding agents;   c) detecting the specific binding of the labeled binding agent to the one or more tumor-associated carbohydrate antigens, wherein if the detected cells are bound by the binding agent, the cancer is susceptible to treatment with the one or more binding agents that specifically bind to said tumor-associated carbohydrate antigen(s) and wherein said treatment induces apoptosis or inhibits cell proliferation of the cancer stem cells,   wherein the cancer stem cells comprise one or more tumor-associated carbohydrate antigens, and   wherein the one or more tumor-associated carbohydrate antigens comprises SSEA3.   
     
     
         10 .- 15 . (canceled) 
     
     
         16 . A kit for use in a method according to  claim 9 , comprising one or more binding agents each of which specifically binds to one or more tumor-associated carbohydrate antigens, and instructions for use in a method as according to said  claim 9 . 
     
     
         17 . (canceled) 
     
     
         18 . A method for detecting for the presence of cancer comprising detecting expression of β-1,3-galactosyltransferase 5 (β3GalT5) at abnormal levels in cells from a patient, and additionally assaying for the presence of tumor-associated carbohydrate antigen on cells from a patient, wherein both the presence of said tumor-associated carbohydrate antigen on said cells and abnormal levels of β-1,3-galactosyltransferase 5 (β3GalT5) indicates that the cancer is present,
 wherein the tumor-associated carbohydrate antigens comprises SSEA3. 
 
     
     
         19 . A method for detecting for a population of cancer stem cells comprising tumor-associated carbohydrate antigens, the method comprising
 a) providing a starting population of cancer cells,   b) measuring the expression level of one or more tumor-associated carbohydrate antigens,   c) selecting a population of cells whose expression level of said one or more tumor-associated carbohydrate antigens as determined in step b) is increased when compared to control cells, wherein said selected population of cells are cancer stem cells; and   d) optionally isolating and/or enriching for said population of cells selected in step c),   wherein said control cells are cells from the same starting cancer cell population which do not express, or express lower levels of said one or more tumor-associated carbohydrate antigens, and   wherein the tumor-associated carbohydrate antigens comprises SSEA3.   
     
     
         20 . The method of  claim 19 , wherein the cancer stem cells are breast cancer stem cells. 
     
     
         21 . The method of  claim 19 , wherein the step (b) measuring the expression level of one or more tumor-associated carbohydrate antigens, and c) selecting a population of cells whose expression level of said one or more tumor-associated carbohydrate antigens as determined in step (b) is increased when compared to control cells, comprises using flow cytometry and cell sorting. 
     
     
         22 . The method of any of  claim 9 ,  16 ,  18 , or  19 , wherein the one or more tumor-associated carbohydrate antigens further comprises an antigen selected from the group consisting of CD24, CD44, PROCR, and ESA. 
     
     
         23 . A method of detecting a SSEA3 expressing cancer stem cell in a patient, the method comprising:
 (a) obtaining a biological sample from the patient;   (b) labeling the cancer stem cell in the biological sample by contacting the biological sample with antibodies that separately bind to tumor antigens SSEA3 and tumor cell antigens CD44 and CD24 on the cancer stem cell;   (c) detecting the specific binding of the antibodies in step b) and the level of expression of SSEA3 or the level of expression of SSEA3, CD44, and CD24; wherein if the detected cells are SSEA3hi or SSEA3hi/CD44 hi/CD24lo/−, the sample contains a SSEA3 expressing cancer stem cell.   
     
     
         24 . The method of  claim 9 , wherein the one or more labeled binding agents binds to the one or more tumor-associated carbohydrate antigens. 
     
     
         25 . The method of  claim 9 , wherein the one or more labeled binding agents are labelled SSEA-3 binding glycoantibodies. 
     
     
         26 . The method of  claim 25 , wherein the label is a fluorophore.