Maturation of the Human Immunoglobulin Heavy Chain Repertoire With Age

Marie Ghraichy, Jacob D Galson, Aleksandr Kovaltsuk, Valentin von Niederhäusern, Jana Pachlopnik Schmid, Mike Recher, Annaïse J Jauch, Enkelejda Miho, Dominic F Kelly, Charlotte M Deane, Johannes Trück, Marie Ghraichy, Jacob D Galson, Aleksandr Kovaltsuk, Valentin von Niederhäusern, Jana Pachlopnik Schmid, Mike Recher, Annaïse J Jauch, Enkelejda Miho, Dominic F Kelly, Charlotte M Deane, Johannes Trück

Abstract

B cells play a central role in adaptive immune processes, mainly through the production of antibodies. The maturation of the B cell system with age is poorly studied. We extensively investigated age-related alterations of naïve and antigen-experienced immunoglobulin heavy chain (IgH) repertoires. The most significant changes were observed in the first 10 years of life, and were characterized by altered immunoglobulin gene usage and an increased frequency of mutated antibodies structurally diverging from their germline precursors. Older age was associated with an increased usage of downstream IgH constant region genes and fewer antibodies with self-reactive properties. As mutations accumulated with age, the frequency of germline-encoded self-reactive antibodies decreased, indicating a possible beneficial role of self-reactive B cells in the developing immune system. Our results suggest a continuous process of change through childhood across a broad range of parameters characterizing IgH repertoires and stress the importance of using well-selected, age-appropriate controls in IgH studies.

Keywords: B cells; antibody; children; heavy chain; high-throughput sequencing; immunoglobulin; maturation; repertoire.

Copyright © 2020 Ghraichy, Galson, Kovaltsuk, von Niederhäusern, Pachlopnik Schmid, Recher, Jauch, Miho, Kelly, Deane and Trück.

Figures

Figure 1
Figure 1
V family and J gene usage changes in early childhood. (A) V1 family usage was significantly reduced in older compared with younger individuals in all IgH repertoires. (B) J6 gene usage significantly decreased during the first 10 years of life mostly in IgG subsets. (C) Mean junction length significantly decreased in the first 10 years of life exclusively in IgG subsets. Comparison of each age group to the 0–3y group was performed using the Wilcoxon test. *p < 0.05, **p < 0.01, ***p < 0.001.
Figure 2
Figure 2
Age-related changes in somatic hypermutation and predicted antibody structure. (A) Mean number of V gene mutations by individual and B cell subset with fitted logarithmic curves. Somatic hypermutation increased mainly in the first 10 years of life with some differences between cell subsets. (B) The proportion of memory IgD/IgM out of all IgD/IgM transcripts and the proportion of mutated IgG and IgA transcripts within repertoires showed significant increases in the first 10 years of life. Statistical differences between groups were tested using the Kruskal–Wallis test. (C) The proportion of sequences structurally different from germline increased in early childhood in all B cell subsets.
Figure 3
Figure 3
Sharing of sequence and structural clusters among the 53 healthy participants of different ages. (A) Percentage of sequence clusters shared by n individuals. (B) Percentage of structural clusters shared by n individuals. For structural clusters, zeros were replaced by 0.01% to be displayed on a logarithmic scale but labeled as 0%.
Figure 4
Figure 4
Age-related changes in clonal expansions. (A) Example lineage tree with each node representing a sequence and the size of the node indicating the number of identical sequences. The number of mutations between the sequences (nodes) is shown on top of the connecting lines. (B) Correlation between age and mean trunk length with a fitted logarithmic curve. (C) Correlation between mean Gini index and age with a fitted linear model.
Figure 5
Figure 5
Age-related changes in antigen-driven selection. (A) Mean R/S ratio in V gene CDRs as a measure of selection pressure showed an increase in early childhood in all mutated B cell subsets. For sequences with replacement but no silent mutations, the number of silent mutations was set to 1. (B) Mean selection strength in CDRs calculated using BASELINe decreases with age in class switched subsets.
Figure 6
Figure 6
Usage of IgG and IgA subclasses by age group. The IgG and IgA isotype subclass usage changes with age. Error bars represent standard error of the mean.
Figure 7
Figure 7
VH4-34 motifs by age group. Bar plots represent the proportion of sequences with mutated AVY and/or NHS motifs in IgD/IgM, IgG, and IgA. Error bars indicate standard error of the mean. Proportion of sequences with both unmutated motifs decreases with age.
Figure 8
Figure 8
Stratification of IgH repertoires by age group. Principal component analysis by age category including mutation number, R/S ratio, V1 gene family usage, J6 gene usage, junction length and proportion of sequences structurally divergent from germline as variables. For class-switched IgG and IgA, the proportion of IgG2 and IgA1 are included, respectively. Areas are the convex hulls of the age group and the largest point of one color represents the center of that hull.

References

    1. Reich NC. Janeway's immunobiology. 7th ed In: Murphy K, Travers P, Walport M, Editors. Garland Science. New York, NY: Taylor; (2008) p. 135–48.
    1. Rawlings DJ, Metzler G, Wray-Dutra M, Jackson SW. Altered B cell signalling in autoimmunity. Nat Rev Immunol. (2017) 17:421–36. 10.1038/nri.2017.24
    1. Hoffman W, Lakkis FG, Chalasani G. B cells, antibodies, and more. Clin J Am Soc Nephrol. (2016) 11:137–54. 10.2215/CJN.09430915
    1. Ghraichy M, Galson JD, Kelly DF, Trück J. B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review. Immunology. (2018) 153:145–60. 10.1111/imm.12865
    1. Bashford-Rogers RJM, Smith KGC, Thomas DC. Antibody repertoire analysis in polygenic autoimmune diseases. Immunology. (2018) 155:3–17. 10.1111/imm.12927
    1. Jiang N, He J, Weinstein JA, Penland L, Sasaki S, He XS, et al. . Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci Transl Med. (2013) 5:171ra19. 10.1126/scitranslmed.3004794
    1. Galson JD, Trück J, Clutterbuck EA, Fowler A, Cerundolo V, Pollard AJ, et al. B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation. Genome Med. (2016) 8:68 10.1186/s13073-016-0322-z
    1. Galson JD, Trück J, Fowler A, Münz M, Cerundolo V, Pollard AJ, et al. . In-depth assessment of within-individual and inter-individual variation in the B cell receptor repertoire. Front Immunol. (2015) 6:531. 10.3389/fimmu.2015.00531
    1. Galson JD, Clutterbuck E, Trück J, Ramasamy MN, Münz M, Fowler A, et al. . BCR repertoire sequencing: different patterns of B-cell activation after two meningococcal vaccines. Immunol Cell Biol. (2015) 93:885–95. 10.1038/icb.2015.57
    1. Kovaltsuk A, Leem J, Kelm S, Snowden J, Deane CM, Krawczyk K. Observed antibody space: a resource for data mining next-generation sequencing of antibody repertoires. J Immunol. (2018) 201:2502–9. 10.4049/jimmunol.1800708
    1. IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Driessen GJ, Stubbs AP, et al. . Evaluation of the antigen-experienced B-cell receptor repertoire in healthy children and adults. Front Immunol. (2016) 7:410. 10.3389/fimmu.2016.00410
    1. Comans-Bitter WM, De Groot R, Van den Beemd R, Neijens HJ, Hop WCJ, Groeneveld K, et al. . Immunophenotyping of blood lymphocytes in childhood: reference values for lymphocyte subpopulations. J Pediatr. (1997) 130:388–93. 10.1016/S0022-3476(97)70200-2
    1. Vander Heiden JA, Yaari G, Uduman M, Stern JNH, O'Connor KC, Hafler DA, et al. . PRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. (2014) 30:1930–2. 10.1093/bioinformatics/btu138
    1. Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. (2015) 31:3356–8. 10.1093/bioinformatics/btv359
    1. Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. (2013) 41:W34–40. 10.1093/nar/gkt382
    1. Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. (2011) 21:936–9. 10.1101/gr.111120.110
    1. Stern JNH, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, et al. . B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. (2014) 6:248ra107. 10.1126/scitranslmed.3008879
    1. Yaari G, Uduman M, Kleinstein SH. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. (2012) 40:e134. 10.1093/nar/gks457
    1. Kovaltsuk A, Raybould MIJ, Wong WK, Marks C, Kelm S, Snowden J, et al. . Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice. bioRxiv. (2019). 10.1101/762880
    1. Lefranc MP, Pommié C, Ruiz M, Giudicelli V, Foulquier E, Truong L, et al. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol. (2003) 27:55–77. 10.1016/S0145-305X(02)00039-3
    1. Dunbar J, Deane CM. ANARCI: antigen receptor numbering and receptor classification. Bioinformatics. (2015) 32:298–300. 10.1093/bioinformatics/btv552
    1. Kovaltsuk A, Krawczyk K, Kelm S, Snowden J, Deane CM. Filtering next-generation sequencing of the ig gene repertoire data using antibody structural information. J Immunol. (2018) 201:3694–704. 10.4049/jimmunol.1800669
    1. Wong WK, Georges G, Ros F, Kelm S, Lewis AP, Taddese B, et al. . SCALOP: sequence-based antibody canonical loop structure annotation. Bioinformatics. (2019) 35:1774–6. 10.1093/bioinformatics/bty877
    1. Choi Y, Deane CM. FREAD revisited: accurate loop structure prediction using a database search algorithm. Proteins Struct Funct Bioinforma. (2009) 78:1431–40. 10.1002/prot.22658
    1. Berman H, Henrick K, Nakamura H, Markley JL. The worldwide protein data bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. (2007) 35:D301–3. 10.1093/nar/gkl971
    1. R Project for Statistical Computing A Language and Environment for Statistical Computing. R Found. Stat. Comput. 2 (2018) Available online at: (Accessed on 6 April 2020)
    1. Ginestet C. ggplot2: elegant graphics for data analysis. J R Stat Soc Ser A. (2011) 174:245–6. 10.1111/j.1467-985X.2010.00676_9.x
    1. Kassambara A. ggpubr: ggplot2 Based Publication Ready Plots. R Packag version 0.1.8. (2018).
    1. Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. (2016) 32:2847–9. 10.1093/bioinformatics/btw313
    1. Kassambara A, Mundt F. Package factoextra for R: Extract and Visualize the Results of Multivariate Data Analyses. R Package version (2017).
    1. Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, et al. . Inferred allelic variants of immunoglobulin receptor genes: a system for their evaluation, documentation, and naming. Front Immunol. (2019) 10:435. 10.3389/fimmu.2019.00435
    1. Rubelt F, Busse CE, Bukhari SAC, Bürckert J-P, Mariotti-Ferrandiz E, Cowell LG, et al. . Adaptive immune receptor repertoire community recommendations for sharing immune-repertoire sequencing data. Nat Immunol. (2017) 18:1274–8. 10.1038/ni.3873
    1. Glanville J, Kuo TC, von Budingen H.-C., Guey L, Berka J, Sundar PD, et al. . Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation. Proc Natl Acad Sci USA. (2011) 108:20066–71. 10.1073/pnas.1107498108
    1. Briney B, Inderbitzin A, Joyce C, Burton DR. Commonality despite exceptional diversity in the baseline human antibody repertoire. Nature. (2019) 566:393–7. 10.1038/s41586-019-0879-y
    1. Peres A, Gidoni M, Polak P, Yaari G. RAbHIT: R antibody haplotype inference tool. Bioinformatics. (2019) 35:4840–2. 10.1093/bioinformatics/btz481
    1. Donisi PM, Di Lorenzo N, Riccardi M, Paparella A, Sarpellon C, Zupo S, et al. . Pattern and distribution of immunoglobulin VH gene usage in a cohort of B-CLL patients from a northeastern region of italy. Diagnostic Mol Pathol. (2006) 15:206–15. 10.1097/01.pdm.0000213469.85301.d6
    1. Widhopf GF, Rassenti LZ, Toy TL, Gribben JG, Wierda WG, Kipps TJ. Chronic lymphocytic leukemia B cells of more than 1% of patients express virtually identical immunoglobulins. Blood. (2004) 104:2499–504. 10.1182/blood-2004-03-0818
    1. North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol. (2011) 406:228–56. 10.1016/j.jmb.2010.10.030
    1. Chothia C, Lesk AM. Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol. (1987) 196:901–17. 10.1016/0022-2836(87)90412-8
    1. Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, et al. . Neutralizing antibodies against west nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr Biol. (2015) 7:1587–97. 10.1039/C5IB00169B
    1. Wardemann H, Yurasov S, Schaefer A, Young JW, Meffre E, Nussenzweig MC. Predominant autoantibody production by early human B cell precursors. Science. (2003) 301:1374–7. 10.1126/science.1086907
    1. Larimore K, McCormick MW, Robins HS, Greenberg PD. Shaping of human germline IgH repertoires revealed by deep sequencing. J Immunol. (2012) 189:3221–30. 10.4049/jimmunol.1201303
    1. Pugh-Bernard AE, Silverman GJ, Cappione AJ, Villano ME, Ryan DH, Insel RA, et al. . Regulation of inherently autoreactive VH4-34 B cells in the maintenance of human B cell tolerance. J Clin Invest. (2001) 108:1061–70. 10.1172/JCI200112462
    1. Potter KN, Hobby P, Klijn S, Stevenson FK, Sutton BJ. Evidence for involvement of a hydrophobic patch in framework region 1 of human V4-34-encoded Igs in recognition of the red blood cell i antigen. J Immunol. (2002) 169:3777–82. 10.4049/jimmunol.169.7.3777
    1. Reed JH, Jackson J, Christ D, Goodnow CC. Clonal redemption of autoantibodies by somatic hypermutation away from self-reactivity during human immunization. J Exp Med. (2016) 213:1255–65. 10.1084/jem.20151978
    1. Sabouri Z, Schofield P, Horikawa K, Spierings E, Kipling D, Randall KL, et al. . Redemption of autoantibodies on anergic B cells by variable-region glycosylation and mutation away from self-reactivity. Proc Natl Acad Sci USA. (2014) 111:E2567–75. 10.1073/pnas.1406974111
    1. Souto-Carneiro MM, Sims GP, Girschik H, Lee J, Lipsky PE. Developmental changes in the human heavy chain CDR3. J Immunol. (2005) 175:7425–36. 10.4049/jimmunol.175.11.7425
    1. Rogosch T, Kerzel S, Hoß K, Hoersch G, Zemlin C, Heckmann M, et al. . IgA response in preterm neonates shows little evidence of antigen-driven selection. J Immunol. (2012) 189:5449–56. 10.4049/jimmunol.1103347
    1. Zemlin M, Hoersch G, Zemlin C, Pohl-Schickinger A, Hummel M, Berek C, et al. . The postnatal maturation of the immunoglobulin heavy chain IgG repertoire in human preterm neonates is slower than in term neonates. J Immunol. (2007) 178:1180–8. 10.4049/jimmunol.178.2.1180
    1. Rechavi E, Lev A, Lee YN, Simon AJ, Yinon Y, Lipitz S, et al. . Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Sci Transl Med. (2015) 7:276ra25. 10.1126/scitranslmed.aaa0072
    1. Rechavi E, Somech R. Survival of the fetus: fetal B and T cell receptor repertoire development. Semin Immunopathol. (2017) 39:577–83. 10.1007/s00281-017-0626-0
    1. Martin V, (Bryan) Wu Y.-C., Kipling D, Dunn-Walters D. Ageing of the B-cell repertoire. Philos Trans R Soc B Biol Sci. (2015) 370:20140237. 10.1098/rstb.2014.0237
    1. Wu Y.-C. B., Kipling D, Dunn-Walters DK. Age-related changes in human peripheral blood igh repertoire following vaccination. Front Immunol. (2012) 3:193. 10.3389/fimmu.2012.00193
    1. Wang C, Liu Y, Xu LT, Jackson KJL, Roskin KM, Pham TD, et al. . Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires. J Immunol. (2014) 192:603–11. 10.4049/jimmunol.1301384
    1. de Bourcy CFA, Angel CJL, Vollmers C, Dekker CL, Davis MM, Quake SR. Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. Proc Natl Acad Sci USA. (2017) 114:1105–10. 10.1073/pnas.1617959114
    1. Greiff V, Menzel U, Miho E, Weber C, Riedel R, Cook S, et al. . Systems analysis reveals high genetic and antigen-driven predetermination of antibody repertoires throughout B cell development. Cell Rep. (2017) 19:1467–78. 10.1016/j.celrep.2017.04.054
    1. Tabibian-Keissar H, Hazanov L, Schiby G, Rosenthal N, Rakovsky A, Michaeli M, et al. . Aging affects B-cell antigen receptor repertoire diversity in primary and secondary lymphoid tissues. Eur J Immunol. (2016) 46:480–92. 10.1002/eji.201545586
    1. Schatorjé EJ, Driessen GJ, van Hout RW, van der Burg M, de Vries E. Levels of somatic hypermutations in B cell receptors increase during childhood. Clin. Exp. Immunol. (2014) 178:394–8. 10.1111/cei.12419
    1. Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee J-Y, et al. . Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. Sci Transl Med. (2019) 11:eaat2004. 10.1126/scitranslmed.aat2004
    1. Siegrist CA, Aspinall R. B-cell responses to vaccination at the extremes of age. Nat Rev Immunol. (2009) 9:185–94. 10.1038/nri2508
    1. Fecteau JF, Côté G, Néron S. A new memory CD27 – IgG + B cell population in peripheral blood expressing V H genes with low frequency of somatic mutation. J Immunol. (2006) 177:3728–36. 10.4049/jimmunol.177.6.3728
    1. Bauer K, Zemlin M, Hummel M, Pfeiffer S, Karstaedt J, Steinhauser G, et al. . Diversification of Ig heavy chain genes in human preterm neonates prematurely exposed to environmental antigens. J Immunol. (2002) 169:1349–56. 10.4049/jimmunol.169.3.1349
    1. Nagumo H, Agematsu K, Kobayashi N, Shinozaki K, Hokibara S, Nagase H, et al. . The different process of class switching and somatic hypermutation; a novel analysis by CD27- naive B cells. Blood. (2002) 99:567–75. 10.1182/blood.V99.2.567
    1. Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J. How B-cell receptor repertoire sequencing can be enriched with structural antibody data. Front Immunol. (2017) 8:1753. 10.3389/fimmu.2017.01753
    1. Krawczyk K, Kelm S, Kovaltsuk A, Galson JD, Kelly D, Trück J, et al. . Structurally mapping antibody repertoires. Front Immunol. (2018) 9:1698. 10.3389/fimmu.2018.01698
    1. Blanco E, Pérez-Andrés M, Arriba-Méndez S, Contreras-Sanfeliciano T, Criado I, Pelak O, et al. . Age-associated distribution of normal B-cell and plasma cell subsets in peripheral blood. J Allergy Clin Immunol. (2018) 141:2208–19.e16. 10.1016/j.jaci.2018.02.017
    1. Vidarsson G, Dekkers G, Rispens T. IgG subclasses and allotypes: from structure to effector functions. Front Immunol. (2014) 5:520. 10.3389/fimmu.2014.00520
    1. Woof JM, Kerr MA. IgA function - variations on a theme. Immunology. (2004) 113:175–7. 10.1111/j.1365-2567.2004.01958.x
    1. Turner P, Turner C, Green N, Ashton L, Lwe E, Jankhot A, et al. . Serum antibody responses to pneumococcal colonization in the first 2 years of life: results from an SE Asian longitudinal cohort study. Clin Microbiol Infect. (2013) 19:1–8. 10.1111/1469-0691.12286
    1. Xiong H, Dolpady J, Wabl M, Curotto de Lafaille MA, Lafaille JJ. Sequential class switching is required for the generation of high affinity IgE antibodies. J Exp Med. (2012) 209:353–64. 10.1084/jem.20111941
    1. Schickel JN, Glauzy S, Ng YS, Chamberlain N, Massad C, Isnardi I, et al. Self-reactive VH4-34-expressing IgG B cells recognizecommensal bacteria. J Exp Med. (2017) 214:1991–2003. 10.1084/jem.20160201
    1. Hou D, Chen C, Seely EJ, Chen S, Song Y. High-throughput sequencing-based immune repertoire study during infectious disease. Front Immunol. (2016) 7:336. 10.3389/fimmu.2016.00336
    1. Burkholder WF, Newell EW, Poidinger M, Chen S, Fink K. Deep sequencing in infectious diseases: immune and pathogen repertoires for the improvement of patient outcomes. Front Immunol. (2017) 8:593. 10.3389/fimmu.2017.00593
    1. Ghraichy M, Galson JD, Kovaltsuk A, von Niederhäusern V, Schmid JP, Recher M, et al. Maturation of the human B-cell receptor repertoire with age. bioRxiv. (2019) 609651 10.1101/609651

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