Use of aptamers in proteomics

Abstract

The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated.

1 . A method for measuring the amount of at least one molecule in a biological sample, the method comprising:
 a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s);   b) separating bound from unbound molecules; and   c) quantifying the molecule(s) bound to the or each aptamer,   
       wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. 
     
     
         2 . A method according to  claim 1 , wherein the at least one molecule is a protein. 
     
     
         3 . A method according to  claim 1  or  claim 2 , wherein the identity of the molecule is known. 
     
     
         4 . A method according to  claim 1  or  claim 2 , wherein the identity of the molecule is unknown. 
     
     
         5 . A method according to  claim 4 , wherein the method further comprises determining the identity of the molecule. 
     
     
         6 . A method according to any one of  claims 1  to  4 , wherein the sequence of the or each aptamer is known. 
     
     
         7 . A method according to any one of  claims 1  to  6 , wherein each aptamer sequence carries a unique tag. 
     
     
         8 . A method according to  claim 7 , wherein the tag is the sequence of the aptamer. 
     
     
         9 . A method according to  claim 7  or  claim 8 , wherein the tag is part of the sequence of the aptamer. 
     
     
         10 . A method according to any one of  claims 1  to  9 , wherein sequencing is carried out on a single molecule array or a clonal single molecule array. 
     
     
         11 . A method according to any one of  claims 1  to  10 , wherein the method further comprises removing the aptamer(s) bound to the or each molecule and arraying the aptamer(s) on a surface. 
     
     
         12 . A method according to  claim 11 , wherein the method further comprises amplifying the arrayed aptamers. 
     
     
         13 . A method according to any one of  claims 1  to  12 , wherein the one or more aptamers comprise different sequences that bind to the same molecule. 
     
     
         14 . A method according to any one of  claims 1  to  12 , wherein the one or more aptamers comprise panels of aptamer sequences, each panel binding to a different molecule. 
     
     
         15 . A method according to any one of  claims 1  to  14 , wherein the aptamers are derived from polynucleotides or polypeptides. 
     
     
         16 . A method according to  claim 15 , wherein the aptamers are polynucleotides and have between about 30 and about 60 bases. 
     
     
         17 . A method according to  claim 16 , wherein the aptamers have about 40 bases. 
     
     
         18 . A method according to  claim 15 , wherein the aptamers are polypeptides and have between about 30 and about 60 amino acids. 
     
     
         19 . A method according to any one of  claims 1  to  18 , wherein the biological sample is a bodily fluid. 
     
     
         20 . A method according to  claim 19 , wherein the bodily fluid is blood or derived from blood. 
     
     
         21 . A method according to  claim 20 , wherein the bodily fluid is serum or plasma. 
     
     
         22 . A method according to any one of  claims 1  to  21 , wherein the method further comprises:
 d) combining a second biological sample with the quantified aptamers obtained in c);   e) separating bound from unbound molecules;   f) quantifying the molecule(s) bound to aptamers; and   g) comparing quantities obtained in c) with those obtained in f),   
       wherein quantification of aptamers bound to one or more molecules in the second sample is carried out by sequencing at least part of each aptamer. 
     
     
         23 . A method according to any one of  claims 1  to  22 , wherein the method further comprises comparing the quantity of the or each aptamer against a control or baseline quantity. 
     
     
         24 . A method according to  claim 22  or  claim 23 , wherein the second sample is obtained from an individual known to be in a diseased state. 
     
     
         25 . A method according to  claim 22  or  claim 23 , wherein the second sample is obtained from an individual known to be in a healthy state. 
     
     
         26 . A method according to  claim 22  or  claim 23 , wherein the second sample is obtained from an individual after drug treatment. 
     
     
         27 . Use of a method as claimed in any one of  claims 1  to  26  to identify one or more biomarkers. 
     
     
         28 . Use of a method as claimed in any one of  claims 1  to  26  to validate one or more biomarkers. 
     
     
         29 . Use of a method as claimed in any one of  claims 1  to  21  as a diagnostic method. 
     
     
         30 . Use of aptamers identified by the method as claimed in any one of  claims 1  to  26  in a diagnostic kit. 
     
     
         31 . A diagnostic kit for use with the method as claimed in any one of  claims 1  to  26 , wherein the kit comprises one or more aptamers. 
     
     
         32 . A diagnostic kit as claimed in  claim 31 , wherein the one or more aptamers have been identified by the method as claimed in any one of  claims 1  to  26 . 
     
     
         33 . Use of an aptamer as a tag to quantify a molecule in a sample, wherein at least part of the sequence of the aptamer is the tag. 
     
     
         34 . Use according to  claim 33 , wherein the molecule is a protein. 
     
     
         35 . Use according to  claim 33  or  claim 34 , wherein quantification is carried out by sequencing at least part of the tag. 
     
     
         36 . Use according to  claim 35 , wherein sequencing is carried out on a single molecule array or a clonal single molecule array. 
     
     
         37 . A sequencing-enabled aptamer comprising:
 An aptamer sequence; and   At least one adapter sequence,   
       wherein the adapter sequence comprises an attachment sequence for attachment of the aptamer to a surface for sequencing. 
     
     
         38 . An aptamer according to  claim 37 , wherein the adapter sequence further comprises a sequencing primer. 
     
     
         39 . An aptamer according to  claims 37  or  claim 38 , wherein the aptamer sequence is DNA, RNA, PNA or a mixture thereof. 
     
     
         40 . An aptamer according to any one of  claims 37  to  39 , wherein the aptamer further includes a label. 
     
     
         41 . An aptamer according to  claim 40 , wherein the label is a radiolabel or is fluorescent. 
     
     
         42 . An aptamer according to  claim 41 , wherein the label is 6-carboxyfluorescein. 
     
     
         43 . Use of an aptamer according to any one of  claims 37  to  42  in a method according to any one of  claims 1  to  26  or a diagnostic kit according to  claim 31  or  claim 32 .