Transcriptomic and V(D)J profiling at the single cell level of plasmablasts from lymph nodes of mice immunized with bMOG protein

Autoantibodies contribute to many autoimmune diseases, yet there is no therapy to neutralize them selectively. A popular mouse model, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. In this study, we analyzed autoantibody-secreting extrafollicular plasmablasts in mice with EAE induced by immunization with a mutated myelin oligodendrocyte glycoprotein (MOG) antigen called bMOG. These CD138+ cells were enriched from lymph nodes at day 8 post-immunization and analyzed by single-cell RNA sequencing using 10× Genomics technologies. Here we provide the raw and processed data obtained from the gene expression (GEX) and VDJ cDNA libraries. Single-cell suspensions were prepared from inguinal lymph nodes of mice at day 8 post-immunization with bMOG. CD138+ cells were enriched using the EasySep Mouse CD138 Positive Selection Kit (Stemcell Technologies). Cells were processed with the Chromium Single Cell Chip A and Chromium Controller (10× Genomics) with the goal of analyzing ~6,000 cells per mouse. RNA samples were pooled for reverse transcription and amplification to generate gene expression and V(D)J libraries using the Single Cell 5’ Library Kit and Single Cell V(D)J Enrichment Kit (10× Genomics). Libraries were pooled and sequenced using both Illumina Hiseq 2500 PE100 technology (low pass) at the University Hospital Center of Quebec and Illumina NovaSeq 6000 S4 PE150 technology (high pass) at Genome Quebec. Sequencing results from both technologies were combined for bioinformatics analyses.

自身抗体（autoantibodies）可参与多种自身免疫疾病，但目前尚无能够选择性中和此类抗体的治疗方案。实验性自身免疫性脑脊髓炎（experimental autoimmune encephalomyelitis, EAE）作为一类常用小鼠模型，可用于开发此类治疗策略，前提是我们能够更深入地阐明所涉自身抗体的本质与功能重要性。本研究针对经突变型髓鞘少突胶质细胞糖蛋白（myelin oligodendrocyte glycoprotein, MOG，命名为bMOG）免疫诱导的EAE小鼠体内分泌自身抗体的滤泡外浆母细胞（extrafollicular plasmablasts）展开分析，研究人员于免疫后第8天从淋巴结中富集CD138阳性细胞，并通过10× Genomics技术完成单细胞RNA测序（single-cell RNA sequencing）。本研究提供从基因表达（gene expression, GEX）文库与VDJ cDNA文库中获得的原始数据与预处理数据。研究人员从经bMOG免疫后第8天的小鼠腹股沟淋巴结中制备单细胞悬液，使用EasySep小鼠CD138阳性分选试剂盒（Stemcell Technologies）富集CD138阳性细胞；随后采用Chromium单细胞芯片A与Chromium控制器（10× Genomics）处理细胞，目标为每只小鼠分析约6000个细胞。通过单细胞5’文库试剂盒与单细胞V(D)J富集试剂盒（10× Genomics）对RNA样本进行混合逆转录与扩增，以构建基因表达文库与V(D)J文库；将构建好的文库混合后，分别在魁北克大学医院中心采用Illumina Hiseq 2500 PE100技术（低覆盖度测序）完成测序，以及在魁北克基因组中心采用Illumina NovaSeq 6000 S4 PE150技术（高覆盖度测序）完成测序，最终将两种测序技术获得的结果整合，用于后续生物信息学分析。