Methods for producing members of specific binding pairs

• US 5,969,108 A
• Filed: 01/08/1993
• Issued: 10/19/1999
• Est. Priority Date: 07/10/1990
• Status: Expired due to Term

• Current Assignee: UK Research and Innovation
• Original Assignee: Medical Research Council (Government of United Kingdom), Cambridge Silicon Radio Limited (Qualcomm, Inc.)
• Inventors: Bonnert, Timothy Peter, Jackson, Ronald Henry, Marks, James David, Griffiths, Andrew David, Winter, Gregory Paul, Hoogenboom, Henricus Renerus Jacobus Mattheus, Pope, Anthony Richard, Johnson, Kevin Stuart, Chiswell, David John, Clackson, Timothy Piers, McCafferty, John, Holliger, Kaspar Philipp
• Primary Examiner(s): Eisenschenk, Frank C.
• Application Number:
  US07/971,857
• Time in Patent Office: 2,475 Days
• Field of Search: 530/387.1, 530/412, 530/387.3, 530/867, 536/23.1, 536/23.53, 536/23.4, 435/5, 435/252.3, 435/6, 435/69.6, 435/7.1, 435/69.7, 435/9.1, 435/69.1, 435/69.8, 435/230.1, 435/320.1
• US Class Current: 506/14
• CPC Class Codes: B01J 2219/00718 Type of compounds synthesised
• CPC Class Codes: C07K 16/00 Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C07K 16/005 constructed by phage libraries
• CPC Class Codes: C07K 16/18 against material from animals or humans
• CPC Class Codes: C07K 16/26 against hormones ; against hormone releasing or inhibiting factors
• CPC Class Codes: C07K 16/34 against blood group antigens
• CPC Class Codes: C07K 16/40 against enzymes
• CPC Class Codes: C07K 16/44 against material not provided for elsewhere , e.g. haptens, metals, DNA, RNA, amino acids
• CPC Class Codes: C07K 16/462 Igs containing a variable region (Fv) from one specie and a constant region (Fc) from another
• CPC Class Codes: C07K 16/468 Immunoglobulins having two or more different antigen binding sites, e.g. multifunctional antibodies
• CPC Class Codes: C07K 19/00 Hybrid peptides , i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
• CPC Class Codes: C07K 2317/21 from primates, e.g. man
• CPC Class Codes: C07K 2317/24 containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• CPC Class Codes: C07K 2317/34 Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/55 Fab or Fab'
• CPC Class Codes: C07K 2317/62 comprising only variable region components
• CPC Class Codes: C07K 2317/622 Single chain antibody (scFv)
• CPC Class Codes: C07K 2317/92 Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/02 containing a signal sequence
• CPC Class Codes: C07K 2319/41 : containing a Myc-tag
• CPC Class Codes: C07K 2319/735 : containing a domain for self-assembly, e.g. a viral coat protein (includes phage display)
• CPC Class Codes: C12N 15/1037 : Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C12N 15/62 : DNA sequences coding for fusion proteins
• CPC Class Codes: C12N 15/73 : Expression systems using phage (lambda) regulatory sequences
• CPC Class Codes: C40B 40/02 : Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
• CPC Class Codes: G01N 33/53 : Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/6857 : Antibody fragments
• CPC Class Codes: Y10S 530/867 : involving immunoglobulin or antibody produced via recombinant dna technology

Abstract

A member of a specific binding pair (sbp) is identified by expressing DNA encoding a genetically diverse population of such sbp members in recombinant host cells in which the sbp members are displayed in functional form at the surface of a secreted recombinant genetic display package (rgdp) containing DNA encoding the sbp member or a polypeptide component thereof, by virtue of the sbp member or a polypeptide component thereof being expressed as a fusion with a capsid component of the rgdp. The displayed sbps may be selected by affinity with a complementary sbp member, and the DNA recovered from selected rgdps for expression of the selected sbp members. Antibody sbp members may be thus obtained, with the different chains thereof expressed, one fused to the capsid component and the other in free form for association with the fusion partner polypeptide. A phagemid may be used as an expression vector, with said capsid fusion helping to package the phagemid DNA. Using this method libraries of DNA encoding respective chains of such multimeric sbp members may be combined, thereby obtaining a much greater genetic diversity in the sbp members than could easily be obtained by conventional methods.

Claims

1. A method of producing a member of a specific binding pair, which member is a single polypeptide chain comprising a binding domain of an antibody, the binding domain comprising a light chain variable region and a heavy chain variable region, from a nucleic acid library including nucleic acid encoding said specific binding pair member or a genetically diverse population of that type of specific binding pair member, which method comprises:

expressing in recombinant host cells polypeptides encoded by said nucleic acid library fused to a component of a secreted filamentous phage, so that the phage displays said specific binding pair member in functional form at the surface of the phage, said nucleic acid library being contained within the host cells in a form that is packaged using said phage component, whereby the genetic material of a secreted filamentous phage displaying a specific binding pair member contains nucleic acid encoding said specific binding pair member.

6. A method according to claims 1, 2, 3, or 4 wherein the host cell is a mutator strain which introduces genetic diversity into the specific binding pair member nucleic acid.

7. A method according to any one of claims 1, 2, 3, or 4 wherein said library or genetically diverse population is obtained from:

(a) a repertoire of rearranged immunoglobulin genes of an animal immunized with complementary specific binding pair member;

(b) a repertoire of rearranged immunoglobulin genes of an animal not immunized with complementary specific binding pair member;

(c) a repertoire of an artificially rearranged immunoglobulin gene or genes;

(d) a repertoire of an immunoglobulin homolog gene or genes,

in vitro mutagenesis of nucleic acid encoding an immunoglobulin gene or a library of immunoglobulin genes;

or

(f) a mixture of any of (a), (b), (c), and (d).

8. A method according to any one of claims 1, 2, 3, or 4 wherein the host is a bacterium, and said component of the phage is a capsid protein for the bacteriophage.

9. A method according to claim 8, wherein the phage is selected from the class I phages fd, M13, f1, If1, Ike, ZJ/Z, Ff and the class II phages XF, Pf1 and Pf3.

10. A method according to claim 9 wherein said specific binding pair member is expressed as a fusion with the gene III capsid protein of phage fd or its counterpart in another filamentous phage.

11. A method according to claim 10 wherein said specific binding pair member is inserted in the N-terminal region of the mature capsid protein downstream of a secretory leader peptide.

12. A method according to claim 8 wherein the host is E. coli.

13. A method according to claims 1, 2, 3, or 4 wherein nucleic acid encoding a specific binding pair member polypeptide is linked downstream to a phage capsid protein through a suppressible translational stop codon.

14. A method according to claim 1, 2, 3, or 4 wherein the phages formed by said expression are selected or screened to provide an individual specific binding pair member or a mixed population of said specific binding pair members associated in their respective phages with nucleic acid encoding said specific binding pair members.

15. A method according to claim 14 wherein the phages are selected by affinity with a member complementary to said specific binding pair member.

16. A method according to claim 15 which comprises recovering any phages bound to said complementary member by washing with an eluant.

17. A method according to claim 16 wherein the eluant contains a molecule which competes with said phage for binding to the complementary specific binding pair member.

18. A method according to claim 15 wherein the phage is applied to said complementary specific binding pair member in the presence of a molecule which competes with said phage for binding to said complementary specific binding pair member.

19. A method according to claim 14, wherein nucleic acid derived from a selected or screened phage is used to express said specific binding pair member or a fragment or derivative thereof.

20. A method according to claim 19 wherein the expression end product is modified to produce a derivative thereof.

23. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 14; and

(ii) producing by expression from the nucleic acid obtained in step (i) an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain components thereof.

24. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 14; and

(ii) producing from the nucleic acid obtained in step (i) nucleic acid which encodes an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain components thereof.

25. A specific binding pair member or derivative thereof produced by the method of claim 19.

26. A specific binding pair member or derivative thereof produced by the method of claim 23.

27. A specific binding pair member produced by the method of claim 19 or a fragment or derivative thereof.

28. A specific binding pair member produced by the method of claim 23.

30. The method according to claim 1 wherein said fusion is with a bacteriophage capsid protein and wherein a native capsid protein is present in said particle displaying said fusion.

31. The method according to claim 30 wherein a single said fusion is displayed per phage displaying a said fusion.

32. A method according to any claim 30 or 31 wherein said library or genetically diverse population is obtained from:

(a) a repertoire of rearranged immunoglobulin genes of an animal immunized with complementary specific binding pair member;

(b) a repertoire of rearranged immunoglobulin genes of an animal not immunized with complementary specific binding pair member;

(c) a repertoire of an artificially rearranged immunoglobulin gene or genes;

(d) a repertoire of an immunoglobulin homolog gene or genes,

(e) in vitro mutagenesis of nucleic acid encoding an immunoglobulin gene or a library of immunoglobulin genes;

or

(f) a mixture of any of (a), (b), (c), (d), and (r).

33. A method according to claim 32 wherein the phage formed by said expression is selected or screened to provide an individual specific binding pair member or a mixed population of said specific binding pair members associated in their respective phages with nucleic acid encoding said specific binding pair member.

34. A method according to claim 33 wherein the phage is selected by affinity with a member complementary to said specific binding pair member.

35. A method according to claim 34 which comprises recovering any phage bound to said second member by washing with an eluant.

36. A method according to claim 35 wherein the eluant contains a molecule which competes with said phage for binding to the complementary specific binding pair member.

37. A method according to claim 34 wherein the phage is applied to said complementary specific binding pair member in the presence of a molecule which competes with said package for binding to said complementary specific binding pair member.

38. A method according to claim 33, wherein nucleic acid derived from a selected or screened phage is used to express said specific binding pair member or a fragment or derivative thereof in a recombinant host organism.

39. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 33; and

(ii) producing by expression from the nucleic acid obtained in step (i) an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain component thereof.

40. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 33; and

(ii) producing from the nucleic acid obtained in step (i) nucleic acid which encodes an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain component thereof.

41. A specific binding pair member produced by the method of claim 38.

42. A specific binding pair member produced by the method of claim 39.

43. A method according to claim 38 or claim 39 wherein the expression end product is modified to produce a derivative thereof.

44. A method according to claim 30 wherein the phage formed by said expression is selected or screened to provide an individual specific binding pair member or a mixed population of said specific binding pair members associated in their respective phage with nucleic acid encoding said specific binding pair member.

45. A method according to claim 44 wherein the phage is selected by affinity with a member complementary to said specific binding pair member.

46. A method according to claim 44, wherein nucleic acid derived from a selected or screened phage is used to express said specific binding pair member or a fragment or derivative thereof in a recombinant host organism.

47. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 44; and

(ii) producing by expression from the nucleic acid obtained in step (i) an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain component thereof.

48. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 44; and

(ii) producing from the nucleic acid obtained in step (i) nucleic acid which encodes an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain component thereof.

49. A method according to claim 46 wherein the expression end product is modified to produce a derivative thereof.

50. A specific binding pair member produced by the method of claim 46.

51. A specific binding pair member produced by the method of claim 47.

52. A method according to claim 31 wherein the phage formed by said expression is selected or screened to provide an individual specific binding pair member or a mixed population of said specific binding pair members associated in their respective phage with nucleic acid encoding said specific binding pair member or a polypeptide chain thereof.

53. A method according to claim 52 wherein the phage is selected by affinity with a member complementary to said specific binding pair member.

54. A method according to claim 50, wherein nucleic acid derived from a selected or screened phage is used to express said specific binding pair member or a fragment or derivative thereof in a recombinant host organism.

55. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 52; and

(ii) producing by expression from the nucleic acid obtained in step (i) an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain component thereof.

56. A method comprising the steps of:

(i) obtaining nucleic acid from a selected or screened phage produced by a method according to claim 52; and

(ii) producing from the nucleic acid obtained in step (i) nucleic acid which encodes an individual specific binding pair member, a mixed population of specific binding pair members, or polypeptide chain component thereof.

57. A method according to claim 54 wherein the expression end product is modified to produce a derivative thereof.

58. A specific binding pair member produced by the method of claim 54.

59. A specific binding pair member produced by the method of claim 55.

2. A method of producing a member of a specific binding pair, which member is a single polypeptide chain comprising a binding domain of an antibody, the binding domain comprising a light chain variable region and a heavy chain variable region, which method comprises:

expressing in recombinant host cells nucleic acid encoding said specific binding pair member or a genetically diverse population of that type of specific binding pair member, wherein the or each said specific binding pair member is expressed as a fusion with a component of a secreted filamentous phage which displays said specific binding pair member at the surface of the phage, nucleic acid encoding said specific binding pair member being contained within the host cell in a form that is packaged using said phage component, whereby the genetic material of the phage displaying said specific binding pair member encodes said specific binding pair member, said host cell being a mutator strain which introduces genetic diversity into the specific binding pair member to produce said mixed population.

3. A method of producing a member of a specific binding pair, which member is a single polypeptide chain comprising a binding domain of an antibody, the binding domain comprising a light chain variable region and a heavy chain variable region, which method comprises:

expressing in recombinant host cells nucleic acid encoding said specific binding pair member or a genetically diverse population of that type of specific binding pair member, wherein the or each specific binding pair member is expressed as a fusion with a component of a secreted filamentous phage which displays said specific binding pair member in functional form at the surface of the phage, nucleic acid encoding said specific binding pair member being contained within the host cell in a form that is packaged using said phage component, whereby the genetic material of the phage displaying a specific binding pair member encodes said specific binding pair member, said fusions being with phage capsid protein and the phage being formed with said fusions in the absence of said capsid protein expressed in wild-type form.

4. A method of producing a member of a specific binding pair, which member is a single polypeptide chain comprising a binding domain of an antibody, the binding domain comprising a light chain variable region and a heavy chain variable region, which method comprises:

expressing in recombinant host cells nucleic acid encoding said specific binding pair member or a genetically diverse population of that type of specific binding pair member, wherein the or each specific binding pair member is expressed as a fusion with a component of a secreted replicable genetic display package which displays said specific binding pair member at the surface of the package, nucleic acid encoding said specific binding pair member being contained within the host cell in a form that is packaged using said replicable genetic display package component, whereby the genetic material of the replicable genetic display package displaying an specific binding pair member encodes said specific binding pair member, said specific binding pair member being expressed from a phagemid as a capsid fusion, and a helper phage, or a plasmid expressing complementing phage genes, it used along with said capsid fusions to package the phagemid nucleic acid.

5. A method according to claim 4, wherein said capsid protein is absent, defective or conditionally defective in the helper phage.

21. Recombinant host cells harboring a library of nucleic acid fragments comprising fragments encoding a genetically diverse population of a type of member of a specific binding pair which member is a single polypeptide chain comprising a binding domain of an antibody, the binding domain comprising a light chain variable region and a heavy chain variable region, each specific binding pair member being expressed as a fusion with a surface component of a secretable filamentous phage, so that said specific binding pair members are displayed on the surface of the phage in functional form and the genetic material of the phage encode the associated displayed specific binding pair member.

29. Recombinant host cells according to claim 21 wherein said library is obtained from:

(a) a repertoire of rearranged immunoglobulin genes of an animal immunized with complementary specific binding pair member;

(b) a repertoire of rearranged immunoglobulin genes of an animal not immunized with complementary specific binding pair member;

(c) a repertoire of an artificially rearranged immunoglobulin gene or genes;

(d) a repertoire of immunoglobulin gene or genes;

(e) in vitro mutagenesis of nucleic acid encoding an immunoglobulin gene or a library of immunoglobulin genes;

or

(f) a mixture of (a), (b), (c), (d) and (e).

22. A phage having the form of a secreted replicable genetic display package displaying on its surface in functional form a member of a specific binding pair, which member is a single polypeptide chain comprising a binding domain of an antibody, the binding domain comprising a light chain variable region and a heavy chain variable region or a binding domain thereof.