Construction of a rationally designed antibody platform for sequencing-assisted selection

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 45, 2012, Pages 18523-18528

  Larman, H Benjamin ^a,b,c,d   Xu, George Jing ^a,c,d,e   Pavlova, Natalya N ^c,d   Elledge, Stephen J ^c,d  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e HARVARD UNIVERSITY   (United States)

Author keywords

Antibody display; Single framework antibody library; Synthetic antibody library

Indexed keywords

IMMUNOGLOBULIN LIGHT CHAIN; OLIGONUCLEOTIDE; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY;

ANTIBODY LIBRARY; ANTIBODY PRODUCTION; ANTIGEN BINDING; ARTICLE; COMPLEMENTARITY DETERMINING REGION; CONTROLLED STUDY; CRYSTAL STRUCTURE; GENE SEQUENCE; HIDDEN MARKOV MODEL; IMMUNOGLOBULIN HEAVY CHAIN GENE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DATABASE; RIBOSOME;

ANTIBODIES; CELL ADHESION MOLECULES; CLONE CELLS; FLOW CYTOMETRY; HUMANS; MARKOV CHAINS; PEPTIDE LIBRARY; SEQUENCE ANALYSIS, DNA; SINGLE-CHAIN ANTIBODIES;

EID: 84868543068     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1215549109     Document Type: Article

References (28)

1. Ravn U, et al. (2010) By-passing in vitro screening - Next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res 38:e193.
2. Zhang H, et al. (2011) Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems. Proc Natl Acad Sci USA 108:13456-13461.
3. Barbas CF, 3rd, Bain JD, Hoekstra DM, Lerner RA (1992) Semisynthetic combinatorial antibody libraries: A chemical solution to the diversity problem. Proc Natl Acad Sci USA 89:4457-4461.
4. Barbas CF, 3rd (1995) Synthetic human antibodies. Nat Med 1:837-839.
5. Vargas-Madrazo E, Lara-Ochoa F, Almagro JC (1995) Canonical structure repertoire of the antigen-binding site of immunoglobulins suggests strong geometrical restrictions associated to the mechanism of immune recognition. J Mol Biol 254:497-504. (Pubitemid 26001786)
6. Lee CV, et al. (2004) High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J Mol Biol 340:1073-1093. (Pubitemid 38976491)
7. Lloyd C, et al. (2009) Modelling the human immune response: Performance of a 1011 human antibody repertoire against a broad panel of therapeutically relevant antigens. Protein Eng Des Sel 22:159-168.
8. Zhai W, et al. (2011) Synthetic antibodies designed on natural sequence landscapes. J Mol Biol 412:55-71.
9. Kaas Q, Ruiz M, Lefranc MP (2004) IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res 32(Database issue):D208-D210. (Pubitemid 38081640)
10. Ehrenmann F, Kaas Q, Lefranc MP (2010) IMGT/3Dstructure-DB and IMGT/DomainGapAlign: A database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res 38(Database issue):D301-D307.
11. Hanes J, Schaffitzel C, Knappik A, Plückthun A (2000) Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat Biotechnol 18:1287-1292.
12. Ofran Y, Schlessinger A, Rost B (2008) Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes. J Immunol 181:6230-6235.
13. Schütz F, Delorenzi M (2008) MAMOT: Hidden Markov modeling tool. Bioinformatics 24:1399-1400. (Pubitemid 351737148)
14. Bond CJ, Wiesmann C, Marsters JC, Jr., Sidhu SS (2005) A structure-based database of antibody variable domain diversity. J Mol Biol 348:699-709.
15. Lara-Ochoa F, Vargas-Madrazo E, Jimenez-Montano MA, Almagro JC (1994) Patterns in the complementary determining regions of immunoglobulins (CDRs). Biosystems 32:1-9. (Pubitemid 24084397)
16. Singh H, Raghava GP (2001) ProPred: Prediction of HLA-DR binding sites. Bioinformatics 17:1236-1237. (Pubitemid 33735355)
17. Fabre-Lafay S, et al. (2007) Nectin-4 is a new histological and serological tumor associated marker for breast cancer. BMC Cancer 7:73. (Pubitemid 46785011)
18. Athanassiadou AM, Patsouris E, Tsipis A, Gonidi M, Athanassiadou P (2011) The significance of Survivin and Nectin-4 expression in the prognosis of breast carcinoma. Folia Histochem Cytobiol 49:26-33.
19. Chodorge M, Fourage L, Ravot G, Jermutus L, Minter R (2008) In vitro DNA recombination by L-Shuffling during ribosome display affinity maturation of an anti-Fas antibody increases the population of improved variants. Protein Eng Des Sel 21:343-351.
20. Hoogenboom HR (2005) Selecting and screening recombinant antibody libraries. Nat Biotechnol 23:1105-1116.
21. Beck A, Wurch T, Bailly C, Corvaia N (2010) Strategies and challenges for the next generation of therapeutic antibodies. Nat Rev Immunol 10:345-352.
22. Erlich Y, et al. (2009) DNA Sudoku - Harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 19:1243-1253.
23. Prabhu S, Pe'er I (2009) Overlapping pools for high-throughput targeted resequencing. Genome Res 19:1254-1261.
24. Bowley DR, Jones TM, Burton DR, Lerner RA (2009) Libraries against libraries for combinatorial selection of replicating antigen-antibody pairs. Proc Natl Acad Sci USA 106:1380-1385.
25. Whitehead TA, et al. (2012) Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 30:543-548.
26. Schofield DJ, et al. (2007) Application of phage display to high throughput antibody generation and characterization. Genome Biol 8:R254.
27. Zacchi P, Sblattero D, Florian F, Marzari R, Bradbury AR (2003) Selecting open reading frames from DNA. Genome Res 13:980-990. (Pubitemid 36621757)
28. Gibson DG, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345.