Dynamic human antibody light chain libraries
Provided herein are libraries containing polynucleotides, where one of the polynucleotides encodes an antibody light chain with specific hypervariable regions HVR-L1, HVR-L2, and HVR-L3. Further provided herein are libraries containing polynucleotides encoding a plurality of unique antibodies, wherein each antibody comprises a heavy chain variable region and a light chain variable region. Also provided are antibodies, polypeptide libraries, vector libraries, cells, non-human animals, antibody light chains, methods of making an antibody library, kits, and methods of generating a bispecific antibody related thereto.
1. A library comprising polynucleotides that encode antibody light chain variable regions (V L s), wherein each of the V L s comprises a HVR-L1, a HVR-L2 and a HVR-L3, and wherein at least one V L comprises
a. an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:5-9 and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:10-23;
b. an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-4 and an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:5-9;
c. an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-4 and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:10-23;
d. an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-4, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:5-9, and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NO:10-23;
e. the HVR-L1, the HVR-L2, and the HVR-L3 are selected from the group consisting of: (1) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 selected from the group consisting of SEQ ID NOS:10-23; (2) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:10-23; (3) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:2, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:10-23; (4) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:2, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:18; (5) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; (6) an HVR-L 1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 sequence selected form the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:20; (7) an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:18; (8) an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; (9) an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:20; (10) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:3, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:10-23; (11) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:6, and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:10-23; (11b) an HVR-L 1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:7, and an HVR-L3 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:10-23; (12) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; (13) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:14; (14) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:18; (15) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:3, an HVR-L2 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:5-9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:20; (16) an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:14; (17) an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:6, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; and (18) an HVR-L1 that comprises an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:7, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23;
f. the HVR-L1, the HVR-L2, and the HVR-L3 are selected from the group consisting of: (1) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:2, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:18; (2) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; (3) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:20; (4) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:14; (5) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:3, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:20; (6) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:1, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:9, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:18; (7) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:7, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; (8) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:6, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:23; (9) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:6, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:17; (10) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:5, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:20; and (11) an HVR-L1 that comprises the amino acid sequence of SEQ ID NO:4, an HVR-L2 that comprises the amino acid sequence of SEQ ID NO:8, and an HVR-L3 that comprises the amino acid sequence of SEQ ID NO:11; or
g. an HVR-L1, an HVR-L2, and an HVR-L3 of an antibody listed in Table 2.
2. The library of claim 1 , wherein at least two, at least three, at least four, at least five, or at least ten of the V LS each comprises a unique combination of HVR-L1, HVR-L2, and/or HVR-L3 sequences set forth in claim 1 (a), 1(b), 1(c), 1(d), 1(e)(1), 1(e)(2), 1(e)(3), 1(e)(4), 1(e)(5), 1(e)(6), 1(e)(7), 1(e)(8), 1(e)(9), 1(e)(10), 1(e)(11), 1(e)(11b), 1(e)(12), 1(e)(13), 1(e)(14), 1(e)(15), 1(e)(16), 1(e)(17), 1(e)(18), 1(f)(1), 1(f)(2), 1(f)(3), 1(f)(4), 1(f)(5), 1(f)(6), 1(f)(7), 1(f)(8), 1(f)(9), 1(f)(10), 1(f)(11), or 1(g).
3. The library of claim 1 , wherein each of the V LS comprises a unique combination of HVR-L1, HVR-L2, and HVR-L3 sequences set forth in claim 1 (a), 1(b), 1(c), 1(d), 1(e)(1), 1(e)(2), 1(e)(3), 1(e)(4), 1(e)(5), 1(e)(6), 1(e)(7), 1(e)(8), 1(e)(9), 1(e)(10), 1(e)(11), 1(e)(11b), 1(e)(12), 1(e)(13), 1(e)(14), 1(e)(15), 1(e)(16), 1(e)(17), 1(e)(18), 1(f)(1), 1(f)(2), 1(f)(3), 1(f)(4), 1(f)(5), 1(f)(6), 1(f)(7), 1(f)(8), 1(f)(9), 1(f)(10), 1(f)(11), or 1(g).
4. The library of claim 1 , wherein the V LS comprise fewer than about 1000 unique combinations of HVR-L1, HVR-L2, and HVR-L3 sequences.
5. The library of claim 4 , wherein the V LS comprise about 280 or fewer unique combinations of HVR-L1, HVR-L2, and HVR-L3 sequences.
6. The library of claim 1 , wherein the at the least one V L comprises a FW-L1 comprising the amino acid sequence of SEQ ID NO:24, a FW-L2 comprising the amino acid sequence of SEQ ID NO:25, a FW-L3 comprising the amino acid sequence of SEQ ID NO:26, and a FW-L4 comprising the amino acid sequence of SEQ ID NO:27.
7. The library of claim 1 , wherein the at the least one V L comprises a sequence selected from the group consisting of SEQ ID NOS:28-50.
8. The library of claim 1 , wherein the polynucleotides encode full-length antibody light chains.
9. The library of claim 1 , further comprising polynucleotides that encode antibody heavy chain variable regions (V HS .
10. The library of claim 9 , wherein the polynucleotides that encode the V HS include at least one unique sequence, at least 100 unique sequences, at least 1000 unique sequences, or at least about 10 9 unique sequences.
11. The library of claim 9 , wherein the polynucleotides that encode the V LS and the polynucleotides that encode the V HS together encode a plurality of unique antibodies, wherein the V L of each antibody of the plurality comprises an identical sequence.
12. The library of claim 1 , wherein the polynucleotides of the library are synthetic polynucleotides.
13. The library of claim 1 , wherein at least one of the HVR-L1, HVR-L2, and HVR-L3 of the at least one V L adopts multiple conformations, as assayed by structural determination and/or computational modeling.
14. The library of claim 1 , wherein at least one of the polynucleotides that encode the V LS is in a vector.
15. The library of claim 14 , wherein the vector is an expression vector.
16. The library of claim 14 , wherein the vector is a display vector.
17. The library of claim 1 , wherein at least one of the polynucleotides encoding the antibody light chain variable region is in a cell.
18. The library of claim 17 , wherein the cell is a bacterial, yeast, or mammalian cell.
19. A method of preparing a library comprising providing and assembling the polynucleotide sequences of the library of claim 1 .
20. A kit comprising the library of polynucleotides of claim 1 .
21. The library of claim 6 , wherein all of the V LS comprise a FW-L1 comprising the amino acid sequence of SEQ ID NO:24, a FW-L2 comprising the amino acid sequence of SEQ ID NO:25, a FW-L3 comprising the amino acid sequence of SEQ ID NO:26, and a FW-L4 comprising the amino acid sequence of SEQ ID NO:27.
22. The library of claim 6 , wherein each of the polynucleotides that encode the V LS is in a vector.
23. The library of claim 11 , wherein the polynucleotides that encode the V HS include at least one unique sequence, at least 100 unique sequences, at least 1000 unique sequences, or at least about 10 9 unique sequences.