A model of somatic hypermutation targeting in mice based on high-throughput immunoglobulin sequencing data (TECH2P.910)

Abstract

Abstract Analyses of somatic hypermutation (SHM) patterns in B-cell immunoglobulin (Ig) genes have important basic science and clinical applications, but are often confounded by the intrinsic biases of SHM targeting on DNA motifs (i.e., hot/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 heavy-chain transgenic mice with nitrophenyl (NP) to generate NP-specific λ+ B cells, and used next-generation sequencing to examine the unproductive κ light chains. Most of these sequences had out-of-frame junctions and were presumed uninfluenced by selection. Despite being non-functionally rearranged, they were targeted by SHM and displayed a higher mutation frequency than functional sequences. We identified 29,005 mutations and used them to construct a quantitative SHM targeting model, which was consistent with classic hot/cold-spots, but revealed additional highly mutable motifs. We observed comparable targeting for functional and non-functional sequences, suggesting similar biological processes operate at both loci. In contrast, the level of C to T transitions in mice was higher than in human κ chains, suggesting lower levels of DNA repair activities. In summary, our model of SHM targeting for mice provides insights into the SHM process and supports future analyses of mutation patterns.