Boyer François, Boutouil Hend, Dalloul Iman, Dalloul Zeinab, Cook-Moreau Jeanne, Aldigier Jean-Claude, Carrion Claire, Herve Bastien, Scaon Erwan, Cogné Michel, Péron Sophie
Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
J Immunol. 2017 May 15;198(10):4148-4155. doi: 10.4049/jimmunol.1601924. Epub 2017 Apr 17.
B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study.
B细胞通过产生抗原特异性记忆B细胞和分泌抗体的浆细胞来确保体液免疫反应。在次级淋巴器官中，抗原驱动的B细胞活化诱导终末成熟和Ig同种型类别转换（类别转换重组[CSR]）。CSR通过每个C区基因上游的两个转换（S）区域之间的染色体内重组，在每个B细胞克隆中创建一个几乎独特的位点。CSR连接点的数量和结构特征揭示了有关CSR机制的有价值信息，并且CSR连接点的分析在B细胞功能的基础和临床研究中很有用。为了提供一种能够分析高通量测序（HTS）产生的大量CSR连接序列数据集的自动化工具，我们设计了CSReport，这是一个专门用于支持对基于HTS协议（Ion Torrent技术）测序的CSR重组连接点进行分析的软件程序。使用CSR连接点的模拟数据集对CSReport进行评估，然后分别用于分析CH12F3细胞和原代小鼠B细胞的Sμ-Sα和Sμ-Sγ1连接点。CSReport可识别参考序列上的连接片段断点和连接结构（平端连接或有插入或微同源性的连接）。除了能够分析前所未有的大量连接序列文库外，CSReport还将为CSR连接点研究提供一个统一的框架。我们的结果表明，CSReport是一种准确的工具，可用于分析基于HTS协议的CSR连接点序列，从而促进和加速对它们的研究。
