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Prediction of antibody response using recombinant human protein fragments as antigen
KTH, School of Biotechnology (BIO), Proteomics.ORCID iD: 0000-0002-9977-5724
KTH, School of Biotechnology (BIO), Proteomics.ORCID iD: 0000-0001-8993-048X
2009 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 18, no 11, 2346-2355 p.Article in journal (Refereed) Published
Abstract [en]

A great need exists for prediction of antibody response for the generation of antibodies toward protein targets. Earlier studies have suggested that prediction methods based on hydrophilicity propensity scale, in which the degree of exposure of the amino acid in an aqueous solvent is calculated, has limited value. Here, we show a comparative analysis based on 12,634 affinity-purified antibodies generated in a standardized manner against human recombinant protein fragments. The antibody response (yield) was measured and compared to theoretical predictions based on a large number (544) of published propensity scales. The results show that some of the scales have predictive power, although the overall Pearson correlation coefficient is relatively low (0.2) even for the best performing amino acid indices. Based on the current data set, a new propensity scale was calculated with a Pearson correlation coefficient of 0.25. The values correlated in some extent to earlier scales, including large penalty for hydrophobic and cysteine residues and high positive contribution from acidic residues, but with relatively low positive contribution from basic residues. The fraction of immunogens generating low antibody responses was reduced from 30% to around 10% if immunogens with a high propensity score (>0.48) were selected as compared to immunogens with lower scores (<0.29). The study demonstrates that a propensity scale might be useful for prediction of antibody response generated by immunization of recombinant protein fragments. The data set presented here can be used for further studies to design new prediction tools for the generation of antibodies to specific protein targets.

Place, publisher, year, edition, pages
2009. Vol. 18, no 11, 2346-2355 p.
Keyword [en]
antibody response, immunogenicity, immunization, prediction, b-cell epitopes, human genome, sequence, system, determinants, generation, proteomics, character, selection, peptides
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-18937DOI: 10.1002/pro.245ISI: 000271518100015Scopus ID: 2-s2.0-70350519382OAI: oai:DiVA.org:kth-18937DiVA: diva2:336984
Note
QC 20100525. Tidigare titel: Prediction of antibody response using recombinant human protein fragmentsAvailable from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Methods for Generation and Characterization of Monospecific Antibodies
Open this publication in new window or tab >>Methods for Generation and Characterization of Monospecific Antibodies
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Recent advances in biotechnology have generated possibilities to investigate and measure parts of life previously left for believers to explain. Utilizing the same book of recipes, the genome, our cells produce selections of proteins at a time and thereby niche into a multitude of specialized cell types, tissues and organs comprising our body. Knowledge of the precise protein composition in a given organ at normal and disease condition would be of invaluable importance, both for identification of disease causes and the design of new pharmaceuticals, as well as for a deeper understanding of the processes of life. This doctoral thesis describes the start and progress of a visionary project (HPR) to localize all human proteins in our body, with emphasis on the generation and characterization of antibodies used as protein targeting missiles. To facilitate the identification of one human protein in a complex environment like our body, it is of significant importance to have precise and specific means of detection. The first two papers (I-II), describe software developed for generation of monospecific antibodies satisfying such needs, using a set of rules for antigen optimization. Five years after project start a large amount of antibodies with documented characteristics have been generated. The third paper (III), illustrates an attempt to sieve these antibody characteristics to develop a tool, for further improvement of antigen selection, based on the correlation between antigen sequence and amount of specific antibody generated.Having a panel of protein-specific antibodies is a possession of a great value, not only for localization studies, but also as possible target-directed pharmaceuticals. In such cases, knowledge of the precise epitope recognized by the antibody on its target protein, is an important aid, both for understanding its effect as well as unwanted cross-reactivity. Paper (IV) describes the development of a high-resolution method for epitope mapping of antibodies using staphylococcal display. An application of the method is described in the last paper (V) where it is used to map an anti-HER2 monospecific antibody with growth-inhibiting effects on breast cancer cells. The monospecific antibody was fractionated into separate populations and five novel epitopes related to cancer cell growth-inhibition was determined.Altogether these methods are valuable tools for generation and characterization of monospecific antibodies.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. xii, 66 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:20
Keyword
antibody, epitope mapping, HER2, human protein atlas, immunogenicity, proteomics
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-9338 (URN)978-91-7415-139-8 (ISBN)
Public defence
2008-10-31, F3, KTH, Lindstedtsvägen 26, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20100907Available from: 2008-10-21 Created: 2008-10-21 Last updated: 2010-09-07Bibliographically approved

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