Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.
Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.
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DOI：
10.3389/fimmu.2017.00537
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发表时间：
2017
影响因子：
7.3
通讯作者：
Shapiro L
中科院分区：
文献类型：
--
作者：
Sheng Z;Schramm CA;Kong R;NISC Comparative Sequencing Program;Mullikin JC;Mascola JR;Kwong PD;Shapiro L
体细胞超突变(SHM)在抗体的成熟过程中起着关键作用，它优化了V(D)J基因重组所引发的识别。以前的研究表明，突变的倾向受到周围核苷酸环境的影响，SHM机制产生有偏见的替换。为了在氨基酸水平上研究SHM的内在突变频率和替换偏向，我们分析了功能性人类抗体谱，并开发了一种从下一代测序确定的B细胞转录物中构建氨基酸替换谱的方法mGSSP(gene-Specitic Subsidence Profile)。我们证明了这些基因特异的替换图谱(GSSP)对于每个V基因都是唯一的，并且在供体之间高度一致。我们还表明，由功能性抗体库构建的GSSP与从非生产性重排的乘客等位基因扩增的抗体序列构建的GSSP高度相似，后者不经历功能选择。这表明SHM机制采样的大多数氨基酸变化的类型和频率，或突变空间，可以很好地被GSSP捕获。我们进一步观察到一些氨基酸之间的突变交换速率是不对称的和上下文相关的，并且与它们的生化性质之间的相关性很弱。GSSP提供了一种改进的、与位置相关的替代标准替代矩阵，并可用于开发精确模拟SHM过程的软件。GSSP还可用于预测可用于抗原驱动选择的氨基酸突变空间，以及在基因特定的背景下理解调节抗体谱系成熟途径的因素。MGSSP方法可用于构建、比较和绘制GSSPs1；我们报告了为69个常见的人类V基因构建的GSSP(DOI：)，并为每个基因提供了高分辨率的LOGO图(DOI：)。
Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts. We demonstrated that these gene-specific substitution profiles (GSSPs) are unique to each V gene and highly consistent between donors. We also showed that the GSSPs constructed from functional antibody repertoires are highly similar to those constructed from antibody sequences amplified from non-productively rearranged passenger alleles, which do not undergo functional selection. This suggests the types and frequencies, or mutational space, of a majority of amino acid changes sampled by the SHM machinery to be well captured by GSSPs. We further observed the rates of mutational exchange between some amino acids to be both asymmetric and context dependent and to correlate weakly with their biochemical properties. GSSPs provide an improved, position-dependent alternative to standard substitution matrices, and can be utilized to developing software for accurately modeling the SHM process. GSSPs can also be used for predicting the amino acid mutational space available for antigen-driven selection and for understanding factors modulating the maturation pathways of antibody lineages in a gene-specific context. The mGSSP method can be used to build, compare, and plot GSSPs1; we report the GSSPs constructed for 69 common human V genes (DOI: ) and provide high-resolution logo plots for each (DOI: ).