Methods to specifically profile protease activity at lymph nodes

Abstract

In some aspects, the disclosure provides compositions and methods for detecting and monitoring the activity of proteases in vivo using affinity assays. The disclosure relates, in part, to the discovery that biomarker nanoparticles targeted to the lymph nodes of a subject are useful for the diagnosis and monitoring of certain medical conditions (e.g., metastatic cancer, infection with certain pathogenic agents).

1 - 53 . (canceled) 
     
     
         54 . A method for detecting cancer comprising:
 a) administering to a subject a biomarker particle, wherein the biomarker particle comprises a modular structure having a carrier domain comprising a trafficking carrier linked via an enzyme substrate to a detectable marker, and wherein the biomarker particle, when exposed to an enzyme, releases the detectable marker from the carrier domain;   b) analyzing a biological sample from the subject; and   c) determining whether the detectable marker is in the biological sample, wherein the presence of the detectable marker in the biological sample is indicative of a cancer.   
     
     
         55 . The method of  claim 54 , wherein the trafficking carrier comprises an antibody, a protein, a polymeric scaffold, or a nanoparticle. 
     
     
         56 . The method of  claim 54 , wherein the trafficking carrier is a lymph node trafficking carrier. 
     
     
         57 . The method of  claim 54 , wherein the trafficking carrier is non-immunogenic. 
     
     
         58 . The method of  claim 54 , wherein the enzyme substrate is a cancer enzyme substrate. 
     
     
         59 . The method of  claim 58 , wherein the cancer enzyme substrate is ADAM28, MMP9 or MMP12. 
     
     
         60 . The method of  claim 54 , wherein the enzyme substrate is a an immune-associated substrate. 
     
     
         61 . The method of  claim 54 , wherein the enzyme substrate is a granzyme substrate. 
     
     
         62 . The method of  claim 54 , wherein the biological sample is urine. 
     
     
         63 . The method of  claim 54 , wherein the lymph node biomarker nanoparticle is a multiplexed library of lymph node specific enzyme susceptible detectable markers. 
     
     
         64 . (canceled) 
     
     
         65 . The method of  claim 54 , wherein the detectable marker is a mass encoded protease substrate or a ligand encoded protease substrate. 
     
     
         66 . The method of  claim 54 , wherein the presence of the detectable marker in the biological sample is indicative of an immune status. 
     
     
         67 . The method of  claim 66 , wherein the immune status indicates sensitivity to immune therapy. 
     
     
         68 . (canceled) 
     
     
         69 . The method of  claim 54 , wherein the analysis of step (b) comprises using mass spectrometry. 
     
     
         70 . The method of  claim 54 , wherein the analysis of step (b) comprises measuring fluorescence of the detectable marker. 
     
     
         71 . The method of  claim 54 , wherein the analysis of step (b) occurs in vitro. 
     
     
         72 . The method of  claim 54 , wherein the analysis of step (b) occurs ex vivo. 
     
     
         73 . The method of  claim 54 , wherein the analysis of step (b) occurs in vivo. 
     
     
         74 . The method of  claim 54 , wherein the cancer is a pancreatic cancer, a prostate cancer, a breast cancer, a colon cancer, an ovarian cancer, an oral cancer, an endometrial cancer, a skin cancer, a gastric cancer, an esophageal cancer, or a lung cancer. 
     
     
         75 . A method for determining a metastatic stage of a cancer comprising:
 a) administering to a subject a biomarker particle, wherein the biomarker particle comprises a modular structure having a carrier domain comprising a trafficking carrier linked via an enzyme substrate to a detectable marker, and wherein the biomarker particle, when exposed to an enzyme, releases the detectable marker from the carrier domain;   b) analyzing a biological sample from the subject; and   c) determining whether the detectable marker is in the biological sample, wherein the presence of the detectable marker in the biological sample is indicative of the metastatic stage of the cancer.   
     
     
         76 - 95 . (canceled) 
     
     
         96 . The method of  claim 54 , wherein the presence of the detectable marker in the biological sample is further indicative of a metastatic stage of the cancer.