IMMUNOHEMATOLOGY
Relationship between B-cell epitope structural properties and the immunogenicity of blood group antigens: Outlier properties of the Kell K1 antigen
John G. Howe,
Gary Stack,
John G. Howe
Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
Search for more papers by this authorCorresponding Author
Gary Stack
Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
Pathology and Laboratory Medicine Service, VA Connecticut Healthcare System, West Haven, Connecticut, USA
Correspondence
Gary Stack, Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.
Email: [email protected], [email protected]
Search for more papers by this authorJohn G. Howe,
Gary Stack,
John G. Howe
Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
Search for more papers by this authorCorresponding Author
Gary Stack
Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
Pathology and Laboratory Medicine Service, VA Connecticut Healthcare System, West Haven, Connecticut, USA
Correspondence
Gary Stack, Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.
Email: [email protected], [email protected]
Search for more papers by this authorThe views expressed in this article are those of the authors and do not necessarily reflect the position or policy of the Department of Veterans Affairs or the United States government.
Abstract
Background
The immunogenicities of polypeptide blood group antigens vary, despite most being created by single amino acid (AA) substitutions. To study the basis of these differences, we employed an immunoinformatics approach to determine whether AA substitution sites of blood group antigens have structural features typical of B-cell epitopes and whether the extent of B-cell epitope properties is positively related to immunogenicity.
Study design and methods
Fifteen structural property prediction programs were used to determine the likelihood of β-turns, surface accessibility, flexibility, hydrophilicity, particular AA composition and AA pairs, and other B-cell epitope properties at AA substitution sites of polypeptide blood group antigens.
Results
AA substitution sites of Lua, Jka, E, c, M, Fya, C, and S were each located in regions with at least two structural features typical of B-cell epitopes. The substitution site of K, the most immunogenic non-ABO/D antigen, scored the lowest for most B-cell epitope properties and was the only one not predicted to be part of a linear B-cell epitope. The most immunogenic antigens studied (K, Jka, Lua, E) had B-cell epitope structural properties determined by the fewest programs; the least immunogenic antigens (e.g., Fya, S, C, c) had B-cell epitope properties according to the most programs.
Discussion
Counter to prediction, the immunogenicity of polypeptide blood group antigens was not positively related to B-cell epitope structural features present at their AA-substitution sites. Instead, it tended to be negatively related. The AA-substitution site of the most immunogenic non-ABO/D antigen, K, had the least B-cell epitope features.
CONFLICT OF INTEREST
The authors declare that they have no conflict of interest relevant to the manuscript submitted to TRANSFUSION.
Supporting Information
| Filename | Description |
|---|---|
| trf17110-sup-0001-Tables.docxWord 2007 document , 22.9 KB | Table S1 Scores of the highest scoring peptides containing exofacial AA substitutions that create blood group antigens Table S2 Average scores of peptides containing AA substitutions at each position of the peptide sequence |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1Van Regenmortel MH. What is a B-cell epitope? Methods Mol Biol. 2009; 524: 3–20.
- 2Kringelum JV, Nielsen M, Padkjaer SB, Lund O. Structural analysis of B-cell epitopes in antibody: protein complexes. Mol Immunol. 2013; 53: 24–34.
- 3Stave JW, Lindpainter K. Antibody and antigen contact residues define epitope and paratope size and structure. J Immunol. 2013; 191: 1428–35.
- 4Sela M. Antigenicity: some molecular aspects. Science. 1969; 166: 1365–74.
- 5Barlow DJ, Edwards MS, Thornton JM. Continuous and discontinuous protein antigenic determinants. Nature. 1986; 322: 747–8.
- 6Sivalingam GN, Shepherd AJ. An analysis of B-cell epitope discontinuity. Mol Immunol. 2012; 51: 304–9.
- 7Haste Andersen P, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci. 2006; 15: 2558–67.
- 8Avent ND, Jones JW, Liu W, et al. Molecular basis of the D variant phenotypes DNU and DII allows localization of critical amino acids required for expression of Rh D epitopes epD3, 4 and 9 to the sixth external domain of the Rh D protein. Br J Haematol. 1997; 97: 366–71.
- 9Zhu A, Haller S, Li H, et al. Use of RhD fusion protein expressed on K562 cell surface in the study of molecular basis for D antigenic epitopes. J Biol Chem. 1999; 274: 5731–7.
- 10Liu W, Smythe JS, Scott ML, et al. Site-directed mutagenesis of the human D antigen: definition of D epitopes on the sixth external domain of the D protein expressed on K562 cells. Transfusion. 1999; 39: 17–25.
- 11Liu W, Avent ND, Jones JW, et al. Molecular configuration of Rh D epitopes as defined by site-directed mutagenesis and expression of mutant Rh constructs in K562 erythroleukemia cells. Blood. 1999; 94: 3986–96.
- 12Cartron J-P, Rouillac C, Le Van Kim C, et al. Tentative model for the mapping of D epitopes on the RhD polypeptide. Transfus Clin Biol. 1996; 6: 497–503.
- 13Lomas C, Tippett P, Thompson KM, et al. Demonstration of seven epitopes on the Rh antigen D using human monoclonal anti-D antibodies and red cells from D categories. Vox Sang. 1989; 57: 261–4.
- 14Scott ML, Voak D, Jones JW, et al. A structural model for 30 Rh D epitopes based on serological and DNA sequence data from partial D phenotypes. Transfus Clin Biol. 1996; 6: 391–6.
- 15Avent ND, Liu W, Warner KM, et al. Immunochemical analysis of the human erythrocyte Rh polypeptides. J Biol Chem. 1996; 271: 14233–9.
- 16Apoil PA, Reid ME, Halverson G, et al. A human monoclonal anti-D antibody which detects a nonconformation-dependent epitope on the RhD protein by immunoblot. Br J Haematol. 1997; 98: 365–74.
- 17Wasniowska K, Lisowska E, Halverson GR, et al. The Fya, Fy6, Fy3 epitopes of the Duffy blood group system recognized by new monoclonal antibodies: identification of a linear Fy3 epitope. Br J Haematol. 2004; 124: 118–22.
- 18Tournamille C, Filipe A, Wasniowska K, et al. Structure-function analysis of the extracellular domains of the Duffy antigen/receptor for chemokines: characterization of antibody and chemokine binding sites. Br J Haematol. 2003; 122: 1014–23.
- 19Bigbee WL, Vanderlaan M, Fong SSN, Jensen RH. Monoclonal antibodies specific for the M- and N-forms of human glycophorin a. Mol Immunol. 1983; 20: 1353–62.
- 20Nichols ME, Rosenfield RE, Rubinstein P. Two blood group M epitopes disclosed by monoclonal antibodies. Vox Sang. 1985; 49: 138–48.
- 21Lu Y-Q, Nichols ME, Bigbee WL, et al. Structural polymorphism of glycophorins demonstrated by immunoblotting techniques. Blood. 1987; 69: 618–24.
- 22Lisowska E, Messeter L, Duk M, et al. A monoclonal anti-glycophorin a antibody recognizing the blood group M determinant: studies on the subspecificity. Mol Immunol. 1987; 24: 606–13.
- 23Jaskiewicz E, Moulds JJ, Kraemer K, et al. Characterization of the epitope recognized by a monoclonal antibody specific for blood group M antigen. Transfusion. 1990; 30: 230–5.
- 24Pedersen JT, Kaplan H, Wedeck L, et al. Octapeptide segments from the amino terminus of glycophorin A contain the antigenic determinants of the M and N blood group systems. J Lab Clin Med. 1990; 116: 527–34.
- 25Duk M, Sticher U, Brossmer R, Lisowska E. The differences in significance of α2,3Gal-linked and α2,6GalNAc-linked sialic acid residues in blood group M- and N-related epitopes recognized by various monoclonal antibodies. Glycobiology. 1994; 4: 175–81.
- 26Duk M, Lisowska E. Subspecificities of anti-M and anti-N antibodies tested with chemically-modified antigens. Transfus Clin Biol. 1997; 1: 69–71.
- 27Jaskiewicz E, Lisowska E, Lundblad A. The role of carbohydrate in the blood group N-related epitopes recognized by three new monoclonal antibodies. Glyconjugate J. 1990; 7: 255–68.
- 28Halverson GR, Tossas E, Velliquette RW, et al. Murine monoclonal anti-s and other anti-glycophorin B antibodies resulting from immunizations with a GPB.S peptide. Transfusion. 2009; 49: 485–94.
- 29Van Regenmortel MHV. Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. METHODS: a companion to. Methods Enzymol. 1996; 9: 465–72.
- 30El-Manzalawy Y, Honavar V. Recent advances in B-cell epitope prediction methods. Immunome Res. 2010; 6(Suppl 2): S2.
- 31Berzofsky JA. Intrinsic and extrinsic factors in protein antigenic structure. Science. 1985; 229: 932–40.
- 32Rubinstein ND, Mayrose I, Halperin D, et al. Computational characterization of B-cell epitopes. Mol Immunol. 2008; 45: 3477–89.
- 33Daniels G. The molecular genetics of blood group polymorphism. Hum Genet. 2009; 126: 729–42.
- 34Reid ME, Lomas-Francis C, Olsson ML. The Blood Group Antigen Facts Book. New York: Academic Press; 2012.
- 35Howe JG, Stack G. Structural and functional impacts of AA substitutions that create blood group antigens: implications for immunogenicity. Transfusion. 2017; 57: 541–53.
- 36Howe JG, Stack G. Relationship of epitope glycosylation and other properties of blood group proteins to the immunogenicity of blood group antigens. Transfusion. 2018; 58: 1739–51.
- 37Lee S, Wu X, Reid ME, et al. Molecular basis of the Kell (K1) phenotype. Blood. 1995; 85: 912–6.
- 38Stephen J, Cairns LS, Pickford WJ, et al. Identification, immunomodulatory activity, and immunogenicity of the major helper T-cell epitope on the K blood group antigen. Blood. 2012; 119: 5563–74.
- 39Stack G, Tormey CA. Estimating the immunogenicity of blood group antigens: a modified calculation that corrects for transfusion exposures. Br J Haematol. 2016; 175: 154–60.
- 40 Uniprot Consortium. Uniprot [Internet]. [cited 2018 Aug 8]. Available from: http://www.uniprot.org/
- 41Chou PY, Fasman GD. Conformational parameters for amino acids in helical, -sheet, and random coil regions calculated from proteins. Biochemistry. 1974; 13: 211–22.
- 42 Chou and Fasman Beta-Turn Prediction. Immune Epitope Database (IEDB). [cited 2018 June 20]. Available from: http://tools.iedb.org/bcell/
- 43Petersen B, Lundegaard C, Petersen TN. NetTurnP—neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features. PLoS ONE. 2010; 5(11):e15079. https://doi.org/10.1371/journal.pone.0015079
- 44 NetTurnP 1.0. Prediction of Beta-Turn Regions in Protein Sequences. [cited 2018 Oct 18]. Available from: http://www.cbs.dtu.dk/services/NetTurnP/
- 45Kountouris P, Hirst JD. Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics. 2010; 11:407. https://doi.org/10.1186/1471-2105-11-407
- 46 DEBT: Dihedrally Enhanced Beta Turn Prediction. [cited 2018 June 20]. Available from: http://comp.chem.nottingham.ac.uk/debt/
- 47Emini E, Hughes J, Perlow D, Boger J. Induction of hepatitis virus-neutralizing antibody by a virus specific synthetic peptide. J Virol. 1985; 55: 836–9.
- 48 Emini Surface Accessibility Prediction. Immune Epitope Database (IEDB) [cited 2018 Oct 23]. Available from: http://tools.iedb.org/bcell/
- 49Heffernan R, Dehzangi A, Lyons J, et al. Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinformatics. 2016; 32: 843–9.
- 50 SPIDER2: Sequence-Based Prediction of Local and Nonlocal Structural Features for Proteins. [cited 2018 May 30]. Available from: http://sparks-lab.org/server/SPIDER2/
- 51Klausen MS, Jespersen MC, Nielsen H, et al. NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning. Proteins. 2019; 87: 520–7. https://doi.org/10.1002/prot.25674
- 52 NetSurfP-2.0: NetSurfP 2.0 Server Predicts the Surface Accessibility, Secondary Structure, Disorder, and Phi/Psi Dihedral Angles of Amino Acids in an Amino Acid Sequence. [cited 2018 June 20]. Available from: http://www.cbs.dtu.dk/services/NetSurfP/
- 53Karplus P, Schulz G. Prediction of chain flexibility in proteins. Naturwissenschaften. 1985; 72: 212–3.
- 54 Karplus and Schulz flexibility prediction. Immune Epitope Database (IEDB). [cited 2018 June 20]. Available from: http://tools.iedb.org/bcell/
- 55de Brevern AG, Bornot A, Craveur P, et al. PredyFlexy: flexibility and local structure prediction from sequence. Nucleic Acids Res. 2012; 40(Web Server issue): W317–22. https://doi.org/10.1093/nar/gks482
- 56 PredyFlexy Server: Flexibility and Local Structure Prediction from Sequence. [cited 2018 Oct 18]. Available from: http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/
- 57Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics. 2006; 22: 2948–9.
- 58 FoldUnfold: Webserver for Prediction of Disordered Regions in Protein Chain. [cited 2018 May 30]. Available from: http://bioinfo.protres.ru/ogu/
- 59Cilia E, Pancsa R, Tompa P, et al. The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acid Res. 2014; 42(W1): W264–70. [cited 2019 July 1]. https://doi.org/10.1093/nar/gku629
- 60 DynaMine Webserver: Predicting Protein Backbone Dynamics Using Only Sequence Information as Input. [cited 2018 June 20]. Available from: http://dynamine.ibsquare.be/
- 61Davydov YI, Tonevitsky AG. Prediction of linear B-cell epitopes. Mol Biol (Mosk). 2009; 43: 166–74.
- 62 AAPPred Epitope Prediction Software. [cited 2018 Aug 22]. Available from: http://www.bioinf.ru/aappred/
- 63Kolaskar A, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett. 1990; 276: 172–4.
- 64 Kolaskar and Tongaonkar antigenicity prediction. Immune Epitope Database (IEDB). [cited 2018 Oct 23]. Available from: http://tools.iedb.org/bcell/10/23/18
- 65Parker JM, Guo D, Hodges RS. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray derived accessible sites. Biochemistry. 1986; 25: 5425–32.
- 66 Parker Hydrophilicity prediction. Immune Epitope Database (IEDB). [cited 2018 June 20]. Available from: http://tools.iedb.org/bcell/
- 67Larsen JE, Lund O, Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006; 2:2. https://doi.org/10.1186/1745-7580-2-2
- 68 BepiPred Linear Epitope Prediction. Immune Epitope Database (IEDB). [cited 2018 Oct 18]. Available from: http://tools.iedb.org/bcell/
- 69Singh H, Ansari HR, Raghava GPS. Improved method for linear B-cell epitope prediction using antigen's primary sequence. PLoS ONE. 2013; 8(5):e62219.
- 70 LBtope: Linear B-Cell Epitope Prediction Server. [cited 2018 Aug 15]. Available from: https://webs.iiitd.edu.in/raghava/lbtope/protein.php
- 71 VassarStats: Website for Statistical Computation, Richard Lowry. [cited 2016 Oct 4]. Available from: http://vassarstats.net/
- 72Pellequer JL, Westhof E, Van Regenmortel MH. Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett. 1993; 36: 83–9.
- 73Rahman KS, Chowdhury EU, Sachse K, Kaltenboeck B. Inadequate reference datasets biased toward short non-epitopes confound B-cell epitope prediction. J Biol Chem. 2016; 291: 14585–99.
- 74Sun J, Xu T, Wang S, et al. Does difference exist between epitope and non-epitope residues? Analysis of the physicochemical and structural properties on conformational epitopes from B-cell protein antigens. Immunome Res. 2011; 7: 1–11.
- 75Advani H, Zamor J, Judd WJ, et al. Inactivation of Kell blood group antigens by 2-aminoethylisothiouronium bromide. Br J Haematol. 1982; 51: 107–15.
- 76Branch DR, Petz LD. A new reagent (ZZAP) having multiple applications in immunohematology. Am J Clin Pathol. 1982; 78: 161–7.
- 77Branch DR, Muensch HA, Sy Siok Hian AL, Petz LD. Disulfide bonds are a requirement for Kell and cartwright (Yta) blood group antigen intergrity. Br J Haematol. 1983; 54: 573–8.
- 78Redman CM, Avellino G, Pfeffer SR, et al. Kell blood group antigens are part of a 93,000-Dalton red cell membrane protein. J Biol Chem. 1986; 261: 9521–5.
- 79Weber CA, Mehta PJ, Ardito M, et al. T cell epitope: friend or foe? Immunogenicity of biologics in context. Adv Drug Deliv Rev. 2009; 61: 965–76.
- 80Rossjohn J, Gras S, Miles JJ, et al. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol. 2015; 33: 169–200.
- 81Sette A, Vitiello A, Reherman B, et al. The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes. J Immunol. 1994; 153: 5586–92.
- 82Blum JS, Wearsch PA, Cresswell P. Pathways of antigen processing. Annu Rev Immunol. 2013; 31: 443–73.
- 83Lazarski CA, Chaves FA, Jenks SA, et al. The kinetic stability of MHC class II: peptide complexes is a key parameter that dictates immunodominance. Immunity. 2005; 23: 29–40.
- 84Southwood S, Sidney J, Kondo A, et al. Several common HLA-DR types share largely overlapping peptide binding repertoires. J Immunol. 1998; 160: 3363–73.
- 85Cano P, Klitz W, Mack SJ, et al. Common and well-documented HLA alleles: report of the ad-hoc Committee of the American Society of histocompatibility and Immunogenetics. Hum Immunol. 2007; 68: 392–417.
- 86Reviron D, Dettori I, Ferrara V, et al. HLA-DRB1 alleles and Jka immunization. Transfusion. 2005; 45: 956–9.
- 87Schonewille H, Doxiadis II, Levering WH, et al. HLA-DRB1 associations in individuals with single and multiple clinically relevant red blood cell antibodies. Transfusion. 2014; 54: 1971–80.
- 88Hudson KE, Lin E, Hendrickson JE, et al. Regulation of primary alloantibody response through antecedent exposure to a microbial T-cell epitope. Blood. 2010; 115: 3989–96.
Citing Literature
