A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data

Abstract

Analyses of somatic hypermutation (SHM) patterns in B-cell immunoglobulin (Ig) sequences have important basic science and clinical applications, but are often confounded by the intrinsic biases of SHM targeting on specific DNA motifs (i.e., hot- and cold-spots). Modeling these biases has been hindered by the difficulty in identifying mutated Ig sequences in vivo in the absence of selection pressures, which skew the observed mutation patterns. To generate a large number of unselected mutations, we immunized B1-8 heavy-chain transgenic mice with nitrophenyl (NP) to stimulate NP-specific λ+ germinal center B cells, and sequenced the unexpressed κ light chains using next-generation methods. Most of these κ sequences had out-of-frame junctions and were presumably uninfluenced by selection. Despite being non-functionally rearranged, they were targeted by SHM and displayed a higher mutation frequency than functional sequences. We used 39,173 mutations to construct a quantitative SHM targeting model. The model showed targeting biases that were consistent with classic hot- and cold-spots, yet revealed additional highly mutable motifs. We observed comparable targeting for functional and non-functional sequences, suggesting similar biological processes operate at both loci. However, we observed species-specific and chain-specific targeting patterns, demonstrating the need for multiple SHM targeting models. Interestingly, the targeting of C/G bases and the frequency of transition mutations at C/G bases was higher in mice compared with humans, suggesting lower levels of DNA repair activity in mice. Our models of SHM targeting provide insights into the SHM process and support future analyses of mutation patterns.

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

“…Much effort has been invested in building context-dependent models to predict the mutation propensity of Ig genes at nucleotide level (14–19, 24). These models have emphasized the difference between the generation of mutations by SHM machinery and the selection of those mutations into the functional repertoire.…”

Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data

“…The analysis described here uses the S5F targeting model for SHM that was previously constructed (Yaari et al, 2013). However, while hot-and cold-spot biases are generally conserved across individuals, these intrinsic biases can be altered by age (Hoehn et al, 2019), and may also differ across species (Cui et al, 2016). Clonal identification could be improved by using a data-specific targeting model that can be built using toolkits available in the Immcantation framework (www.immcantation.org).…”

Improving immunological insights into the ferret model of human viral infectious disease

“…The identification of SNPs in immunoglobulin genes is useful for distinguishing between somatically mutated B‐cell receptor sequences and germline variants in affinity‐matured antigen‐specific B‐cell populations. There are currently databases of immunoglobulin sequences for well‐established animal models such as those found in the international ImMunoGeneTics (IMGT) information system database and have been useful for identifying somatic hypermutations in immunoglobulin sequences . A curated and annotated database of immune gene sequences is a prerequisite for PCR primer design and post‐sequencing data analysis used to recover and express antibodies from single‐sorted B cells and recombinant T‐cell receptors…”