Detection of neoantigens using peptide arrays

Abstract

The present disclosure provides a method of identifying a peptide antigen, including: contacting an antibody-comprising composition to a peptide microarray having an array surface and a plurality of feature pairs disposed thereon. Each of the feature pairs includes a first feature of wild-type peptides having a defined sequence and a second feature of mutant peptides having the defined sequence with a single amino acid mutation. Each of the wild-type peptides and the mutant peptides has an array-coupled terminus coupled to the array surface and an opposing free terminus, and the position of the amino acid mutation in the mutant peptides is located closer to the array-coupled terminus of the mutant peptides than tire free terminus. The method further includes detecting binding of an antibody in the antibody-comprising composition to at least one of the feature pairs on the peptide microarray, and identifying feature pairs exhibiting differential binding.

1 .- 20 . (canceled) 
     
     
         21 . A method of identifying a neoantigen in a subject, comprising
 (a) contacting an antibody-comprising composition derived from a subject to a peptide microarray having addressable features on the peptide microarray surface, wherein each feature comprises a wild-type peptide or a mutant peptide;   (b) detecting binding of an antibody in the antibody-comprising composition to at least one of the features on the peptide microarray surface;   (c) identifying features containing: (i) a mutant peptide where binding has occurred, and (ii) a corresponding wild-type peptide where binding has not occurred; and   (d) identifying the mutant peptide from the feature of step (c), as a neoantigen.   
     
     
         22 . The method of  claim 21 , wherein the antibody-comprising composition is blood serum. 
     
     
         23 . The method of  claim 21 , wherein the position of the mutation in the mutant peptide is placed 5 amino acids away from its C-terminus. 
     
     
         24 . The method of  claim 21 , wherein the mutant on the mutant peptide is single amino acid mutation. 
     
     
         25 . The method of  claim 24 , wherein the single amino acid mutation is selected from one of a substitution, a modification, a deletion, and an insertion. 
     
     
         26 . The method of  claim 21 , wherein each of the array-coupled termini are coupled to the peptide microarray surface via one of a linker and a spacer. 
     
     
         27 . The method of  claim 26 , wherein the spacer includes at least one amino acid selected from glycine and serine. 
     
     
         28 . The method of  claim 26 , wherein the linker includes at least one 6-hexanoic acid molecule. 
     
     
         29 . The method of  claim 21 , wherein each of the wild-type peptides and each of the mutant peptides has a length of at least 12 amino acids. 
     
     
         30 . The method of  claim 29 , wherein the position of the amino acid mutation in the mutant peptides is located within the first 6 amino acid positions numbered from the array-coupled terminus of the mutant peptides. 
     
     
         31 . The method of  claim 21 , wherein each of the wild-type peptides and each of the mutant peptides has a length of at least 16 amino acids. 
     
     
         32 . The method of  claim 21 , wherein the antibody that binds to the neoantigen of step (d) is identified as an antibody specific to the neoantigen. 
     
     
         33 . A method of detecting an antibody specific to a neoantigen in a subject, comprising:
 (a) contacting an antibody-comprising composition derived from a subject to a peptide microarray having addressable features on the peptide microarray surface, wherein each feature comprises a wild-type peptide or a mutant peptide;   (b) detecting binding of an antibody in the antibody-comprising composition to at least one of the features on the peptide microarray surface;   (c) identifying features containing: (i) a mutant peptide where binding has occurred, and (ii) a corresponding wild-type peptide where binding has not occurred;   (d) identifying the mutant peptide from the feature of step (c), as a neoantigen; and   (e) identifying the antibody that binds to the neoantigen of step (d), as an antibody specific to the neoantigen.   
     
     
         34 . The method of  claim 33 , wherein the antibody-comprising composition is blood serum. 
     
     
         35 . The method of  claim 33 , wherein the position of the mutation in the mutant peptide is placed 5 amino acids away from its C-terminus. 
     
     
         36 . The method of  claim 33 , wherein the mutant on the mutant peptide is single amino acid mutation. 
     
     
         37 . The method of  claim 36 , wherein the single amino acid mutation is selected from one of a substitution, a modification, a deletion, and an insertion. 
     
     
         38 . The method of  claim 33 , wherein each of the array-coupled termini are coupled to the peptide microarray surface via one of a linker and a spacer. 
     
     
         39 . The method of  claim 38 , wherein the spacer includes at least one amino acid selected from glycine and serine. 
     
     
         40 . The method of  claim 38 , wherein the linker includes at least one 6-hexanoic acid molecule. 
     
     
         41 . The method of  claim 33 , wherein each of the wild-type peptides and each of the mutant peptides has a length of at least 12 amino acids. 
     
     
         42 . The method of  claim 41 , wherein the position of the amino acid mutation in the mutant peptides is located within the first 6 amino acid positions numbered from the array-coupled terminus of the mutant peptides. 
     
     
         43 . The method of  claim 33 , wherein each of the wild-type peptides and each of the mutant peptides has a length of at least 16 amino acids. 
     
     
         44 . A method of detecting an autoantibody in a subject, comprising:
 (a) contacting an antibody-comprising composition derived from a subject to a peptide microarray having addressable features on the peptide microarray surface, wherein each feature comprises a wild-type peptide or a mutant peptide;   (b) detecting binding of an antibody in the antibody-comprising composition to at least one of the features on the peptide microarray surface;   (c) identifying features containing: (i) a wild-type peptide where binding has occurred, and (ii) a corresponding mutant peptide where binding has not occurred; and   (d) identifying the antibody that binds to the wild-type peptide of step (c), as an autoantibody of step (d), as an autoantibody.   
     
     
         45 . The method of  claim 44 , wherein the antibody-comprising composition is blood serum. 
     
     
         46 . The method of  claim 44 , wherein the position of the mutation in the mutant peptide is placed 5 amino acids away from its C-terminus. 
     
     
         47 . The method of  claim 44 , wherein the mutant on the mutant peptide is single amino acid mutation. 
     
     
         48 . The method of  claim 47 , wherein the single amino acid mutation is selected from one of a substitution, a modification, a deletion, and an insertion.