The space of antibody reactivities modelled by mimotope libraries - IgOme

Antibody repertoires can be studied by BCR sequencing or by selection of sets of random peptides - IgOme or phage immunoprecipitation sequencing (PhIP-Seq).

Apart from the much more popular repertoire sequencing (AIRR-Seq)

What is IgOme?

The term IgOme was coined in a paper from the Jonathan Gershony’s lab¹. It consists of bulk mimotope selection from a random peptide phage display library, adsorption on non-specific monoclonals, and NGS of the regions coding for the peptide inserts. This technique can be coupled with bioinformatic analyses of the mimotope libraries for finding of clusters and motifs. It also helps infer properties of the global shape of the reactivity space.

Why this is more than a reframing

Three things follow that the binary picture cannot give:

• Polyreactivity becomes a measurable quantity, not a nuisance — an entropy, not an error bar.
• Mimotope arrays become samples from the space of peptides. A microarray of peptides probes the landscape \(E(\varepsilon)\) at many points at once; the measured reactivities are an empirical sketch of the distribution. Scalable mimotope libraries make this sampling practical at the scale of the public repertoire².
• The repertoire becomes an ensemble of distributions, opening the door to genuinely statistical-mechanical questions about the population of antibodies as a whole.

None of this is settled. The epitope space is not obviously enumerable, the parameters are not yet estimated or measured, and whether the equilibrium reading is the right one in a dynamic immune system is an open question. But as a way to organise mimotope and microarray data — and as a bridge to the repertoire-physics program — treating specificity as a shape has been more productive than treating it as a switch.

Viewing specificity as a distribution of binding energies may seem hard to reconcile with negative selection. Each monoclonal antibody can select thousands of short peptides from a random peptide library with a biologically relevant affinity. These peptides are found to span the entire peptide space. If each individual reaction can have biological consequences, then the probability of an antibody surviving negative selection would become negligible. Indeed, up to 70% of the early immature B cells in the bone marrow are self-reactive³ and most of them are eliminated by negative selection.

How can these views be reconciled:

• The affinities for small peptides are below the threshold for negative selection, the epitopes above that threshold are less frequent.
• The tolerogenic signals have typically been found to depend on high avidity⁴ .
• The accessible self-antigens, presented at sufficient concentration and local density, are probably many orders of magnitude fewer than the random peptide species in a phage library.
• The frequency of self-reactive BCR rearrangements is surprisingly high.Indeed, up to 70% of the early immature B cells in the bone marrow are self-reactive³ and most of them are eliminated by negative selection.

Thus, falsifying this concept would require careful modeling and definition of the model’s parameters.

References

1.

Ryvkin, A., A. & Gershoni, J. M. Deep Panning: Steps towards probing the IgOme. PLoS One 7, e41469 (2012).

2.

Pashov, A. et al. Diagnostic profiling of the human public IgM repertoire with scalable mimotope libraries. Frontiers in Immunology 10, 2796 (2019).

3.

Wardemann, H. et al. Predominant autoantibody production by early human b cell precursors. Science 301, 1374–7 (2003).

4.

Desaymard, C., Pearce, B. & Feldmann, M. Role of epitope density in the induction of tolerance and immunity with thymus-independent antigens. III. Interaction of epitope density and receptor avidity. Eur J Immunol 6, 646–50 (1976).