Spatially Encoded Biological Assays

Abstract

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

1 . (canceled) 
     
     
         2 . A system for analyzing a target biological molecule of a tissue section, the system comprising:
 a laser configured to deliver radiation to a tissue section comprising a plurality of probes, wherein a probe of the plurality of probes comprises an antibody that specifically binds a target biological molecule of the tissue section and a plurality of labeling moieties conjugated to the antibody, wherein each of the plurality of labeling moieties comprising a chelated metal;   a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) detection apparatus comprising a mass analyzer configured to:
 receive a detection moiety comprising at least a portion of the plurality of labeling moieties after irradiation by the laser from a location of interest in the tissue section; and 
 detect and mass analyze the at least a portion of the labeling moiety. 
   
     
     
         3 . The system of  claim 2 , wherein the system is configured to determine a relative abundance of the at least a portion of the labeling moieties from the location of interest in the tissue section. 
     
     
         4 . The system of  claim 2 , wherein the laser is configured to liberate the detection moiety from the location of interest in the tissue section. 
     
     
         5 . The system of  claim 2 , wherein one or more of the chelated metals comprises a chelated metal ion. 
     
     
         6 . The system of  claim 2 , wherein the chelated metals of each of the multiple labeling moieties are the same. 
     
     
         7 . The method of  claim 2 , wherein one or more of the labeling moieties comprise a structure comprising at least one metal-coordinating atom. 
     
     
         8 . The method of  claim 7 , wherein the structure comprises multiple metal-coordinating atoms. 
     
     
         9 . The method of  claim 8 , wherein the structure comprises four metal-coordinating nitrogen atoms. 
     
     
         10 . The method of  claim 7 , wherein at least one of the metal-coordinating atoms is a nitrogen atom. 
     
     
         11 . The method of  claim 7 , wherein each of the at least one metal-coordinating atoms is a nitrogen atom. 
     
     
         12 . The method of  claim 7 , wherein the structure is a closed ring structure. 
     
     
         13 . The method of  claim 7 , wherein the structure is capable of conjugating iron. 
     
     
         14 . The system of  claim 2 , wherein the detection moiety is a metal or a metal ion of the chelated metal. 
     
     
         15 . The system of  claim 2 , wherein the detection moiety is liberated from the tissue section in an oxidized form relative to a corresponding moiety prior to directing radiation to the tissue section. 
     
     
         16 . The system of  claim 2 , wherein the probe is a first probe comprising a first antibody that specifically binds a first target biological molecule of the tissue section and a first labeling moiety conjugated to the first antibody, and wherein a second probe of the plurality of probes comprises a second antibody that specifically binds a second target biological molecule of the tissue section and a second labeling moiety conjugated to the second antibody. 
     
     
         17 . The system of  claim 16 , wherein the first and second labeling moieties are different. 
     
     
         18 . The system of  claim 16 , wherein the first and second target biological molecules are the same. 
     
     
         19 . The system of  claim 16 , wherein the first and second target biological molecules are different. 
     
     
         20 . The system of  claim 2 , wherein the probe comprises:
 a primary antibody that specifically binds the target biological molecule of the tissue section; and   a secondary antibody conjugated to the plurality of labeling moieties that specifically binds the primary antibody.   
     
     
         21 . The system of  claim 2 , wherein the detection moiety is liberated from a location in the tissue section that is within 200 angstroms of the target protein of the tissue section. 
     
     
         22 . The system of  claim 2 , wherein the multiple labeling moieties are conjugated to the antibody indirectly through linking moieties. 
     
     
         23 . The system of  claim 22 , wherein the linking moieties comprise a polymer. 
     
     
         24 . The system of  claim 2 , further comprising a processing circuit comprising instructions that, when executed, cause the processing circuit to obtain information about the location of interest in the tissue section. 
     
     
         25 . The system of  claim 24 , wherein the processing circuit is configured to obtain information about multiple locations of interest in the tissue section, and the detection apparatus is configured to determine information corresponding to a relative abundance of the at least a portion of the labeling moiety at different locations in the tissue section corresponding to the multiple locations of interest. 
     
     
         26 . The system of  claim 24 , wherein the processing circuit comprises instructions that, when executed, cause the processing circuit to receive the information about the location of interest in the tissue section from a user of the system. 
     
     
         27 . The system of  claim 2 , wherein the target biological molecule comprises a protein. 
     
     
         28 . The system of  claim 2 , wherein the tissue section comprises a fresh-frozen or formalin-fixed paraffin embedded (FFPE) tissue section. 
     
     
         29 . The system of  claim 25 , wherein each of the multiple locations of interest corresponds to a different group of one or more cells in the tissue section. 
     
     
         30 . The system of  claim 25 , wherein each of the multiple locations of interest corresponds to a different cell type in the tissue section or a different cell in the tissue section. 
     
     
         31 . The system of  claim 25 , wherein each of the multiple locations of interest is less than the entire tissue section.