Method for identifying an intestinal phenotype

Abstract

The present invention relates to a method for identifying cells having a predisposition to develop an intestinal phenotype, wherein the cells are characterized by the loss of expression of the RUNX3 gene and the expression of one or more intestinal marker genes. In particular, the invention is directed to the identification of cells, which exhibit an intestinal phenotype representing a precursor of gastric cancer. Furthermore, the invention discloses a method for identifying a compound inhibiting the development of an intestinal phenotype in cells having a predisposition to develop an intestinal phenotype. Finally, the invention also relates to kits of parts for performing these methods.

1 . A method for identifying one or more cells having a predisposition to develop an intestinal phenotype, the method comprising detecting in said one or more cells:
 (a) the loss of expression of the RUNX3 gene; and   (b) the expression of one or more intestinal marker genes.   
   
   
       2 . The method of  claim 1 , further comprising:
 (c) comparing the result of the measurements obtained in steps (a) and (b) with those obtained in a control cell.   
   
   
       3 . The method of  claim 1 , wherein the one or more cells are epithelial cells. 
   
   
       4 . The method of  claim 3 , wherein the cells are gastric epithelial cells. 
   
   
       5 . The method of  claim 4 , wherein the cells are gastric mucous neck cells. 
   
   
       6 . The method of  claim 1 , wherein the intestinal phenotype is characterized by a retained capacity to proliferate. 
   
   
       7 . The method of  claim 6 , wherein the intestinal phenotype is a precursor of gastric cancer. 
   
   
       8 . The method of  claim 6 , wherein the intestinal phenotype is INTESTINAL METAPLASIA. 
   
   
       9 . The method of  claim 1 , wherein the loss of expression of the RUNX3 gene is detected by measuring the degree of methylation of the exon 1 region of the RUNX3 gene and/or determining the absence of a RUNX3 gene product, wherein the gene product is selected from the group consisting of an mRNA and a protein. 
   
   
       10 . The method of  claim 9 , wherein the absence of the RUNX3 protein is determined by using a specific antibody. 
   
   
       11 . The method of  claim 1 , wherein the one or more intestinal marker genes are selected from the group of genes encoding a member of the group consisting of MUC2, and CDX2. 
   
   
       12 . The method of  claim 1 , wherein (b) further comprises detecting the expression of one or more gastric marker genes. 
   
   
       13 . The method of  claim 12 , wherein the one or more gastric marker genes are selected from the group of genes encoding a member of the group consisting of MUC6 and MUC5AC. 
   
   
       14 . The method of  claim 12 , wherein the loss of expression of the RUNX3 gene, the expression of the intestinal marker genes MUC2 and CDX2, and the expression of the gastric marker gene MUC5AC is detected. 
   
   
       15 . The method of  claim 1 , wherein the expression of the one or more intestinal marker genes is detected by determining the presence of the gene products encoding said marker genes, wherein the gene products are selected from the group consisting of an mRNA and a protein. 
   
   
       16 . The method of  claim 15 , wherein the presence of a protein encoding an intestinal marker gene is determined by using a specific antibody. 
   
   
       17 . A kit of parts for performing the method as defined in  claim 1 . 
   
   
       18 . The kit of  claim 17  for performing the method as defined in  claim 12 . 
   
   
       19 . A kit of parts for performing a method for identifying a compound inhibiting the development of an intestinal phenotype in one or more cells having a predisposition to develop an intestinal phenotype, wherein said cells are characterized by the loss of expression of the RUNX3 gene and the expression of one or more intestinal marker genes, the method comprising:
 (a) contacting said one or more cells with a solution supposed to contain at least one compound to be identified;   (b) incubating said cells for a predetermined period of time; and   (c) measuring the expression of the RUNX3 gene as well as the expression of said one or more intestinal marker genes.   
   
   
       20 . A kit of parts for performing a method for identifying a compound inhibiting the development of an intestinal phenotype in one or more gastric cells which are in a precancerous state, the method comprising:
 (a) contacting said one or more gastric cells with a solution supposed to contain at least one compound to be identified;   (b) incubating said cells for a predetermined period of time; and   (c) measuring the expression of the RUNX3 gene and the expression of said one or more intestinal marker genes,   wherein said intestinal phenotype is characterized by the loss of expression of the RUNX3 gene and a change in the expression of one or more intestinal marker genes such that the level of said one or more marker genes is characteristic of said intestinal phenotype;   wherein a compound inhibiting the development of an intestinal phenotype of one or more gastric cells is identified.