First-in-human clinical trial of personalized neoantigen vaccines as early intervention in untreated patients with lymphoplasmacytic lymphoma

We performed single cell RNA-seq gene expression analysis on bone marrow of 9 lymphoplasmacytic lymphoma patients before and after vaccination with personalized idiotype DNA vaccine to study changes in tumor microenvironment Overall design: Bone marrow samples before and after vaccination of 8 patients and one sample of pre vaccination sample for one patient were processed for single cell RNA seq using 10x genomics 5' chromium kit. For all except one patient samples of pre and post for a given patient were processed together on the same day and loaded separately into a well of 10x Genomics chip. For one patient (LPL008) samples of pre and post were first stained with two hashing antibodies, and then samples were mixed together at 1:1 ratio and loaded into a single well of 10x Genomics chip (additional data files are included for that patient for cell surface barcode sequencing). Bone marrow samples before and after vaccination of 9 patients were processed for single cell RNA seq paired with single cell TCR and single cell BCR seq using 10x genomics 5' chromium kit.

本研究针对9例淋巴浆细胞淋巴瘤（lymphoplasmacytic lymphoma, LPL）患者，在其接种个性化独特型DNA疫苗的前后阶段，采集骨髓样本开展单细胞RNA测序（single cell RNA-seq, scRNA-seq）基因表达分析，旨在揭示肿瘤微环境的动态变化。
整体实验设计：采用10x Genomics 5' Chromium试剂盒，对8例患者的疫苗接种前后骨髓样本，以及1例患者的接种前骨髓样本进行单细胞RNA测序建库处理。除患者LPL008外，其余所有患者的接种前后样本均于同日同步处理，并分别上样至10x Genomics芯片的单个孔位。针对患者LPL008，其接种前后样本首先经两种哈希抗体（hashing antibodies）标记，随后以1:1比例混合后上样至10x Genomics芯片的单个孔位（该患者的细胞表面条形码测序附加数据文件已随数据集一并提供）。
本数据集全部9例患者的疫苗接种前后骨髓样本，均通过10x Genomics 5' Chromium试剂盒完成单细胞RNA测序，并同步配套单细胞T细胞受体（T cell receptor, TCR）与单细胞B细胞受体（B cell receptor, BCR）测序。