Compositions and methods for rapid production of versatile nanobody repertoires

Abstract

Provided are compositions and methods for producing large repertoires of recombinant nanobodies with high affinities and specificities against any antigen. Included are methods for making and identifying nanobodies produced by camelids, the nanobodies themselves, modifications of the nanobodies, expression vectors encoding the nanobodies, cDNAs encoding the nanobodies, cells comprising the expression vectors and/or cDNA, and methods of making the nanobodies recombinantly. Antigen-specific nanobodies and antigen binding fragments thereof having a Kd for the antigen in a sub-micromolar range are provided.

What is claimed is: 
     
         1 . A method for identifying nanobodies that bind with specificity to an antigen (heavy chain only IgG class of antibodies (Ag-specific HCAbs)), the method comprising:
 i) introducing into a camelid an antigen such that a plurality of Ag-specific HCAbs is produced by the camelid;   ii) testing lymphocytes obtained from the camelid to determine polynucleotide sequences encoding the variable region (V H H) of a mixed population of HCAbs that includes the plurality of Ag-specific HCAbs and HCAbs that are not specific for the antigen (non-specific HCAbs), and deducing the amino acid sequences of the V H H regions of the Ag-specific HCAbs and non-specific HCAbs in the mixed population from the polynucleotide sequences;   iii) processing a sample from the camelid to separate Ag-specific HCAbs from non-specific HCAbs and determining the amino acid sequences of at least a portion of the V H H regions of the Ag-specific HCAbs; and   iv) comparing deduced amino acid sequences of ii) with amino acid sequences of iii) to identify amino acid sequences of ii) that are the same as the amino acid sequences of iii), thereby identifying the Ag-specific V H H regions that are members of the mixed population of HCAbs.   
     
     
         2 . The method of  claim 1 , wherein the determining the amino acid sequences of iii) comprises mass spectrometric analysis of the Ag-specific V H H regions. 
     
     
         3 . The method of  claim 1 , wherein the determining the polynucleotide sequences of ii) comprises generating and sequencing a plurality of cDNA sequences that encode at least 100 unique V H H regions. 
     
     
         4 . The method of  claim 1 , wherein identifying the deduced amino acid sequences of ii) that are the same as the amino acid sequences of iii) comprises a microprocessor implemented comparison of the amino acid sequences of ii) and iii). 
     
     
         5 . The method of  claim 1 , wherein identifying the deduced amino acid sequences of ii) that are the same as the amino acid sequences of iii) comprises a microprocessor implemented comparison of calculated fragmentation patterns of deduced amino acid sequences of ii) and the fragmentation pattern of the amino acid sequences of iii) measured by tandem mass spectrometry. 
     
     
         6 . The method of  claim 1 , wherein separating Ag-specific antibodies from the non-specific antibodies comprises affinity purification of the Ag-specific antibodies using the antigen as an affinity capture agent. 
     
     
         7 . The method of  claim 1 , wherein the lymphocytes of ii) are obtained from bone marrow of the camelid, or are separated from a liquid biological sample obtained from the camelid. 
     
     
         8 . The method of  claim 1 , wherein the lymphocytes of ii) comprise B plasma cells. 
     
     
         9 . The method of  claim 1 , wherein the sample of iii) comprises serum from the camelid. 
     
     
         10 . The method of  claim 1 , further comprising providing and introducing distinct expression vectors encoding distinct Ag-specific nanobodies into host cells, wherein the nanobody sequences are designed based on the deduced Ag-specific V H H regions allowing expression of the distinct Ag-specific nanobodies from the host cells, separating the Ag-specific nanobodies from the host cells, and testing the Ag-specific nanobodies for binding to the antigen. 
     
     
         11 . The method of  claim 10 , wherein the testing the Ag-specific nanobodies for binding to the antigen comprises testing for affinity and/or specificity for the antigen. 
     
     
         12 . The method of  claim 11 , wherein the testing comprises identifying one or more of the Ag-specific nanobodies that have a Kd in a sub-micromolar range. 
     
     
         13 . The method of  claim 1 , wherein the camelid is selected from camels, alpacas and llamas. 
     
     
         14 . The method of  claim 1 , wherein the determining the amino acid sequences of at least a portion of the V H H regions of the Ag-specific HCAbs is performed without proteolytic digestion of the Ag-specific HCAbs.