# Patent

## Title
Donor specific antibody libraries

## Abstract

The present invention 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 invention also concerns the method of making and using the donor-specific antibodies. The present invention 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.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This is a continuation-in-part of U.S. application Ser. No. 11/748,980, filed on May 15, 2007, now abandoned, which claims priority under 35 U.S.C. §119(e) from U.S. provisional patent application Nos. 60/800,787, filed May 15, 2006 and 60/855,679, filed Oct. 30, 2006, the entire disclosures of which are expressly incorporated by reference herein.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 26, 2010, is named SLN-0004.txt, and is 233,503 bytes in size.
FIELD OF THE INVENTION
The present invention concerns donor-specific antibody libraries and methods of making and using thereof. The present invention also concerns neutralizing antibodies obtained from such donor-specific antibody libraries and methods of using the antibodies obtained for the prevention and/or treatment of various human diseases and conditions.
BACKGROUND OF THE INVENTION
The generation and identification of specific agents for the diagnosis, prevention, and treatment of human diseases requires access to vast collections of useful chemistries. With the advent and rapid development of a variety of techniques for the creation and screening of antibody libraries, monoclonal antibodies against disease targets have become one of the major categories of new drug candidates. Since for human use, in addition to specificity and efficacy, safety is of primary concern, libraries of human monoclonal antibodies have become of particular importance.
At present, the development of human antibody-based drug candidates are typically identified by screening of human antibody libraries comprising a random collection of antibody sequences from human repertoires that are typically unrelated to their intended application or applications. Each antibody library created from a specific human donor potentially contains antibodies to every component, physiology, and metabolic alteration stemming from, or creating, every unique challenge that the donor has encountered, challenged, and surmounted over the course of that individual's lifetime. As typical human antibody libraries made with the current approaches are constructed without the knowledge of the health history of donors, little is known of what would be expected in the resulting immunoglobulin repertoires.
Thus, it is of great interest to create antibody libraries from individuals who have successfully survived or are surviving an encounter with specific diseases because their resulting repertoires include antibodies that were used by the donor to defend specifically against a relevant disease. It is also important to provide methods for the efficient screening and handling of such libraries, including the ability to remove or isolate negative or positive elements, eliminate undesirable content, and produce human antibodies with improved properties.
The present invention addresses these needs by providing methods and means for the creation, screening and handling of donor-specific antibody libraries from individuals who have been exposed to and survived or are surviving an encounter with a specific target disease.
SUMMARY OF THE INVENTION
In one aspect, the invention concerns 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 the collection is identified with a unique barcode.
In one embodiment, the vector collection comprises a repertoire of nucleic acid molecules encoding antibody light chains or fragments thereof, such as antibody λ light chains, or antibody κ light chains, or fragments thereof.
In another embodiment, the vector collection comprises a repertoire of nucleic acid molecules encoding antibody heavy chains or fragments thereof.
In yet another embodiment, 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 the nucleic acid molecules.
Thus, the barcode may be contiguous non-coding nucleotide sequence of one to about 24 nucleotides, which may, for example, be linked to the 3′ or 5′ non-coding region of the nucleic acid molecules.
In a further embodiment, the barcode is a nucleotide sequence that 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.
In a still further embodiment, the barcode is a non-contiguous nucleotide sequence. At least part of the non-contiguous nucleotide sequence may be linked to or incorporated in the vectors present in the collection. Alternatively, at least part of the non-contiguous nucleotide sequence may be 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.
In another embodiment, the barcode is a peptide or polypeptide sequence.
In a different embodiment, the vectors present in the vector collection are phagemid vectors, which may, for example, 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, and may have a barcode, such as a non-coding contiguous nucleotide sequence inserted in the untranslated region following the stop codon.
In another aspect, the invention concerns host cells comprising the vector collection of the present invention. The host cells may by eukaryotic or prokaryotic host cells, such as, for example, E. coli cells.
In a further aspect, the invention concerns a donor-specific antibody library comprising library members expressing a collection of antibodies or antibody fragments to a target antigen wherein the 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.
In one embodiment, the antibody heavy and light chains are separately identified each with a barcode unique to the human donor from whom it derived.
In another embodiment, the donor-specific antibody library is identified with one unique barcode.
In yet another embodiment, the antibodies or antibody fragments are composed of antibody heavy and light chains or fragments thereof encoded by nucleic acid molecules present in a vector.
In a further embodiment, 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 the nucleic acid molecules.
In a still further embodiment, the barcode is a contiguous non-coding nucleotide sequence of one to about 24 nucleotides, which may, for example, be linked to the 3′ or 5′ non-coding region of the nucleic acid molecules.
In a different embodiment, the barcode is encoded by 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.
In another embodiment, the barcode is encoded by a non-contiguous nucleotide sequence.
In a further embodiment, a least part of the non-contiguous sequence encoding the barcode is linked to or incorporated in the vectors present in the library.
In a still further embodiment, at least part of the non-contiguous sequence encoding the barcode 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 such nucleic acid molecules.
In different embodiment, the barcode is a peptide or polypeptide sequence.
In another embodiment, vectors are phagemid vectors, may, for example, 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.
In yet another embodiment, the medical history of the human patient donor shows that the donor has suffered from, or is suffering from said disease. In some embodiments, it is independently confirmed that the human donor suffered from, or is suffering from the disease.
In an additional embodiment, the donor-specific antibody library is substantially devoid of antibodies and antibody fragments specifically binding antigens different from said target antigen.
In one embodiment, the target antigen is an influenza A virus, such as an isolate of influenza A virus H1, H2, H3, H5, H7, or H9 subtype.
In another embodiment, the library expresses at least one antibody or antibody fragment specifically binding to more than one influenza A virus subtype.
In yet another embodiment, the library expresses at least one antibody or antibody fragment binding to and neutralizing the H5N1 subtype of influenza virus A.
In a further embodiment, the human donor has suffered from, or is suffering from a disease selected from the group consisting of the diseases listed in Table 1 below.
In a still further embodiment, the antibody library expresses at least one antibody or antibody fragment binding to an antigen associated with the target disease.
In an additional embodiment, the antibody library expresses at least one antibody or antibody fragment binding to and neutralizing an antigen associated with the target disease.
The donor-specific antibody library may, for example, be a phage library, in an embodiment, it may contain sequences encoding more than 106 different members of antibodies or antibody fragments, or more than 109 different members of antibodies or antibody fragments.
In other embodiments, the donor-specific antibody library is, without limitation, a spore-display library, a ribosome display library, a mRNA display library, a microbial cell display library, a yeast display library, or a mammalian display library.
In an embodiment, the nucleic acid encoding the antibodies or antibody fragments present in the library is reverse-transcribed from mRNA extracted from lymphocytes of the human patient donor, where the lymphocytes may, for example, originate from bone marrow, blood, spleen, or lymph node.
If desired, a serological profile of said human donor may be generated prior to extraction of said mRNA.
Alternatively, or in addition, the medical history of the human donor, and optionally the donor's family, is examined prior to or following extraction of the mRNA.
In another aspect, the invention concerns 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 the patient by reverse transcription of said obtained mRNA; and
        c) identifying the donor-specific library with an unique barcode labeling said nucleic acids.
    
    


The method may further comprise steps of generating a serological profile of said patient and/or examining medical history of the patient prior or subsequent to step a).
The method may further comprise the steps of d) inserting said nucleic acids into expression vector; e) expressing the immunoglobulin repertoire; and f) displaying the immunoglobulin repertoire in a display system.
In another embodiment, the method further comprises the step of selecting members of the library based their ability to neutralize or activate the target antigen.
In a still further embodiment, the method yields at least one neutralizing antibody.
In another embodiment, the method further comprises the step of creating one or more sub-libraries comprising library members that were found to neutralize or activate the target antigen.
In yet another embodiment, the method comprises the step of sequencing at least one library member identified.
In a further aspect, the invention concerns a method of treating or preventing a disease associated with a target antigen neutralized or activated by an antibody selected by the method described above, comprising administering to a human patient in need an effective amount of the antibody selected.
The antibody may, for example, be a neutralizing antibody, such as a neutralizing antibody to at least one influenza A virus subtype.
In another embodiment, the disease is selected from the group consisting of the diseases listed in Table 1 below.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a flow chart schematically illustrating a typical method for the creation of the human antibody libraries of the present invention.
FIG. 2 illustrates a typical panning enrichment scheme for increasing the reactive strength towards two different targets, A and B. Each round of enrichment increases the reactive strength of the pool towards the individual target(s).
FIG. 3 illustrates a strategy for the selection of clones cross-reactive with targets A and B, in which each successive round reinforces the reactive strength of the resulting pool towards both targets.
FIG. 4 illustrates a strategy for increasing the reactive strengths towards two different targets (targets A and B), by recombining parallel discovery pools to generate/increase cross-reactivity. Each round of selection of the recombined antibody library increases the reactive strength of the resulting pool towards both targets.
FIG. 5 illustrates a strategy for increasing cross-reactivity to a target B while maintaining reactivity to a target A. First, a clone reactive with target A is selected, then a mutagenic library of the clones reactive with target A is prepared, and selection is performed as shown, yielding one or more antibody clones that show strong reactivity with both target A and target B.
FIG. 6 illustrates a representative mutagenesis method for generating a diverse multifunctional antibody collection by the “destinational mutagenesis” method. FIG. 6 discloses SEQ ID NOS 5, 4, 8, 6 and 7, respectively, in order of appearance. Consensus peptide disclosed as SEQ ID NO: 9.
FIG. 7 shows the amino acid sequences of 15 known hemagglutinin (H) protein subtypes (SEQ ID NOS 10-25, respectively, in order of appearance).
FIG. 8 shows the H5 hemagglutinin (HA) serology results for blood samples obtained from six human survivors of a Turkish H5N1 bird flu outbreak. The data demonstrate the presence of antibodies to the HA antigen.
FIG. 9 shows serology results obtained with serum samples of twelve local donors, tested on H5 antigen (A/Vietnam/1203/2004) and H1N1 (A/New Caledonia/20/99) and H3N2 (A/Panama/2007/99) viruses.
FIG. 10 illustrates the unique barcoding approach used in the construction of antibody phage libraries.
FIG. 11 shows the results of a scFv ELISA test of five distinct clones obtained from pooled libraries of Turkish bird flu survivors on H5 protein and H5N1 virus.
FIG. 12 shows sequence alignments comparing the sequences of H5 hemagglutinin proteins from reported Turkish isolates (SEQ ID NOS 26-29, respectively, in order of appearance) and one Vietnamese isolate (SEQ ID NO: 30) downloaded from the Los Alamos National Laboratory sequence database.
FIGS. 13 and 14 show heavy chain variable region sequences of unique clones identified in pooled antibody libraries of Turkish donors, along with the corresponding light chain and germline origin sequences. The sequences shown in FIG. 13 (3-23 heavy chain clones) originate from a pooled library of all heavy and light chains of all Turkish donors after three rounds of panning. FIG. 13 discloses SEQ ID NOS 31-34, 31-32, 35-37, 32, 38-40, 32 and 41-42, respectively, in order of appearance. The sequences shown in FIG. 14 (3-30 heavy chain clones) originate from a pooled library of all heavy and light chains of all Turkish donors after two rounds of panning. FIG. 14 discloses SEQ ID NOS 43-47, 44, 48-50, 44, 51-53, 44 and 54-55, respectively, in order of appearance.
FIGS. 15A-D show additional unique H5N1-specific antibody heavy chain variable region sequences (SEQ ID NOS 56-94, respectively, in order of appearance) identified from antibody libraries of individual Turkish donors, after four rounds of panning.
FIGS. 16 and 17 illustrate the use of destinational mutagenesis to create diverse antibody heavy and light chain libraries using the antibody heavy (FIG. 16) and light chain (FIG. 17) sequences identified by analysis of sera and bone marrow of Turkish bird flu survivors. FIG. 16 discloses SEQ ID NOS 95 and 95-100, respectively, in order of appearance. FIG. 17 discloses SEQ ID NOS 101-106, respectively, in order of appearance.
FIGS. 18 and 19 show ELISA results confirming cross-reactivity of certain Fab fragments obtained from an H5N1 Vietnam virus scFv antibody with Turkish and Indonesian variants of the HA protein.



DETAILED DESCRIPTION
A. Definitions
Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994), provides one skilled in the art with a general guide to many of the terms used in the present application.
One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. Indeed, the present invention is in no way limited to the methods and materials described. For purposes of the present invention, the following terms are defined below.
The phrase “conserved amino acid residues” is used to refer to amino acid residues that are identical between two or more amino acid sequences aligned with each other.
The terms “disease,” “disorder” and “condition” are used interchangeably herein, and refer to any disruption of normal body function, or the appearance of any type of pathology. The etiological agent causing the disruption of normal physiology may or may not be known. Furthermore, although two patients may be diagnosed with the same disorder, the particular symptoms displayed by those individuals may or may not be identical.
An “effective amount” is an amount sufficient to effect beneficial or desired therapeutic (including preventative) results. An effective amount can be administered in one or more administrations.
A “composition,” as used herein, is defined as comprising an active ingredient, such as a neutralizing antibody generated from the present invention, and at least one additive, such as a pharmaceutically acceptable carrier, including, without limitation, water, minerals, proteins, and/or other excipients known to one skilled in the art.
As used herein, the term “treating” or “treatment” is intended to mean an amelioration of a clinical symptom indicative of a disease.
As used herein, the term “preventing” or “prevention” is intended to mean a forestalling of a clinical symptom indicative of a disease
The terms “subject” and “patient,” as used herein, are used interchangeably, and can refer to any to animal, and preferably a mammal, that is the subject of an examination, treatment, analysis, test or diagnosis. Thus, subjects or patients include humans, non-human primates and other mammals, who may or may not have a disease or other pathological condition.
The term “amino acid” or “amino acid residue” typically refers to an amino acid having its art recognized definition such as an amino acid selected from the group consisting of: alanine (Ala); arginine (Arg); asparagine (Asn); aspartic acid (Asp); cysteine (Cys); glutamine (Gln); glutamic acid (Glu); glycine (Gly); histidine (His); isoleucine (Ile): leucine (Leu); lysine (Lys); methionine (Met); phenylalanine (Phe); proline (Pro); serine (Ser); threonine (Thr); tryptophan (Trp); tyrosine (Tyr); and valine (Val) although modified, synthetic, or rare amino acids may be used as desired. Thus, modified and unusual amino acids listed in 37 CFR 1.822(b)(4) are included within this definition and expressly incorporated herein by reference. Amino acids can be subdivided into various sub-groups. Thus, amino acids can be grouped as having a nonpolar side chain (e.g., Ala, Cys, Ile, Leu, Met, Phe, Pro, Val); a negatively charged side chain (e.g., Asp, Glu); a positively charged side chain (e.g., Arg, His, Lys); or an uncharged polar side chain (e.g., Asn, Cys, Gln, Gly, His, Met, Phe, Ser, Thr, Trp, and Tyr). Amino acids can also be grouped as small amino acids (Gly, Ala), nucleophilic amino acids (Ser, His, Thr, Cys), hydrophobic amino acids (Val, Leu, Ile, Met, Pro), aromatic amino acids (Phe, Tyr, Trp, Asp, Glu), amides (Asp, Glu), and basic amino acids (Lys, Arg).
The term “variant” with respect to a reference polypeptide refers to a polypeptide that possesses at least one amino acid mutation or modification (i.e., alteration) as compared to a native polypeptide. Variants generated by “amino acid modifications” can be produced, for example, by substituting, deleting, inserting and/or chemically modifying at least one amino acid in the native amino acid sequence.
An “amino acid modification” refers to a change in the amino acid sequence of a predetermined amino acid sequence. Exemplary modifications include an amino acid substitution, insertion and/or deletion.
An “amino acid modification at” a specified position, refers to the substitution or deletion of the specified residue, or the insertion of at least one amino acid residue adjacent to the specified residue. By insertion “adjacent” to a specified residue is meant insertion within one to two residues thereof. The insertion may be N-terminal or C-terminal to the specified residue.
An “amino acid substitution” refers to the replacement of at least one existing amino acid residue in a predetermined amino acid sequence with another different “replacement” amino acid residue. The replacement residue or residues may be “naturally occurring amino acid residues” (i.e. encoded by the genetic code) and selected from the group consisting of: alanine (Ala); arginine (Arg); asparagine (Asn); aspartic acid (Asp); cysteine (Cys); glutamine (Gln); glutamic acid (Glu); glycine (Gly); histidine (His); isoleucine (Ile): leucine (Leu); lysine (Lys); methionine (Met); phenylalanine (Phe); proline (Pro); serine (Ser); threonine (Thr); tryptophan (Trp); tyrosine (Tyr); and valine (Val). Substitution with one or more non-naturally occurring amino acid residues is also encompassed by the definition of an amino acid substitution herein.
A “non-naturally occurring amino acid residue” refers to a residue, other than those naturally occurring amino acid residues listed above, which is able to covalently bind adjacent amino acid residues(s) in a polypeptide chain. Examples of non-naturally occurring amino acid residues include norleucine, ornithine, norvaline, homoserine and other amino acid residue analogues such as those described in Ellman et al. Meth. Enzym. 202:301 336 (1991). To generate such non-naturally occurring amino acid residues, the procedures of Noren et al. Science 244:182 (1989) and Ellman et al., supra, can be used. Briefly, these procedures involve chemically activating a suppressor tRNA with a non-naturally occurring amino acid residue followed by in vitro transcription and translation of the RNA.
An “amino acid insertion” refers to the incorporation of at least one amino acid into a predetermined amino acid sequence. While the insertion will usually consist of the insertion of one or two amino acid residues, the present application contemplates larger “peptide insertions”, e.g. insertion of about three to about five or even up to about ten amino acid residues. The inserted residue(s) may be naturally occurring or non-naturally occurring as disclosed above.
An “amino acid deletion” refers to the removal of at least one amino acid residue from a predetermined amino acid sequence.
The term “polynucleotide(s)” refers to nucleic acids such as DNA molecules and RNA molecules and analogs thereof (e.g., DNA or RNA generated using nucleotide analogs or using nucleic acid chemistry). As desired, the polynucleotides may be made synthetically, e.g., using art-recognized nucleic acid chemistry or enzymatically using, e.g., a polymerase, and, if desired, be modified. Typical modifications include methylation, biotinylation, and other art-known modifications. In addition, the nucleic acid molecule can be single-stranded or double-stranded and, where desired, linked to a detectable moiety.
The term “mutagenesis” refers to, unless otherwise specified, any art recognized technique for altering a polynucleotide or polypeptide sequence. Preferred types of mutagenesis include error prone PCR mutagenesis, saturation mutagenesis, or other site directed mutagenesis.
“Site-directed mutagenesis” is a technique standard in the art, and is conducted using a synthetic oligonucleotide primer complementary to a single-stranded phage DNA to be mutagenized except for limited mismatching, representing the desired mutation. Briefly, the synthetic oligonucleotide is used as a primer to direct synthesis of a strand complementary to the single-stranded phage DNA, and the resulting double-stranded DNA is transformed into a phage-supporting host bacterium. Cultures of the transformed bacteria are plated in top agar, permitting plaque formation from single cells that harbor the phage. Theoretically, 50% of the new plaques will contain the phage having, as a single strand, the mutated form; 50% will have the original sequence. Plaques of interest are selected by hybridizing with kinased synthetic primer at a temperature that permits hybridization of an exact match, but at which the mismatches with the original strand are sufficient to prevent hybridization. Plaques that hybridize with the probe are then selected, sequenced and cultured, and the DNA is recovered.
The term “vector” is used to refer to a rDNA molecule capable of autonomous replication in a cell and to which a DNA segment, e.g., gene or polynucleotide, can be operatively linked so as to bring about replication of the attached segment. Vectors capable of directing the expression of genes encoding for one or more polypeptides are referred to herein as “expression vectors. The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
Percent amino acid sequence identity may be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov or otherwise obtained from the National Institute of Health, Bethesda, Md. NCBI-BLAST2 uses several search parameters, wherein all of those search parameters are set to default values including, for example, unmask=yes, strand=all, expected occurrences=10, minimum low complexity length=15/5, multi-pass e-value=0.01, constant for multi-pass=25, dropoff for final gapped alignment=25 and scoring matrix=BLOSUM62.
“Antibody-dependent cell-mediated cytotoxicity” and “ADCC” are used herein to refer to a cell-mediated reaction in which nonspecific cytotoxic cells that express FcRs (e.g. Natural Killer (NK) cells, neutrophils, and macrophages) recognize bound antibody on a target cell and subsequently cause lysis of the target cell. Various immune cells express different Fc receptors (FcRs). Thus, the primary cells for mediating ADCC, NK cells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII and FcγRIII.
The terms “influenza A subtype” or “influenza A virus subtype” are used interchangeably, and refer to influenza A virus variants that are characterized by various combinations of the hemagglutinin (H) and neuraminidase (N) viral surface proteins, and thus are labeled by a combination of an H number and an N number, such as, for example, H1N1 and H3N2. The terms specifically include all strains (including extinct strains) within each subtype, which usually result from mutations and show different pathogenic profiles. Such strains will also be referred to as various “isolates” of a viral subtype, including all past, present and future isolates. Accordingly, in this context, the terms “strain” and “isolate” are used interchangeably.
The term “influenza” is used to refer to a contagious disease caused by an influenza virus.
B. General Techniques
Techniques for performing the methods of the present invention are well known in the art and described in standard laboratory textbooks, including, for example, Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997); Molecular Cloning: A Laboratory Manual, Third Edition, J. Sambrook and D. W. Russell, eds., Cold Spring Harbor, N.Y., USA, Cold Spring Harbor Laboratory Press, 2001; O'Brian et al., Analytical Chemistry of Bacillus Thuringiensis, Hickle and Fitch, eds., Am. Chem. Soc., 1990; Bacillus thuringiensis: biology, ecology and safety, T. R. Glare and M. O'Callaghan, eds., John Wiley, 2000; Antibody Phage Display, Methods and Protocols, Humana Press, 2001; and Antibodies, G. Subramanian, ed., Kluwer Academic, 2004. Mutagenesis can, for example, be performed using site-directed mutagenesis (Kunkel et al., Proc. Natl. Acad. Sci USA 82:488-492 (1985)). PCR amplification methods are described in U.S. Pat. Nos. 4,683,192, 4,683,202, 4,800,159, and 4,965,188, and in several textbooks including “PCR Technology: Principles and Applications for DNA Amplification”, H. Erlich, ed., Stockton Press, New York (1989); and PCR Protocols: A Guide to Methods and Applications, Innis et al., eds., Academic Press, San Diego, Calif. (1990).
The methods of the present invention are not limited by any particular technology used for the display of antibodies. Although the invention is illustrated with reference to phage display, antibodies of the present invention can also be identified by other display and enrichment technologies, such as, for example, ribosome or mRNA display (Mattheakis et al., Proc. Natl. Acad. Sci. USA 91:9022-9026 (1994); Hanes and Pluckthun, Proc. Natl. Acad. Sci. USA 94:4937-4942 (1997)), microbial cell display, such as bacterial display (Georgiou et al., Nature Biotech. 15:29-34 (1997)), or yeast cell display (Kieke et al., Protein Eng. 10:1303-1310 (1997)), display on mammalian cells, spore display (Isticato et al., J. Bacteriol. 183:6294-6301 (2001); Cheng et al., Appl. Environ. Microbiol. 71:3337-3341 (2005) and co-pending provisional application Ser. No. 60/955,592, filed Aug. 13, 2007), viral display, such as retroviral display (Urban et al., Nucleic Acids Res. 33:e35 (2005), display based on protein-DNA linkage (Odegrip et al., Proc. Acad. Natl. Sci. USA 101:2806-2810 (2004); Reiersen et al., Nucleic Acids Res. 33:e10 (2005)), and microbead display (Sepp et al., FEBS Lett. 532:455-458 (2002)).
In ribosome display, the antibody and the encoding mRNA are linked by the ribosome, which at the end of translating the mRNA is made to stop without releasing the polypeptide. Selection is based on the ternary complex as a whole.
In a mRNA display library, a covalent bond between an antibody and the encoding mRNA is established via puromycin, used as an adaptor molecule (Wilson et al., Proc. Natl. Acad. Sci. USA 98:3750-3755 (2001)). For use of this technique to display antibodies, see, e.g., Lipovsek and Pluckthun, J. Immunol. Methods. 290:51-67 (2004).
Microbial cell display techniques include surface display on a yeast, such as Saccharomyces cerevisiae (Boder and Wittrup, Nat. Biotechnol. 15:553-557 (1997)). Thus, for example, antibodies can be displayed on the surface of S. cerevisiae via fusion to the α-agglutinin yeast adhesion receptor, which is located on the yeast cell wall. This method provides the possibility of selecting repertoires by flow cytometry. By staining the cells by fluorescently labeled antigen and an anti-epitope tag reagent, the yeast cells can be sorted according to the level of antigen binding and antibody expression on the cell surface. Yeast display platforms can also be combined with phage (see, e.g., Van den Beucken et al., FEBS Lett. 546:288-294 (2003)).
For a review of techniques for selecting and screening antibody libraries see, e.g., Hoogenboom, Nature Biotechnol. 23(9):1105-1116 (2005).
C. Detailed Description of Preferred Embodiments
I. Preparation of Donor-Specific Antibody Libraries
The present invention concerns donor-specific antibody libraries from individuals who have successfully survived or are surviving an encounter with a specific disease. The resulting antibody repertoires will include antibodies that were used by the donor to defend specifically against a relevant disease, and thus are important tools, for example, for developing neutralizing antibodies for the prevention and/or treatment of a target disease.
While the present invention is applicable to any target disease that evokes antibody production in a human subject, representative, non-limiting, examples of such diseases are listed in Table 1.








TABLE 1





Type of disorder
Representative examples







infectious disorder
Influenza viral infection, hepatitis C virus



(HCV) infection, herpes simplex virus (HSV)



infection, human immunodeficiency virus



(HIV) infection, Methicillin-resistant



Staphylococcus aureus (MRSA) infection,



Epstein-Barr virus (EBV) infection, respiratory



syncytial virus (RSV) infection, Pseudomonas,



Candida infections


Respiratory disorder
Asthma, Allergies, chronic obstructive



pulmonary disease (COPD), idiopathic



pulmonary fibrosis (IPF), adult respiratory



distress syndrome (ARDS)


metabolic disorder
Frailty, cachexia, sarcopenia, Obesity, type II



diabedyslipidemia, metabolic syndrome-



associated myocardial infarction (MI), chronic



renal failure (CRF), osteoporosis


digestive disorder
irritable bowel syndrome (IBS), inflammatory



bowel disease (IBD), Chron's disease, fatty liver



disease, fibrosis, drug-induced liver disease


Neurological disorder
Alzheimer's disease, multiple sclerosis (MS),



Parkinson's disease, bovine spongiform



encephalopathy (BSE, mad cow disease)


Cancer
e.g., breast, renal, stomach, melanoma, lung,



colon, glioma, lymphoma









A method of creating the donor-specific libraries of the present invention is schematically illustrated in FIG. 1. As a first step, potential donors are identified. The patient donor may currently suffer from or may have recovered from and survived a target disease. Thus, for example, as illustrated in the Examples, the donor-specific libraries herein may be created from the bone marrow of convalescent patients of prior influenza infections, including seasonal influenza outbreaks, epidemics, and pandemics.
When selecting or identifying a patient donor, it is important to confirm that the patient indeed had or is having the target disease. Part of the confirmation is the examination of the medical history of the patient donor. In addition to the medical history, various other factors, such as the medical history of the patient's family, the patient's sex, weight, health state, etc., should be taken into consideration. If the patient history is not available or unreliable, or for any other reason, such as a further confirmation measure, the serological profile of the patient may be determined. Serological assays are well known in the art and can be performed in various formats, such as in the form of various ELISA assay formats. Thus, for example, the presence of antibodies to an influenza virus can be detected by the well-known hemagglutinin inhibition (HAI) assay (Kendal, A. P., M. S. Pereira, and J. J. Skehel. 1982. Concepts and procedures for laboratory-based influenza surveillance. U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control, Atlanta, Ga.), or the microneutralization assay (Harmon et al., J. Clin. Microbiol. 26:333-337 (1988)). This step might not be necessary if the serum sample has already been confirmed to contain influenza neutralizing antibodies.
In order to prepare donor-specific human antibody libraries, samples containing lymphocytes are collected from individuals (patient donors) known to have developed a target disease, such as at least one disease from those listed in Table 1. The sample may, for example, derive from bone marrow, blood, spleen, lymph nodes, tonsils, thymus, and the like. Bone marrow is a preferred source of the antibody libraries herein, since it represents the complete “fossil archive” of individual donor's mature antibody repertoire.
Samples containing lymphocytes can be collected from the patient donor at various time points. In one embodiment, lymphocytes are collected from a patient who has recovered from the targeted disease(s) at least for 1, 5, 10, 15, 20, 25 days, at least for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 months, or at least for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 years. In another embodiment, lymphocytes are collected from a patient who is having the targeted disease(s) at the time of collection, and has been diagnosed as having the disease(s) at least 1, 5, 10, 15, 20, 25 days, or at least 1, 2, 3, 4, 5, 6, 8, 9, 10 months, or 1, 2, 3, 4, or 5 years prior to collection.
Peripheral blood samples, especially from geographically distant sources, may need to be stabilized prior to transportation and use. Kits for this purpose are well known and commercially available, such as, for example, BD Vacutainer® CPTTM cell preparation tubes can be used for centrifugal purification of lymphocytes, and guanidium, Trizol, or RNAlater used to stabilize the samples. Methods and kits for isolating lymphocytes from other sources, such as lymphoid organs are also well known and commercially available.
Upon receipt of the stabilized lymphocytes or whole bone marrow, RNA is extracted and RT-PCR is performed to rescue antibody heavy and light chain repertoires, using immunoglobulin oligo primers known in the art.
Methods for preparation of RNA from bone marrow lymphocytes, or lymphocytes from any other source, are well known in the art. General methods for mRNA extraction are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). RNA purification kits are available from commercial manufacturers, such as Qiagen, and can be used according to the manufacturer's instructions.
Since RNA cannot serve as a template for PCR, it is first reverse transcribed into cDNA, which is subjected to PCR amplification. The two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling. For example, extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit (Perkin Elmer, Calif., USA), following the manufacturer's instructions. The derived cDNA can then be used as a template in the subsequent PCR reaction.
In order to create phage-display libraries, the PCR repertoire products may be combined with linker oligos to generate scFv libraries to clone directly in frame with m13 pIII protein, following procedures known in the art. Libraries using other display techniques, such as those discussed above, can be prepared by methods well known in the art.
In a typical protocol, whole RNA is extracted by Tri BD reagent (Sigma) from fresh or RNAlater stabilized tissue. Subsequently, the isolated donor total RNA is further purified to mRNA using Oligotex purification (Qiagen). Next first strand cDNA synthesis, is generated by using random nonamer oligonucleotides and or oligo (dT)18 primers (SEQ ID NO: 1) according to the protocol of AccuScript reverse transcriptase (Stratagene). Briefly, 100 ng mRNA, 0.5 mM dNTPs and 300 ng random nonamers and or 500 ng oligo (dT)18 primers (SEQ ID NO: 1) in Accuscript RT buffer (Stratagene) are incubated at 65° C. for 5 mM, followed by rapid cooling to 4° C. Then, 100 mM DTT, Accuscript RT, and RNAse Block are added to each reaction and incubated at 42° C. for 1 h, and the reverse transcriptase is inactivated by heating at 70° C. for 15 minutes. The cDNA obtained can be used as a template for RT-PCR amplification of the antibody heavy and light chain V genes, which can then be cloned into a vector, or, if phage display library is intended, into a phagemid vector. This procedure generates a repertoire of antibody heavy and light chain variable region clones (VH and VL libraries), which can be kept separate or combined for screening purposes. The vector, such as a phagemid vector, can then be introduced into a host cell, such as an E. coli host, to generate a vector collection comprising a repertoire of nucleic acid molecules encoding antibody light chains or heavy chains or fragments thereof. In each case, the vector collection may comprise a single or more than one antibody light chain or heavy chain subtype. Thus, the vector collection may comprise sequences encoding antibody κ and/or λ light chains.
In the methods of the present invention, typically antibody light chains and antibody heavy chains are at first cloned separately, as discussed above, also separating the κ and λ light chain libraries. The libraries can be archived, and, when needed, the heavy chain library can be combined with the segregated κ and λ light chain libraries and heavy and light chain pairings can be identified, e.g. by panning, in the case of phage display. It is possible to repeat these steps multiple times with various libraries or sub-libraries, depending on the goal to be attained. The methods of the present invention provide great flexibility in including or excluding libraries, sub-libraries or clones, as needed during panning in order to maximize success.
In particular, because the sequences present in the vector collection harbor the coding sequences of the antibody heavy and light chains (or fragments) separately, the sequences may be excised and inserted into one or more expression vectors for expression of the antibody heavy and light chains, or fragments thereof. Preferably, the coding sequences of the antibody heavy and light chains, or fragments thereof, are inserted into the same expression vector for coexpression of the heavy and light chains to produce the library of the antibodies or antibody fragments.
The expression vectors of the present invention contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2μ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
Expression vectors will typically contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli. 
An example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the antibodies-encoding nucleic acid, such as DHFR or thymidine kinase. An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980). A suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)]. The trp1 gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].
Expression and cloning vectors usually contain a promoter operably linked to the antibody-encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the β-lactamase and lactose promoter systems [Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and hybrid promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding antibodies
Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman et al., J. Biol. Chem., 255:2073 (1980)] or other glycolytic enzymes [Hess et al., J. Adv. Enzyme Reg., 7:149 (1968); Holland, Biochemistry, 17:4900 (1978)], such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.
Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
Transcription of the heavy chain or light chain genes in the expression vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
Transcription of a DNA encoding the antibody genes by higher eukaryotes may be increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer may be spliced into the vector at a position 5′ or 3′ to the antibody coding sequence, but is preferably located at a site 5′ from the promoter.
Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding antibody heavy and light chains.
Still other methods, vectors, and host cells suitable for adaptation to the synthesis of polypeptide, in recombinant vertebrate cell culture are described in Gething et al., Nature, 293:620-625 (1981); Mantei et al., Nature, 281:40-46 (1979); EP 117,060; and EP 117,058.
In a particular embodiment, the antibody library is produced in the form of a phage library, where the coding sequences of the antibody heavy and light chains, or fragments thereof, are cloned into a phagemid vector, such as a vector comprising the bacteriophage gene III. Phagemid vectors are well known and commercially available, including, for example, the pBluescript vector SKII+ (Stratagene, Genbank Accession X52328), and other pBluescript vectors. Phage display technology enables the generation of large repertoires of human antibodies, and the biopanning procedure allows the selection of individual antibodies with any desired specificity or other properties.
For example, immunoglobulin repertoires from peripheral lymphocytes of survivors of earlier epidemics and pandemics, such as the 1918 Spanish Flu, can be retrieved, stabilized, rescued and expressed in a manner similar to that described above. For additional H1 and H3 libraries, repertoires can be recovered from properly timed vaccinated locally-sourced donors. As an additional option, commercially available bone marrow total RNA or mRNA can be purchased from commercial sources to produce libraries suitable for H1 and H3, and, depending upon the background of donor, also suitable for H2 antibody screening. In general, for target diseases where vaccination is an available treatment option, antibodies can be isolated from biological samples obtained from immunized human donors as well. From immunized patients that have developed titers of antibody recognizing the particular antigen, bone marrow, blood, or another source of lymphocytes, is collected, and antibodies produced are isolated, amplified and expressed as described above.
As discussed above, for each donor, antibody light and heavy chain libraries can be cloned separately. Thus, for each donor, various κ and λ light chain families can be separately pooled and cloned in equimolar amounts. Similarly, for each donor, various heavy chain families can be pooled and cloned in equimolar amounts. By enabling gene family specific rescue of antibodies, the methods of the present invention yield libraries more completely representing the antibody repertoire of the donor, including antibodies that are less abundant and, in the case of pooled antibody libraries, guaranteeing immunoglobulin contributions from any and all individuals. For example, as illustrated in Example 1 by the Examples, in preparing the influenza heavy and light chain libraries herein, 6 κ light chain families, 11λ light chain families and 4 heavy chain families were rescued.
A typical screen can yield zero, one, or more than one target specific positive clone(s). If a particular combinatorial antibody library or libraries have been exhaustively screened and no further solutions seem attainable this may not be a failure of the heavy and light chain repertoire(s) ability to bind target, but rather the collection may have failed to bring together the necessary heavy and light chain pair required to bind target. A typical rescued repertoire of light chains from any individual may contain between about 105-106 unique light chains and between about 106-108 unique heavy chains. The possible combinatorial products of such pairings range from 1011 to 1014. Such a collection exceeds the practical limits of most display systems, such as phage display, by several orders of magnitude. Consequently, with current display technologies (such as phage display), only a fraction of the combinatorial possibilities are captured and assessed in any single phage antibody library. Therefore, recloning the original set of heavy chains with the original collection of light chains will generate an entirely new set of shuffled heavy and light chain combinations with likely novel antibodies to a particular target. Such newly reshuffled collections were found to transform previously existing poorly performing donor specific libraries into highly productive collections. Specifically, for a collection from a single donor previously only 0.3×-fold enrichment could be achieved compared to background after three rounds of selection. However, when this collection was recloned and reshuffled it became capable of 15-fold enrichment following 3 rounds of panning resulting in 55 novel sequences from 92 selected clones.
As mentioned previously, a typical screen can yield any number of target specific positive clones. The present invention enables the identification of the origins of any clone by their embedded barcode. As a typical antibody screen may combine phage antibodies from numerous donor specific libraries it is possible that some of the libraries and their combinatorial clones are not completely represented as antibody bearing phage particles. In which case a positive clone may have resulted from only a limited physical set of all the possible cloned solutions present in the sub-library phage population being screened. In such an instance it is of considerable interest to more fully interrogate the collection of donor specific phage. In this case the barcode from a positive clone guides one to the specific library responsible for the clone and allows to exclusively and more deeply screen the collection of interest.
In instances where desired antibodies must have functional capabilities beyond those initially used as the basis for the initial library construction, such as neutralization, or activation, we can prospectively profile individual donor sera for evidence of such activities. If the desired activities are present at reasonable titers in any particular donor sera, one can select those corresponding libraries are selected to screen against the target of interest. In other instances the relevant selection criteria may be unrelated to serology, but related to donor characteristics such as age, gender, or medical histories. In any event, donor profiles are logical guides for library selection and possible only in donor specific and segregated antibody libraries.
It is not unusual to complete a phage panning screen and discover the presence of immunodominant clones. Furthermore, it is also not unusual to rediscover such clone upon repeated panning screening regimens. In the case of a dominant clone or clones, where either more or different clones are desirable, it is important to avoid the library material responsible for the presence of this clone. In typical phage antibody libraries the specific library or materials responsible for the clones origin are not separable from the collection, however in donor specific libraries it is possible to rescreen the libraries and simply omit the undesirable donor sublibrary or sublibraries, thereby forcing positive selection away from previously identified dominant clones.
Although, for simplicity, the libraries are described as heavy or light chain libraries, it will be apparent to those of ordinary skill in the art that the same description applies to the libraries of antibody fragments, fragments of antibody heavy and/or light chains, and libraries of antibody-like molecules.
In a particular embodiment, antibodies with dual specificities, such as, for example, showing reactivity with two different influenza A subtypes and/or with two strains (isolates) of the same subtype, and/or with human and non-human isolates, can be discovered and optimized through controlled cross-reactive selection and/or directed combinatorial and/or mutagenic engineering.
In a typical enrichment scheme, illustrated in FIG. 2, a library including antibodies showing cross-reactivity to two targets, designated as targets A and B, are subjected to multiple rounds of enrichment. If enrichment is based on reactivity with target A, each round of enrichment will increase the reactive strength of the pool towards target A. Similarly, if enrichment is based on reactivity with target B, each round of enrichment will increase the reactive strength of the pool towards target B. Although FIG. 2 refers to panning, which is the selection method used when screening phage display libraries (see below), the approach is equally applicable to any type of library discussed above, or otherwise known in the art, and to any type of display technique. Targets A and B include any targets to which antibodies bind, including but not limited to various isolates, types and sub-types of influenza viruses.
If the goal is to identify neutralizing antibodies with multiple specificities, a cross-reactive discovery selection scheme can be used. In the interest of simplicity, this scheme is illustrated in FIG. 3 showing the selection of antibodies with dual specificities. In this case, an antibody library including antibodies showing reactivity with two targets, targets A and B, is first selected for reactivity with one of the targets, e.g., target A, followed by selection for reactivity with the other target, e.g., target B. Each successive selection round reinforces the reactive strength of the resulting pool towards both targets. Accordingly, this method is particularly useful for identifying antibodies with dual specificity. Of course, the method can be extended to identifying antibodies showing reactivity towards further targets, by including additional rounds of enrichment towards the additional target(s). Again, if the library screened is a phage display library, selection is performed by cross-reactive panning, but other libraries and other selection methods can also be used.
A combination of the two methods discussed above includes two separate enrichment rounds for reactivity towards target A and target B, respectively, recombining the two pools obtained, and subsequent cross-reactive selection rounds, as described above. This approach is illustrated in FIG. 4. Just as in the pure cross-reactive selection, each round of selection of the recombined library increases the reactive strength of the resulting pool towards both targets.
In a further embodiment, illustrated in FIG. 5, first a clone showing strong reactivity with a target A, and having detectable cross-reactivity with target B is identified. Based on this clone, a mutagenic library is prepared, which is then selected, in alternating rounds, for reactivity with target B and target A respectively. This scheme will result in antibodies that maintain strong reactivity with target A, and have increased reactivity with target B. Just as before, selection is performed by panning, if the libraries screened are phage display libraries, but other libraries, other display techniques, and other selection methods can also be used, following the same strategy.
As discussed above, targets A and B can, for example, be two different subtypes of the influenza A virus, two different strains (isolates) of the same influenza A virus, subtypes or isolates from two different species, where one species is preferably human. Thus, for example, target A may be an isolate of the 2004 Vietnam isolate of the H5N1 virus, and target B may be a 1997 Hong Kong isolate of the H5N1 virus. It is emphasized that these examples are merely illustrative, and antibodies with dual and multiple specificities to any two or multiple targets can be identified, selected and optimized in an analogous manner.
Once neutralizing antibodies with the desired properties have been identified, it might be desirable to identify the dominant epitope or epitopes recognized by the majority of such antibodies. Methods for epitope mapping are well known in the art and are disclosed, for example, in Morris, Glenn E., Epitope Mapping Protocols, Totowa, N.J. ed., Humana Press, 1996; and Epitope Mapping: A Practical Approach, Westwood and Hay, eds., Oxford University Press, 2001.
II. Identifying Donor-Specific Antibody Library with Unique Barcoding
According to the present invention, following amplification of the antibody heavy and light chain repertoires from cDNA, such as bone marrow cDNA, prepared as described above, preferably antibody heavy and light chain libraries are cloned separately for each patient donor, where the individual libraries can be distinguished using unique barcodes.
The barcodes preferably are selected such that they are capable of propagating along with the clone(s) labeled, without interfering with the expression of the desired antibody chain or fragment thereof. In an exemplary embodiment of the present invention, the barcode is inserted into the sequence of the expression vector, preferably, the 3′ untranslated region following the terminal pIII stop codon when a phagemid vector is used. Upon clonal isolation, a vector's unique sequence is determined and subsequently dedicated to a single defined library. This defined library can be derived not only from a single donor, but also from discrete pools of donors, or a synthetic repertoire or a semi-synthetic collection. In another embodiment, the barcode is inserted into the coding sequence of the antibody heavy and/or light chain or fragment thereof, at a position or in a form that does not interfere with the expression of the respective chains.
Thus the barcodes can be non-coding DNA sequences of about 1-24 contiguous non-coding nucleotides in length that can be deconvoluted by sequencing or specific PCR primers. This way, a collection of nucleic acids, such as an antibody repertoire, can be linked at the cloning step. In a exemplary embodiment of the present invention, the barcode is 3 or 5 bases of randomly generated sequence.
In another example, the barcodes are coding sequences of silent mutations. If the libraries utilize restriction enzymes that recognize interrupted palidromes (e.g. Sfi GGCC GGCC (SEQ ID NO: 2)), distinct nucleotides can be incorporated in place of the “N's” to distinguish various collections of clones, such as antibody libraries. This barcoding approach has the advantage that the repertoire is linked at the amplification step.
In a further embodiment, the barcodes are non-contiguous nucleotide sequences, which may be present in the vector sequence and/or the coding sequence of the desired antibody chain. Thus, a barcode with a non-contiguous sequence provides a great degree of flexibility in identifying the origins of the various individual sequences, and monitoring their subsequent handling.
In a different example, the barcodes are coding sequences that encode immunologically distinct peptide or protein sequences fused to phage particles. Examples include, for example, epitope (e.g. Myc, HA, FLAG) fusions to pIII, pVIII, pVII, or pIX phages. The epitopes can be used singly or in various combinations, and can be provided in cis (on the library-encoding plasmid) or in trans (specifically modified helper phage) configuration.
Other examples of possible barcodes include, without limitation, chemical and enzymatic phage modifications (for phage libraries) with haptens or fluorescent chromophores. Such tags are preferred for a single round of selection.
The individual heavy and light chain libraries obtained from individual donors, or other barcoded clone or collections, can be pooled, without losing the ability to distinguish the source of individual sequences.
III. Optimizing Neutralizing Antibodies From the Donor-Specific Antibody Libraries
If desired, cross-reactivity of the neutralizing antibodies with dual or multiple specificity can be further improved by methods known in the art, such as, for example, by Look Through Mutagenesis (LTM), as described in US. Patent Application Publication No. 20050136428, published Jun. 23, 2005, the entire disclosure of which is hereby expressly incorporated by reference.
Look-through mutagenesis (LTM) is a multidimensional mutagenesis method that simultaneously assesses and optimizes combinatorial mutations of selected amino acids. The process focuses on a precise distribution within one or more complementarity determining region (CDR) domains and explores the synergistic contribution of amino acid side-chain chemistry. LTM generates a positional series of single mutations within a CDR where each wild type residue is systematically substituted by one of a number of selected amino acids. Mutated CDRs are combined to generate combinatorial single-chain variable fragment (scFv) libraries of increasing complexity and size without becoming prohibitive to the quantitative display of all variants. After positive selection, clones with improved properties are sequenced, and those beneficial mutations are mapped. To identify synergistic mutations for improved binding properties, combinatorial libraries (combinatorial beneficial mutations, CBMs) expressing all beneficial permutations can be produced by mixed DNA probes, positively selected, and analyzed to identify a panel of optimized scFv candidates. The procedure can be performed in a similar manner with Fv and other antibody libraries.
Mutagenesis can also be performed by walk-through mutagenesis (WTM), as described above.
Another useful mutagenic method to intentionally design cross-reactivity of the antibodies herein with more than one influenza A subtype and/or more than one isolate of the same subtype, is referred herein as “destinational” mutagenesis. Destinational mutagenesis can be used to rationally engineer a collection of antibodies based upon one or more antibody clones, preferably of differing reactivities. In the context of the present invention, destinational mutagenesis is used to encode single or multiple residues defined by analogous positions on like sequences such as those in the individual CDRs of antibodies. In this case, these collections are generated using oligo degeneracy to capture the range of residues found in the comparable positions. It is expected that within this collection a continuum of specificities will exist between or even beyond those of the parental clones. The objective of destinational mutagenesis is to generate diverse multifunctional antibody collections, or libraries, between two or more discrete entities or collections. To create a destinational mutagenesis library, the CDR sequences for both antibodies are first attained and aligned. Next all positions of conserved identity are fixed with a single codon to the matched residue. At non-conserved positions a degenerate codon is incorporated to encode both residues. In some instances the degenerate codon will only encode the two parental residues at this position. However, in some instances additional co-products are produced. The level of co-product production can be dialed in to force co-product production or eliminate this production dependent upon size limits or goals.
Thus, for example, if the first position of the two antibodies respectively are threonine and alanine, the degenerate codon with A/G-C- in the first two positions would only encode threonine or alanine, irrespective of the base in the third position. If, for example, the next position residues are lysine and arginine the degenerate codon A-A/G-A/G will only encode lysine or arginine. However, if the degenerate codon A/C-A/G-A/G/C/T were used then asparagine, histidine, glutamine, and serine coproducts will be generated as well.
As a convenience it is simpler to use only antibodies with matched CDR lengths. One way to force this is to screen a size restricted library for the second antigen, based on the CDR length and potentially even framework restrictions imparted by the initially discovered antibody. It is noted, however, that using CDRs of equal length is only a convenience and not a requirement. It is easy to see that, while this method will be useful to create large functionally diverse libraries of influenza A virus neutralizing antibodies, its applicability is much broader. This mutagenesis technique can be used to produce functionally diverse libraries or collections of any antibody. Thus, FIG. 6 is included herein to illustrate the use of the destinational mutagenesis method using CDRs of a TNF-α antibody and a CD11a antibody as the parental sequences mutagenized.
Other exemplary mutagenesis methods include saturation mutagenesis and error prone PCR.
Saturation mutagenesis (Hayashi et al., Biotechniques 17:310-315 (1994)) is a technique in which all 20 amino acids are substituted in a particular position in a protein and clones corresponding to each variant are assayed for a particular phenotype. (See, also U.S. Pat. Nos. 6,171,820; 6,358,709 and 6,361,974.)
Error prone PCR (Leung et al., Technique 1:11-15 (1989); Cadwell and Joyce, PCR Method Applic. 2:28-33 (1992)) is a modified polymerase chain reaction (PCR) technique introducing random point mutations into cloned genes. The resulting PCR products can be cloned to produce random mutant libraries or transcribed directly if a T7 promoter is incorporated within the appropriate PCR primer.
Other mutagenesis techniques are also well known and described, for example, in In Vitro Mutagenesis Protocols, J. Braman, Ed., Humana Press, 2001.
Optimization can be based on any of the libraries discussed above, or any other types of libraries known in the art, alone or in any combination.
IV. Production of Neutralizing Antibodies
Once antibodies with the desired neutralizing properties are identified, such antibodies, including antibody fragments can be produced by methods well known in the art, including, for example, hybridoma techniques or recombinant DNA technology.
In the hybridoma method, a mouse or other appropriate host animal, such as a hamster, is immunized to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the protein used for immunization. Alternatively, lymphocytes may be immunized in vitro. Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986)).
The hybridoma cells thus prepared are seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells. For example, if the parental myeloma cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
Preferred myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. Among these, preferred myeloma cell lines are murine myeloma lines, such as those derived from MOPC-21 and MPC-11 mouse tumors available from the Salk Institute Cell Distribution Center, San Diego, Calif. USA, and SP-2 or X63-Ag8-653 cells available from the American Type Culture Collection, Rockville, Md. USA. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol. 133:3001 (1984); and Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987)).
Culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against the antigen. Preferably, the binding specificity of monoclonal antibodies produced by hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA).
Recombinant monoclonal antibodies can, for example, be produced by isolating the DNA encoding the required antibody chains and co-transfecting a recombinant host cell with the coding sequences for co-expression, using well known recombinant expression vectors. Recombinant host cells can be prokaryotic and eukaryotic cells, such as those described above.
The choice of human variable domains, both light and heavy, to be used in making the humanized antibodies is very important to reduce antigenicity. According to the so-called “best-fit” method, the sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable-domain sequences. The human sequence which is closest to that of the rodent is then accepted as the human framework region (FR) for the humanized antibody (Sims et al., J. Immunol. 151:2296 (1993); Chothia et al., J. Mol. Biol. 196:901 (1987)). It is important that antibodies be humanized with retention of high affinity for the antigen and other favorable biological properties. To achieve this goal, according to a preferred method, humanized antibodies are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences.
In addition, human antibodies can be generated following methods known in the art. For example, transgenic animals (e.g., mice) can be made that are capable, upon immunization, of producing a full repertoire of human antibodies in the absence of endogenous immunoglobulin production. See, e.g., Jakobovits et al., Proc. Natl. Acad. Sci. USA 90:2551 (1993); Jakobovits et al., Nature 362:255-258 (1993); Bruggermann et al., Year in Immuno. 7:33 (1993); and U.S. Pat. Nos. 5,591,669, 5,589,369 and 5,545,807.
V. Use of Neutralizing Antibodies
The neutralizing antibodies of the present invention can be used for the prevention and/or treatment of the targeted diseases. For therapeutic applications, the antibodies or other molecules, the delivery of which is facilitated by using the antibodies or antibody-based transport sequences, are usually used in the form of pharmaceutical compositions. Techniques and formulations generally may be found in Remington's Pharmaceutical Sciences, 18th Edition, Mack Publishing Co. (Easton, Pa. 1990). See also, Wang and Hanson “Parenteral Formulations of Proteins and Peptides: Stability and Stabilizers,” Journal of Parenteral Science and Technology, Technical Report No. 10, Supp. 42-2S (1988).
Antibodies are typically formulated in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEENTM, PLURONICSTM or polyethylene glycol (PEG).
The antibodies also may be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization (for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively), in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nanoparticles and nanocapsules), or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, supra.
The neutralizing antibodies disclosed herein may also be formulated as immunoliposomes. Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al., Proc. Natl. Acad. Sci. USA 82:3688 (1985); Hwang et al., Proc. Natl Acad. Sci. USA 77:4030 (1980); U.S. Pat. Nos. 4,485,045 and 4,544,545; and WO97/38731 published Oct. 23, 1997. Liposomes with enhanced circulation time are disclosed in U.S. Pat. No. 5,013,556.
Particularly useful liposomes can be generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter. Fab′ fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et al. J. Biol. Chem. 257:286-288 (1982) via a disulfide interchange reaction. A chemotherapeutic agent is optionally contained within the liposome. See Gabizon et al. J. National Cancer Inst. 81(19)1484 (1989).
For the prevention or treatment of disease, the appropriate dosage of antibody will depend on the type of infection to be treated, the severity and course of the disease, and whether the antibody is administered for preventive or therapeutic purposes. The antibody is suitably administered to the patient at one time or over a series of treatments. Depending on the type and severity of the disease, about 1 μg/kg to about 15 mg/kg of antibody is a typical initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion.
Further details of the invention are illustrated by the following non-limiting Examples.
EXAMPLE 1
Antibody Libraries from Survivors of Prior Bird Flu Outbreaks and Preparation of Neutralizing Antibodies
Materials and Methods
Bone Marrow Protocol and Sera Preparation
Blood was obtained by standard venopuncture, allowed to clot, and processed to recover serum. The serum was stored at −20° C. for 3-4 days until they were shipped on dry ice. Donors were anaesthetized with an injection of a local anesthetic and 5 ml of bone marrow was removed from the pelvic bone of each H5N1 survivor. Next the 5 ml of bone marrow was placed into a sterile 50-ml tube containing 45 ml RNAlater (Ambion). The mixture was gently inverted approximately 8-20 times, until there were no visible clumps and the marrow and RNAlater were mixed well. Next the specimen was refrigerated the between 2-10° C. overnight. Following the overnight refrigeration, the specimens were stored at −20° C. for 3-4 days until they were shipped on dry ice. Upon receipt the RNAlater/marrow and sera containing tubes were stored at −80° C. until processed.
Serology: HA ELISA
ELISA plates (Thermo, Immulon 4HBX 96W) were coated with 100 μl of 100 ng/mL H5 hemagglutinin (Protein Sciences, A/Vietnam/1203/2004) in 1× ELISA Plate Coating Solution (BioFX) by overnight incubation at room temperature. The next day plates were washed three times with 300 μPBS/0.05% Tween-20 (PBST). Following the wash, 300 μl of a blocking solution (4% Non-Fat dry Milk in PBS/0.05% Tween-20) was added and incubated for 1 hour at RT. Following the blocking step, the plates were washed three times with 300 μl PBS/0.05% Tween-20. Next, 100 μl serum samples diluted 1:20,000 in PBS/0.05% Tween were incubated for 1-2 hours at RT and then washed three times with 300 μl PBS/0.05% Tween-20. 100 μl of an anti-human Fc-HRP conjugate diluted 1:5,000 in PBS/0.05% Tween was incubated for 1-2 hours at RT and then washed three times with 300 μl PBS/0.05% Tween-20. Following this final wash, 100 μl of chromogenic substrate solution was added (TMB1 Substrate, BioFx) and after sufficient amount of time terminated by the addition of 100 μl of STOP Solution (BioFx). Absorbances at 450 nm were read on a plate reader (Molecular Devices Thermomax microplate reader with Softmax Pro software), data recorded, and subsequently plotted using Excel (Microsoft).
Bone Marrow: RNA Extraction and mRNA Purification
Bone marrow ( ̃2.5 ml in 20 ml RNA later), previously stored at −80° C., was recovered by centrifugation to remove RNA later and then resuspended in 11.25 ml TRI BD reagent (Sigma) containing 300 μl Acetic Acid. The pellet was then vortexed vigorously. Next 1.5 ml BCP (1-bromo-3-chloropropane, Sigma) was added, mixed by vortexing, incubated at RT for 5 min, and then centrifuged at 12000×g for 15 min at 4° C. The aqueous phase was carefully removed to not disturb the interface. Total RNA from the aqueous phase was next precipitated by addition of 25 ml isopropanol, incubation at RT for 10 minutes, and centrifugation at 12000×g for 10 min at 4° C. Following the addition of isopropanol, two phases were formed due to residual RNAlater, resulting in the precipitated RNA settling at the interface. To eliminate the residual RNAlater and allow maximal recovery of RNA, 5 ml aliquots of 50% isopropanol in H2O were added and mixed until no phase separation was noticeable, at which point the RNA was pelleted by centrifugation at 12000×g for 10 min at 4° C. The RNA pellet was washed with 75% EtOH, transferred to an RNAse-free 1.6 ml microcentrifuge tube, and again recovered by centrifugation. Finally the RNA pellet was resuspended in 100 μl 1 mM Na-phosphate, pH 8.2 and the A260 and A280 were read to assess RNA purity.
Prior to reverse transcription mRNA was purified from total RNA according to Qiagen Oligotex mRNA purification kit. Briefly, 50-200 μg bone marrow RNA was brought to 250 μA with RNase-free water and mixed with 250 μA of OBB buffer and Oligotex suspension followed by incubation for 3 min at 70° C. Hybridization between the oligo dT30 (SEQ ID NO: 3) of the Oligotex particle and the mRNA poly-A-tail was carried out at room temperature for 10 min. The hybridized suspensions were then transferred to a spin column and centrifuged for 1 min. The spin column was washed twice with 400 μl Buffer OW2. Purified mRNA was then eluted twice by centrifugation with 20 W hot (70° C.) Buffer OEB. Typical yields were 500 ng to 1.5 μg total RNA.
Reverse Transcription Using N9 and Oligo dT on Bone Marrow mRNA
Reverse transcription (RT) reactions were accomplished by mixing together 75-100 ng mRNA with 2 μl 10× Accuscript RT Buffer (Stratagene), 0.8 μl 100 mM dNTPs, and either N9 (300 ng) or oligo dT primer (100 ng) and then brought to a final volume of 17 μl with water. The mixtures were heated at 65° C. for 5 min, and then allowed to cool to room temperature. Next 2 μl DTT, 0.5 μl RNase Block (Stratagene), 0.5 μl AccuScript RT (Stratagene) were added to each reaction. Next, the N9 primed reactions were incubated for 10 minutes at room temperature and the oligo-dT primed reactions were incubated on ice for 10 minutes. Finally, both reactions were incubated at 42° C. for 60 minutes followed by 70° C. for 15 minutes to kill the enzyme.
PCR from Bone Marrow-Derived cDNA
Antibody heavy and light chain repertoires were amplified from bone marrow cDNA essentially using previously described methods and degenerate primers (O'Brien, P. M., Aitken R. Standard protocols for the construction of scFv Libraries. Antibody Phage Display—Methods and Protocols, vol. 178, 59-71, 2001, Humana Press) based upon human germline V and J regions.
Briefly, PCR reactions using Oligo dT primed cDNA (from 75 ng mRNA) for lambda light chains and N9 primed cDNA (from 75 ng mRNA for kappa light chains, from 100 ng mRNA for heavy chains) were mixed together with 5 μl 10× amplification buffer (Invitrogen), 1.5 μl dNTPs (10 mM), 1 μl MgSO4 (50 mM), 2.5 μl Vregion primers (10 uM) and 2.5 μl Jregion primers (10 uM)-10 uM for VH, 0.5 μl Platinum Pfx Polymerase (Invitrogen), and sterile dH2O to final volume of 50 μl. PCR parameters were as follows: step 1-95° C. 5 minutes, step 2-95° C. 30 seconds, step 3-58° C. 30 seconds, step 4-68° C. 1 minute, step 5-cycle step 2-4 40 times, step 6-68° C. 5 minutes. Light chain PCR products were cleaned up using Qiagen PCR Cleanup kit. Heavy chains PCR products were gel purified from 1.5% agarose gel using Qiagen Gel Extraction Kit and then reamplified. Heavy chain reamplification was carried out as follows: Mixed 10 μl 10× amplification buffer (Invitrogen), 3 μl dNTPs (10 mM), 2 μl MgSO4 (50 mM), 5 μl each VH primers (10 uM) and JH primers (10 uM), 5 μl Heavy chain Primary PCR product, 1 μl Platinum Pfx, volume adjusted to 100 μl with water. Cycling parameters were as follows: step 1-95° C. 5 minutes, step 2-95° C. 30 seconds, step 3-58° C. 30 seconds, step 4-68° C. 1 minute, step 5-cycle step 2-4 20 times, step 6-68° C. 5 minutes. Re-amplified heavy chain PCR products were cleaned up from a 1.5% agarose-TAE gel using Qiagen Extraction Kit.
Antibody Phase Library Construction
Separate antibody libraries for each individual bird flu survivor were constructed using unique identifying 3-nucleotide barcodes inserted in the untranslated region following the stop codon of the pIII gene of filamentous phage.
Light Chain Cloning:
1 μg each of pooled kappa light chain and pooled lambda light chain per donor were digested with NotI and BamHI and gel purified from a 1.5% agarose-TAE gel using Qiagen Gel Extraction Kit. 5 μg of each vector (pAMPFab) was digested with NotI and BamHI and gel purified from a 1% agarose-TAE gel using Qiagen Gel Extraction Kit. Library ligations were performed with 200 ng of gel purified Kappa or Lambda inserts and 1 μg of gel purified vector in 60 μl for 1 hour at RT or overnight at 14° C. Ligations were desalted using Edge BioSystem Perfroma spin columns. The library was transformed in five electroporations in 80 μl TG-1 or XL-1 Blue aliquots, each recovered in 1 ml SOC, pooled and outgrown for one hour at 37° C. Total number of transformants was determined following this outgrowth by plating an aliquot from each of the transformations. The remaining electroporation was amplified by growing overnight at 37° C. in 200 ml 2YT+50 μg/ml Ampicillin+2% glucose. The subsequent light chain library was recovered by plasmid purification from these overnight cultures using a Qiagen High Speed Maxiprep Kit.
Heavy Chain Cloning:
1.5-2 μg each of the donor-specific heavy chains (VH1, VH 2, 5, 6 pool, VH 3, and VH 4) were digested with a 40 Unit excess/μg DNA with SfiI and XhoI and gel purified from a 1.5% agarose-TAE gel using Qiagen Gel Extraction Kit. 15 μg of each light chain library vector was digested with 40 Unit/μg DNA with SfiI and XhoI and gel purified from a 1% agarose-TAE gel using Qiagen Gel Extraction Kit. Library ligations were set up by combining 1.2 μg SfiI/XhoI digested, gel purified heavy chain donor collections and 5 μg of each light chain library (kappa and lambda) overnight at 14° C. The library ligations were then desalted with Edge BioSystem Pefroma spin columns and then transformed through 20 electroporations per library in 80 μl TG-1 aliquots, each recovered in 1 ml SOC, pooled and outgrown for one hour at 37° C. Again following this outgrowth an aliquot of each was used to determine the total number of transformants with the remainder transferred to 1 L 2YT+50 μg/ml Ampicillin+2% glucose and grown at 37 C with vigorous aeration to an OD600 of  ̃0.3. Next M13K07 helper phage was then added at a multiplicity of infection (MOI) of 5:1 and incubated for 1 hour at 37° C., with no agitation. Next the cells were harvested by centrifugation and resuspended in 1 L 2YT+50 μg/ml Ampicillin, 70 μg/ml Kanamycin and grown overnight at 37° C. with vigorous aeration to allow for scFv phagemid production. The next morning the cells were collected by centrifugation and supernatant containing phagemid was collected. The phagemids were precipitated from the supernatant by the addition of 0.2 volumes 20% PEG/5 M NaCl solution and incubation for 1 hour on ice. The phagemid library stocks were then harvested by centrifugation and resuspended in 20 ml sterile PBS. Residual bacteria were removed by an additional centrifugation and the final phagemid libraries were stored at −20° C. in PBS+50% glycerol.
Phagemid Panning and Amplification
ELISA plates (Immulon 4HBX flat bottom, Nunc) were coated with 100 μl of 100 ng/mL H5 hemagglutinin protein (Protein Sciences, A/Vietnam/1203/2004) in ELISA Coating Solution (BioFX) by overnight incubation at room temperature. The next day plates were washed three times with 300 μl PBST. Following the wash, 300 μl of a blocking solution (4% Non-Fat dry Milk in PBS/0.05% Tween-20) was added and incubated for 30 mins on ice. Following the blocking step, the plates were washed three times with 300 μl PBST. Just prior to phage panning, the glycerol was removed from the frozen phagemid stocks using Millipore Amicon Ultra columns and then blocked in 4% nonfat dry milk for 15 minutes. Next, 100 μl aliquots of phagemid were distributed into 8 wells (total phage  ̃1×1012 CFU) and incubated for 2 hours at 4° C. followed by washing 6-8 times with 300 μl PBST. Phagemid were collected following a 10 min at room temperature in 100 μl/well Elution buffer (0.2M glycine-HCl, pH 2.2, 1 mg/ml BSA). The eluate was then neutralized by the addition of 56.25 μl 2M Tris base per ml eluate. Following neutralization, 5 ml TG1 cells (OD600 ̃0.3) were infected with 0.5 ml neutralized phage at 37° C. for 30 minutes in 2-YT with no shaking. Following this step some cells were plated onto LB AMP Glucose plates to determine total phagemid recovery. The remaining inoculum was placed into 10 ml 2-YTAG (final concentration 2% glucose and 50 ug/ml ampicillin) and grown at 37° C. with vigorous aeration to OD600 ̃0.3. Next the cultures were infected with M13K07 helper phage at an MOI of 5:1 and incubated at 37° C. for 30-60 minutes with no shaking. The cells were collected by centrifugation and resuspended in 25 ml 2-YTAK (Ampicillin 50 μg/ml, Kanamycin 70 μg/ml), transferred to a fresh culture flask, and grown ON at 37° C. with shaking. Subsequent rounds were similarly recovered and amplified.
scFv ELISA
Individual colonies of E. coli HB2151 transformed cells from biopanned phage were grown overnight at 37° C. in 1 ml of 2YT+100 μg/ml AMP. The following morning the cells were harvested by centrifugation and resuspended in 1.5 ml periplasmic lysis buffer (1 ml BBS (Teknova)+0.5 ml 10 mg/ml lysozyme+EDTA to 10 mM final concentration). The cells were again pelleted by centrifugation and the scFv containing periplasmic lysates were collected. The scFv lysates were combined 1:1 with dilution buffer (PBS/0.05% BSA) and 100 μl was added to wells that had been previously antigen coated with and blocked with dilution buffer. The samples were incubated for 2 hours at room temperature and then washed three times with PBS/0.05% Tween. Next 100 μl of 1:5000 diluted Biotin Anti-Histidine mouse (Serotec) in dilution buffer was added to each well and incubated for 1 hr at room temperature. Following this incubation the wells were washed three times with PBS/0.05% Tween and then to each well 100 μl of 1:2500 Streptavidin:HRP (Serotec) was added and incubated for 1 hr at room temperature and then washed three times with PBS/0.05% Tween. Following this final wash, 100 μl of chromogenic substrate solution was added (TMB1 Substrate, BioFx) and after sufficient amount of time terminated by the addition of 100 μl of STOP Solution (BioFx). Absorbances at 450 nm were read on a plate reader (Molecular Devices Thermomax microplate reader with Softmax Pro software), data recorded, and subsequently plotted using Excel (Microsoft).
Sequencing
To deduce the heavy and light chain sequences, individual clones were grown and plasmid DNA extracted (Qiagen). The plasmid DNA was subjected to standard DNA sequencing.
Hemagglutinin Inhibition (HAI) Assays
Hemagglutination Inhibition was performed essentially following the method of Rogers et al., Virology 131:394-408 (1983), in round bottom microtiter plates (Corning) using 4 HAU (hemagglutinating units) of virus or protein/well. For HAI determinations 25 μl samples of purified single chain variable fragments (scFv) were mixed with 25 μl of PBS containing 4 HAU of the test virus in each microtiter well. Following a preincubation of 15 minutes at room temperature, 25 μl of 0.75% human erythrocytes were added, and mixed. HAI antibody activity was determined by visual inspection following a 60 min incubation at room temperature.
Results
Bone marrow and blood samples were collected from six survivors of the H5N1 bird flu outbreak that had taken place in Turkey in January 2006, approximately four months after the outbreak. For all six survivors the initial diagnosis of bird flu was made following by physical examination, clinical laboratory testing, and molecular diagnostic determination, sanctioned by the Turkish Ministry of Health. Four of these survivors were additionally confirmed by the World Health Organization (WHO). Serum samples were analyzed to confirm the presence of antibodies to H5 hemagglutinin (A/Vietnam/1203/2004) using the serology protocol described above. As shown in FIG. 8, the blood samples of all six patients (designated SLB H1-H6, respectively) demonstrated the presence of antibodies to the H5 antigen. Following this confirmation, RNA was extracted from the bone marrow samples of these individuals, and bone marrow mRNA was purified and reverse transcribed using the protocols described above. The antibody heavy and light chain repertoires were then amplified from the bone marrow cDNA as described above, and individual antibody heavy and light chain phage libraries were cloned separately for each survivor, using the above-described three-nucleotide bar coding to distinguish the individual libraries.
Bone marrow and blood samples were also collected from twelve local donors who were treated for flu symptoms in the year of 2006. Serology was performed as described above to confirm the presence of antibodies to H1, H3 and H5 hemagglutinin, respectively. As shown in FIG. 8, all serum samples tested positive for antibodies to H1 and/or H3 hemagglutinins, where the dominance of a certain subtype depended on the influenza A virus subtype to which the particular donor was exposed most throughout his or her lifetime. Interestingly, there were donors whose serum contained a significant level of antibodies of H5 hemagglutinin as well (donors SLB1 and SLB5 in FIG. 9). Following this confirmation, RNA was extracted from the bone marrow samples of the donors, and bone marrow mRNA was purified and reverse transcribed using the protocols described above. The antibody heavy and light chain repertoires were then amplified from the bone marrow cDNA as described above, and individual antibody heavy and light chain phage libraries were cloned separately for each donor, using the above-described three-nucleotide bar coding to distinguish the individual libraries.
As illustrated in FIG. 10, using three of the available four nucleotides allows the creation of 64 unique barcodes.
Out of 48 random clones obtained after three rounds of panning of pooled antibody libraries prepared from the bone marrow samples of Turkish bird flu survivors, 40 were tested by ELISA for binding to the H5 hemagglutinin protein (Protein Sciences, A/Vietnam/1203/2004), and to inactivated Vietnamese H5N1 virus (CBER, A/Vietnam/1203/2004). The clones were sequenced. Of the 40 clones, five were found to be different. As shown in FIG. 11, all five distinct clones (clones F5 and G1 have the same sequences) were binding both to the H5 protein and the Vietnamese H5N1 virus. FIG. 12 shows sequence alignments comparing the sequences of H5 hemagglutinin proteins from Turkish donors to the H5 hemagglutinin sequence of the Vietnamese isolate used in the above experiments. The results of these experiments show that, despite differences in the sequences, the antibodies tested bound both the Turkish and the Vietnamese H5 proteins and viruses, and thus showed cross-reactivity with more than one isolate of the H5N1 virus.
Four additional unique clones were identified from among 13 clones produced by the second round of panning.
The heavy chain variable region sequences of the unique clones identified in the pooled antibody libraries of Turkish donors, along with the corresponding light chain and germline origin sequences, are shown in FIGS. 13 and 14. In particular, the sequences shown in FIG. 13 (3-23 heavy chain clones) originate from a pooled library of all heavy and light chains of all Turkish donors after three rounds of panning. The sequences shown in FIG. 14 (3-30 heavy chain clones) originate from a pooled library of all heavy and light chains of all Turkish donors after two rounds of panning.
Additional unique H5N1 specific antibody heavy chain variable region sequences were identified from antibody libraries of individual Turkish donors, using the ELISA protocol described above, after four rounds of panning. The sequences of these H5N1 ELISA positive clones are shown in FIGS. 15A-D.
FIGS. 16 and 17 illustrate the use of destinational mutagenesis to create diverse antibody heavy and light chain libraries using the antibody heavy (FIG. 16) and light chain (FIG. 17) sequences identified by analysis of sera and bone marrow of Turkish bird flu survivors as described above.
FIGS. 18 and 19 show ELISA results confirming cross-reactivity of certain Fab fragments obtained from an H5N1 Vietnam virus scFv antibody with Turkish and Indonesian variants of the HA protein.
EXAMPLE 2
Constructing Donor-Specific Antibody Library for Patients Infected with HIV
Bone Marrow Protocol and Sera Preparation
Blood is obtained by standard venopuncture, allowed to clot, and processed to recover serum. The serum is stored at −20° C. for 3-4 days until they are shipped on dry ice. Donors are anaesthetized with an injection of a local anesthetic and 5 ml of bone marrow is removed from the pelvic bone of each patient donor. Next the 5 ml of bone marrow is placed into a sterile 50-ml tube containing 45 ml RNAlater (Ambion). The mixture is gently inverted approximately 8-20 times, until there are no visible clumps and the marrow and RNAlater are mixed well. Next the specimen is refrigerated the between 2-10° C. overnight. Following the overnight refrigeration, the specimens are stored at −20° C. for 3-4 days until they are shipped on dry ice. Upon receipt the RNAlater/marrow and sera containing tubes are stored at −80° C. until processed. Candidate patient should be tested HIV positive prior to be selected as donors.
Bone marrow extraction and mRNA purification, reverse transcription, PCR, antibody light and heavy chain construction, phagemid panning and amplification, ELISA and sequencing are performed essentially as described in Example 1.
Although in the foregoing description the invention is illustrated with reference to certain embodiments, it is not so limited. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims.
All references cited throughout the specification are hereby expressly incorporated by reference.

## Claims

1. 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 antigen;
b) generating in a vector 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 a unique nucleotide sequence barcode that is linked to and labels said nucleic acids in the vector.

2. The method of claim 1, 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).

3. The method of claim 2, further comprises steps of: d) expressing said immunoglobulin repertoire; and e) displaying said immunoglobulin repertoire in a display system.

4. The method of claim 3, wherein the display system is a phagemid.

5. The method of claim 4 further comprising the step of selecting members of the library based on their ability to neutralize the antigen.

6. The method of claim 5 that yields at least one neutralizing antibody.

7. The method of claim 5 that yields more than one neutralizing antibody.

8. The method of claim 7 further comprising the step of creating one or more sub-libraries comprising library members that were found to neutralize the antigen.

9. The method of claim 5 comprising the step of sequencing at least one library member identified.

10. The method of claim 1 wherein the nucleotide sequence barcode is linked to and labels said nucleic acids such that it does not interfere with the expression of said nucleic acid molecules.

11. The method of claim 1 wherein said nucleotide sequence barcode is a contiguous non-coding sequence of one to about 24 nucleotides.

12. The method of claim 11 wherein said nucleotide sequence barcode is linked to the 3′ or 5′ non-coding region of said nucleic acid molecules.

13. The method of claim 1 wherein said nucleotide sequence barcode is a coding sequence or one or more silent mutations incorporated into the nucleic acid molecules encoding the antibody light or heavy chains or fragments thereof.

14. The method of claim 1 wherein said nucleotide sequence barcode is non-contiguous.

15. The method of claim 14 wherein at least part of said non-contiguous sequence is linked to or incorporated in the vectors present in the library.

16. The method of claim 14 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.

17. The method of claim 1 wherein the barcode encodes a peptide or polypeptide sequence.

18. The method of claim 1, wherein the mRNA is obtained from bone marrow of the donor.