Methods for prognosing and preventing metastatic liver disease

Abstract

The present invention is directed to a method for identifying an individual who is at risk for developing metastatic liver disease that involves measuring, in a sample isolated from the individual, exosomal levels of one or more markers of metastatic liver disease. Kits for carrying out this method are also disclosed. The present invention also relates to a method of preventing metastatic liver disease in an individual who are at risk for developing the disease that involves administering one or more inhibitors of liver premetastatic niche formation.

1 .- 35 . (canceled) 
     
     
         36 . A method of identifying a subject having or at risk of developing metastatic liver disease, said method comprising:
 measuring, in a liver cell sample isolated from the subject, expression levels of one or more markers of liver pre-metastatic niche formation selected from the group consisting of matrix metallopeptidase 9 (MMP9), S100 protein B (S100B), S100 protein A8 (S100A8), connective tissue growth factor (CTGF), endothelin (EDN), platelet-derived growth factor (PDGF), C-C motif chemokine 2 (CCL2), fibroblast growth factor-2 (FGF2), hepatocyte growth factor (HGF), interleukin-1 (IL-1), interleukin-6 (IL-6), insulin-like growth factor (IGF), transforming growth factor-beta (TGFβ) and vascular endothelial growth factor (VEGF);   comparing the measured expression levels of the one or more markers of liver pre-metastatic niche formation to expression levels of the one or more markers of liver pre-metastatic niche formation in a control sample; and   identifying the subject as having or at risk of developing liver metastases when said subject has increased expression levels of the one or more markers of liver pre-metastatic niche formation relative to control expression levels of the one or more markers of liver pre-metastatic niche formation.   
     
     
         37 . The method of  claim 36  further comprising:
 measuring, in a sample isolated from the subject, exosomal levels of one or more markers of metastatic liver disease selected from the group consisting of Annexin Al (ANXA1), CD44, CD47, cadherin 1 (CDH1), filamin A (FLNA), high mobility group box 1 (HMGB1), integrin β3 (ITGB3), lectin galactoside-binding soluble 1 (LGALS1), lectin galactoside-binding soluble 3 (LGALS3), macrophage migration inhibitory factor (MIF), matrix metalloproteinase 14 (MMP14), plasminogen activator urokinase receptor (PLAUR), prostaglandin-endoperoxide synthase 2 (PTGS2), and ras-related C3 botulinum toxin substrate 1 (RAC1); 
 comparing the measured exosomal levels of the one or more markers of metastatic liver disease to exosomal levels of the one or more markers of metastatic liver disease in a control sample to identify increased exosomal levels of the one or more markers of metastatic liver disease in the sample, wherein said subject is identified as having or at risk of developing liver metastases when said subject has increased expression levels of the one or more markers of liver pre-metastatic niche formation relative to control expression levels and increased exosomal levels of the one or more markers of metastatic liver disease relative to control exosomal levels. 
 
     
     
         38 .- 50 . (canceled) 
     
     
         51 . The method of  claim 36 , wherein the subject has a gastrointestinal tract cancer. 
     
     
         52 . The method of  claim 51 , wherein the gastrointestinal tract cancer is in complete or partial remission. 
     
     
         53 . The method of  claim 51 , wherein the gastrointestinal tract cancer is selected from the group consisting of pancreatic cancer, colorectal cancer, stomach cancer, anal cancer, esophageal cancer, gallbladder cancer, and rectal cancer. 
     
     
         54 . The method of  claim 36 , wherein the subject has a pre-tumoral gastrointestinal lesion. 
     
     
         55 . The method of  claim 54 , wherein the pre-tumoral gastrointestinal lesion is selected from the group consisting of pancreatitis, intraductual papillary mucinous neoplasia, pancreatic intraepithelial neoplasia, ulcerative colitis, Chron's disease, inflammatory bowel disease, colon polyps, rectal polyps, helicobacter pylori-associated gastritis, Barrett's esophagus, gallstones, porcelain gallbladder, choledochal cysts, gallbladder polyps, and primary sclerosing cholangitis. 
     
     
         56 . The method of  claim 36 , wherein said measuring comprises:
 measuring expression levels of the one or more markers of liver pre-metastatic niche formation in the sample using an immunoassay.   
     
     
         57 . The method of  claim 56 , wherein the immunoassay is selected from the group consisting of immunohistochemical assay, radioimmunoassay, enzyme-linked immunosorbent assay (ELISA), immunoradiometric assay, gel diffusion precipitation reaction, immunodiffusion assay, in situ immunoassay, Western blot, precipitation reaction, complement fixation assay, immunofluorescence assay, and immunoelectrophoresis assay. 
     
     
         58 . The method of  claim 56 , wherein said measuring comprises:
 contacting the sample with one or more labeled binding reagents, wherein each labeled binding reagent is capable of binding to one of the one or more markers of liver pre-metastatic niche formation;   detecting the one or more labeled binding reagents bound to their respective marker of metastatic liver disease in the sample; and   measuring expression levels of one or more markers of liver pre-metastatic niche formation based on said detecting.   
     
     
         59 . The method of  claim 36 , wherein said measuring comprises:
 measuring expression levels of the one or more markers of liver pre-metastatic niche formation in the sample using a nucleic acid detection assay.   
     
     
         60 . The method of  claim 59 , wherein the nucleic acid detection assay is selected from the group consisting of a quantitative polymerase chain reaction (qPCR) assay, a quantitative reverse-transcription PCR assay, a solid-phase nucleic acid detection assay, and a next-generation sequencing assay. 
     
     
         61 . The method of  claim 59 , wherein mRNA levels are measured. 
     
     
         62 . The method of  claim 61 , wherein said nucleic acid detection assay comprises:
 synthesizing cDNA of the one or more markers of liver pre-metastatic niche formation mRNA of the one or more markers of liver pre-metastatic niche formation present in the sample;   contacting the sample with reagents suitable to detect the synthesized cDNA in the sample;   detecting the synthesized cDNA; and   measuring levels of the synthesized cDNA of the one or more markers of liver pre-metastatic niche formation in the sample based on said detecting.   
     
     
         63 . The method of  claim 36 , wherein the control sample is a sample derived from non-cancerous cells or tissue. 
     
     
         64 . The method of  claim 36 , wherein the control sample is a sample obtained from the subject at an earlier time point.