Donor specific antibody libraries

Abstract

The present application concerns donor-specific antibody libraries derived from a patient donor who has suffered from, or is suffering from one or more diseases discussed herein. The present application also concerns the method of making and using the donor-specific antibodies. The present application further concerns the neutralizing antibodies obtained from the donor-specific antibody libraries and the methods of using these antibodies for the prevention/treatment of human disease.

1 . A vector collection comprising a repertoire of nucleic acid molecules encoding antibody light or heavy chains or fragments thereof, derived from a human patient donor who has suffered from, or is suffering from, a disease evoking antibody production to a target antigen, wherein said collection is identified with a unique barcode. 
     
     
         2 . The vector collection of  claim 1  comprising a repertoire of nucleic acid molecules encoding antibody light chains or fragments thereof. 
     
     
         3 . The vector collection of  claim 2  wherein the antibody light chains are λ chains. 
     
     
         4 . The vector collection of  claim 2  wherein the antibody light chains are κ chains. 
     
     
         5 . The vector collection of  claim 1  comprising a repertoire of nucleic acid molecules encoding antibody heavy chains or fragments thereof. 
     
     
         6 . The vector collection of  claim 1  wherein the barcode is a nucleotide sequence linked to or incorporated in the vectors present in the collection, and/or linked to or incorporated in the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof such that it does not interfere with the expression of said nucleic acid molecules. 
     
     
         7 . The vector collection of  claim 6  wherein said barcode is a contiguous non-coding nucleotide sequence of one to about 24 nucleotides. 
     
     
         8 . The vector collection of  claim 7  wherein said nucleotide sequence is linked to the 3′ or 5′ non-coding region of said nucleic acid molecules. 
     
     
         9 . The vector collection of  claim 6  wherein said nucleotide sequence is a coding sequence of one or more silent mutations incorporated into the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof. 
     
     
         10 . The vector collection of  claim 6  wherein said nucleotide sequence in non-contiguous. 
     
     
         11 . The vector collection of  claim 10  wherein at least part of said non-contiguous nucleotide sequence is linked to or incorporated in the vectors present in the collection. 
     
     
         12 . The vector collection of  claim 10  wherein at least part of said non-contiguous sequence is incorporated into the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof such that it does not interfere with the expression of said nucleic acid molecules. 
     
     
         13 . The vector collection of  claim 1  wherein the barcode is a peptide or polypeptide sequence. 
     
     
         14 . The vector collection of  claim 1  wherein the vectors are phagemid vectors. 
     
     
         15 . The vector collection of  claim 15  wherein the phagemid vectors contain a bacteriophage gene III and a stop codon between the nucleic acid molecules encoding antibody light or heavy chains or fragments thereof and the bacteriophage III gene. 
     
     
         16 . The vector collection of  claim 15  wherein the barcode is a non-coding contiguous nucleotide sequence inserted in the untranslated region following said stop codon. 
     
     
         17 . Host cells comprising the vector collection of  claim 1 . 
     
     
         18 . The host cells of  claim 16  which are  E. coli  host cells. 
     
     
         19 . A donor-specific antibody library comprising library members expressing a collection of antibodies or antibody fragments to a target antigen wherein said antibodies or antibody fragments are derived from a human donor who has suffered from, or is suffering from, a disease evoking antibody production to said target antigen, wherein said antibody library is identified with at least one unique barcode. 
     
     
         20 . The donor-specific antibody library of  claim 19  wherein said antibody heavy and light chains are separately identified each with a barcode unique to the human donor from whom it derived. 
     
     
         21 . The donor-specific antibody library of  claim 19  which is identified with one unique barcode. 
     
     
         22 . The donor-specific antibody library of  claim 19  wherein said antibodies or antibody fragments are composed of antibody heavy and light chains or fragments thereof encoded by nucleic acid molecules present in a vector. 
     
     
         23 . The donor-specific antibody library of  claim 22  wherein the barcode is a nucleotide sequence linked to or incorporated in the vectors present in the library, and/or linked to or incorporated in the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof such that it does not interfere with the expression of said nucleic acid molecules. 
     
     
         24 . The donor-specific antibody library of  claim 23  wherein said barcode is a contiguous non-coding nucleotide sequence of one to about 24 nucleotides. 
     
     
         25 . The donor-specific antibody library of  claim 24  wherein said nucleotide sequence is linked to the 3′ or 5′ non-coding region of said nucleic acid molecules. 
     
     
         26 . The donor-specific antibody library of  claim 23  wherein said nucleotide sequence is a coding sequence of one or more silent mutations incorporated into the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof. 
     
     
         27 . The donor-specific antibody library of  claim 23  wherein said nucleotide sequence in non-contiguous. 
     
     
         28 . The donor-specific antibody library of  claim 27  wherein at least part of said non-contiguous sequence is linked to or incorporated in the vectors present in the library. 
     
     
         29 . The donor-specific antibody library of  claim 27  wherein at least part of said non-contiguous sequence is incorporated into the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof such that it does not interfere with the expression of said nucleic acid molecules. 
     
     
         30 . The donor-specific antibody library of  claim 19  wherein the barcode is a peptide or polypeptide sequence. 
     
     
         31 . The donor-specific antibody library of  claim 22  wherein the vectors are phagemid vectors. 
     
     
         32 . The donor-specific antibody library of  claim 31  wherein the phagemid vectors contain a bacteriophage gene III and a stop codon between the nucleic acid molecules encoding antibody light or heavy chains or fragments thereof and the bacteriophage III gene. 
     
     
         33 . The donor-specific antibody library of  claim 19  expressing a collection of antibody heavy chains or fragments thereof. 
     
     
         34 . The donor specific antibody library of  claim 33  comprising more than one antibody heavy chain family. 
     
     
         35 . The donor-specific antibody library of  claim 19  wherein the medical history of said human donor shows that the patient has suffered from, or is suffering from said disease. 
     
     
         36 . The donor-specific antibody library of  claim 35  wherein it is independently confirmed that said human donor suffered from, or is suffering from said disease. 
     
     
         37 . The donor-specific antibody library of  claim 19 , which is substantially devoid of antibodies and antibody fragments specifically binding antigens different from said target antigen. 
     
     
         38 . The donor-specific antibody library of  claim 19  wherein said target antigen is an influenza A virus. 
     
     
         39 . The donor-specific antibody library of  claim 38  wherein said target antigen is an isolate of influenza A virus H1, H2 or H3 subtype. 
     
     
         40 . The donor-specific antibody library of  claim 38  wherein the target antigen is selected from the group comprising H5, H7 and H9 influenza A virus subtypes. 
     
     
         41 . The donor-specific antibody library of  claim 38  expressing at least one antibody or antibody fragment specifically binding to more than one influenza A virus subtype. 
     
     
         42 . The donor-specific antibody library of  claim 39  expressing at least one antibody or antibody fragment binding to and neutralizing the H5N1 subtype of influenza virus A. 
     
     
         43 . The donor-specific antibody library of  claim 19  wherein the human donor has suffered from, or is suffering from a disease selected from the group consisting of the diseases listed in Table 1. 
     
     
         44 . The donor-specific antibody library of  claim 43  expressing at least one antibody or antibody fragment binding to an antigen associated with said target disease. 
     
     
         45 . The donor-specific antibody library of  claim 43  expressing at least one antibody or antibody fragment binding to and neutralizing an antigen associated with said target disease. 
     
     
         46 . The donor-specific antibody library of  claim 19  expressing a least one neutralizing antibody. 
     
     
         47 . The donor-specific antibody library of Claim  19 , wherein said donor-specific antibody library is a phage library. 
     
     
         48 . The donor-specific antibody library of Claim  47 , wherein said collection contains sequences encoding more than 106 different members of antibodies or antibody fragments. 
     
     
         49 . The donor-specific antibody library of Claim  47 , wherein said collection contains sequences encoding more than 109 different members of antibodies or antibody fragments. 
     
     
         50 . The donor-specific antibody library of  claim 19 , which is selected from the group consisting of a spore-display library, a ribosome display library, a mRNA display library, a microbial cell display library, a yeast display library, and a mammalian display library. 
     
     
         51 . The donor-specific antibody library of Claim  50 , wherein said nucleic acid is reverse-transcribed from mRNA extracted from lymphocytes of said human donor. 
     
     
         52 . The donor-specific antibody library of Claim  51 , wherein said lymphocytes are derived from bone marrow, blood, spleen, or lymph node. 
     
     
         53 . The donor-specific antibody library of Claim  52 , wherein a serological profile of said human donor is generated prior to extraction of said mRNA. 
     
     
         54 . The donor-specific antibody library of Claim  53 , wherein a medical history of said human donor is examined prior to or following extraction of said mRNA. 
     
     
         55 . A method of making a donor-specific library expressing a collection of antibodies or antibody fragments to a target antigen, comprising the steps of:
 a) obtaining mRNA from lymphocytes of a human patient donor who has suffered from, or who is suffering from a disease evoking antibody production to said target antigen;   b) generating a collection of nucleic acids comprising sequences encoding an immunoglobulin repertoire of said patient by reverse transcription of said obtained mRNA: and   c) identifying said donor-specific library with an unique barcode labeling said nucleic acids.   
     
     
         56 . The method of Claim  55 , further comprising steps of generating a serological profile of said patient and/or examining medical history of said patient prior or subsequent to step a). 
     
     
         57 . The method of Claim  56 , further comprises steps of:
 d) inserting said nucleic acids into expression vector;   e) expressing said immunoglobulin repertoire; and   f) displaying said immunoglobulin repertoire in a display system.   
     
     
         58 . The method of Claim  57 , wherein the display system is a phagemid. 
     
     
         59 . The method of  claim 58  further comprising the step of selecting members of the library based their ability to neutralize or activate the target antigen. 
     
     
         60 . The method of  claim 59  that yields at least one neutralizing antibody. 
     
     
         61 . The method of  claim 59  that yields more than one neutralizing antibody. 
     
     
         62 . The method of  claim 61  further comprising the step of creating one or more sub-libraries comprising library members that were found to neutralize or activate the target antigen. 
     
     
         63 . The method of  claim 59  comprising the step of sequencing at least one library member identified. 
     
     
         64 . A method of treating or preventing a disease associated with a target antigen neutralized or activated by an antibody selected by the method of  claim 59 , comprising administering to said human patient in need an effective amount of the antibody selected. 
     
     
         65 . The method of  claim 64  wherein the antibody is a neutralizing antibody. 
     
     
         66 . The method of  claim 65  wherein the disease is an influenza virus A infection. 
     
     
         67 . The method of  claim 64  wherein the disease is selected from the group consisting of the diseases listed in Table 1.