Epitope mapping method

Abstract

Provided herein are methods for mapping immune response to an immunogen, comprising: immunizing a subject with an immunogen and obtaining sera from the immunized subject at multiple time intervals following immunization, wherein the sera comprises one or more immune complexes between the immunogen and serum antibodies; imaging, by electron microscopy, the sera obtained from the immunized subject in each of the time intervals, to obtain structural images of the one or more immune complexes formed between the immunogen and serum antibodies; mapping immune response to the immunogen by measuring differences in structural images obtained at different time intervals to simultaneously visualize diverse antibodies targeting distinct epitopes in the immunized subjects. Further provided herein are vaccine design processes, comprising: administering a proposed vaccine to a test subject; imaging the immune complex formed in the test subject upon administration of the proposed vaccine; processing and visualizing the image to determine the likely immunogenicity of the proposed vaccine, and determining that the proposed vaccine is immunogenic if it binds to an antibody, and determining that the proposed vaccine should be redesigned if it does not bind or binds weakly to the antibody.

What is claimed is: 
     
         1 . A method of forming an immune complex comprising:
 providing an immunoglobulin (Ig) antibody;   enzymatically digesting the Ig into fragment antigen binding (Fab) and complexing the Fab with a soluble pathogen and/or antigen;   quantifying the specific Ig content for immune complex formation; and   forming the immune complex by incubating the pathogen and/or antigen with an excess of Fab.   
     
     
         2 . The method of  claim 1 , wherein the enzyme used for digestion is in solution. 
     
     
         3 . The method of  claim 1 , wherein the enzyme used for digestion is immobilized on a resin. 
     
     
         4 . The method of  claim 1 , wherein the enzymatic digestion is done by a protease. 
     
     
         5 . The method of  claim 1 , wherein the Ig is IgA (immunoglobin A), IgD (immunoglobin D), IgE (immunoglobin E), IgG (immunoglobin G), IgM (immunoglobin M), or combinations thereof. 
     
     
         6 . The method of  claim 5 , wherein the IgA is enzymatically digested using a protease selected from the group consisting of  Clostridium ramosum, Neisseria gonorrhoeae, Neisseria meningitidis, Haemophilus influenzae , and  Streptococcus pneumonia , or combinations thereof. 
     
     
         7 . The method of  claim 5 , wherein the IgM is enzymatically digested using a protease selected from the group consisting of Pepsin, Trypsin or species-specific bacterial IgM proteases. 
     
     
         8 . The method of  claim 5 , wherein the IgG is enzymatically digested using papain or ficin agarose resin or soluble enzyme. 
     
     
         9 . The method of  claim 1 , wherein the antigen is an immunogen. 
     
     
         10 . The method of  claim 1 , wherein the pathogen and/or antigen is a HIV envelope protein. 
     
     
         11 . The method of  claim 1 , wherein the antigen is expressed in a biotinylated BG505 SOSIP.664 trimer. 
     
     
         12 . A vaccine design process, comprising:
 administering a proposed vaccine to a test subject;   imaging the immune complex formed by an elicited antibody in the test subject upon administration of the proposed vaccine;   processing and visualizing the image to determine the likely immunogenicity of the proposed vaccine; and   determining that the proposed vaccine is immunogenic if it binds to an antibody and determining that the proposed vaccine should be redesigned if it does not bind or binds weakly to the antibody.   
     
     
         13 . The vaccine design process of  claim 12 , wherein the elicited antibody is a secreted antibody, and/or an antibody from the tissue or feces of the test subject. 
     
     
         14 . The vaccine design process of  claim 12 , wherein the test subject is a mammal. 
     
     
         15 . The vaccine design process of  claim 12 , wherein the test subject is a rabbit, mouse, rat, and/or monkey. 
     
     
         16 . The vaccine design process of  claim 12 , wherein the mouse or rat is a humanized mouse or a humanized rat that express human naïve precursers. 
     
     
         17 . The vaccine design process of  claim 12 , wherein the test subject is a human. 
     
     
         18 . The vaccine design process of  claim 12 , wherein the visualization step determines whether a single prime or a second prime is given to a patient