Updated SHM targeting model paper

ematsen · December 26, 2016, 4:05pm

A new paper from the @steven.kleinstein group:

ncbi.nlm.nih.gov

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

A Cui, R Di Niro, JA Vander Heiden, AW Briggs, K Adams, T Gilbert, KC O'Connor, F Vigneault, MJ Shlomchik and SH Kleinstein, Journal of immunology (Baltimore, Md. : 1950), 2016 11 01

Analyses of somatic hypermutation (SHM) patterns in B cell Ig sequences have important basic science and clinical applications, but they 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 H chain transgenic mice with nitrophenyl to stimulate nitrophenyl-specific λ+ germinal center B cells and sequenced the unexpressed κ L chains using next-generation methods. Most of these κ sequences had out-of-frame junctions and were presumably uninfluenced by selection. Despite being nonfunctionally 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 nonfunctional sequences, suggesting similar biological processes operate at both loci. However, we observed species- 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.

Despite the title, the paper considers mutation patterns in human as well.

This was my favorite part: how to stimulate a large number of non-functional sequences:

krdav · December 26, 2016, 10:02pm

Cool facts. I didn’t even know that there is a preference for using kappa before lambda. However I wonder how well it has been proven that none of the kappa genes can be a founder of a GC and get maturated in the NP-immunized B1-8 mouse? The Nussenzweig paper which is referred to just seems to take it for granted. All I could find is a paper from 1978 by M. Reth, G.J. Hammerling and K. Rajewsky titled Analysis of the repertoire of anti-NP antibodies in C57BL/6 mice by cell fusion. This is not very high throughput so I imagine that there could easily slip some kappa chains though?

My favourite part is this one:

Overall, these results suggest the SHM targeting mechanism is highly conserved at the functional and nonfunctional loci in both the human and the mouse systems.

ematsen · December 26, 2016, 10:22pm

Well, they do see 20% in-frame kappa sequences, and suggest: