title: 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 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.
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511.
authors.forename: Ang
authors.identifier: 0000-0002-1087-8568
authors.initials: A
authors.lastname: Cui
authors.affiliation: Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213.
authors.forename: Roberto
authors.initials: R
authors.lastname: Di Niro
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511.
authors.forename: Jason A
authors.identifier: 0000-0002-1474-310X
authors.initials: JA
authors.lastname: Vander Heiden
authors.affiliation: AbVitro Inc., Boston, MA 02210.
authors.forename: Adrian W
authors.initials: AW
authors.lastname: Briggs
authors.affiliation: AbVitro Inc., Boston, MA 02210.
authors.forename: Kris
authors.initials: K
authors.lastname: Adams
authors.affiliation: AbVitro Inc., Boston, MA 02210.
authors.forename: Tamara
authors.initials: T
authors.lastname: Gilbert
authors.affiliation: Department of Neurology, Yale School of Medicine, New Haven, CT 06511.|Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511; and.
authors.forename: Kevin C
authors.identifier: 0000-0002-7056-419X
authors.initials: KC
authors.lastname: O'Connor
authors.affiliation: AbVitro Inc., Boston, MA 02210.
authors.forename: Francois
authors.initials: F
authors.lastname: Vigneault
authors.affiliation: Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Shlomchik
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; steven.kleinstein@yale.edu.|Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511; and.|Departments of Pathology and Immunobiology, Yale School of Medicine, New Haven, CT 06511.
authors.forename: Steven H
authors.identifier: 0000-0003-4957-1544
authors.initials: SH
authors.lastname: Kleinstein
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000276:immunology*; D002478:Cells, Cultured; D060966:Clonal Selection, Antigen-Mediated; D004260:DNA Repair; D005260:Female; D018858:Germinal Center / Q000276:immunology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics*; D007135:Immunoglobulin Variable Region / Q000235:genetics*; D051379:Mice; D008807:Mice, Inbred BALB C; D008822:Mice, Transgenic; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D059645:Mutation Rate; D027041:Somatic Hypermutation, Immunoglobulin / Q000235:genetics*
chemical_list: D007143:Immunoglobulin Heavy Chains; D007135:Immunoglobulin Variable Region