Gene expression profiling of B-cell and non-B-cell fractions of follicular lymphoma. Homo sapiens

Excisional biopsies of lymph nodes involved by follicular lymphoma (FL) were obtained from previously-untreated, advanced-stage patients to generate heterohybridomas and idiotype vaccine for a clinical trial (PMID: 21632504). Residual, viably-cryopreserved suspensions of disaggregated cells were magnetically sorted by negative selection into nominal B (CD3-depleted) and non-B (NB; CD19- and CD20-depleted) fractions. Total RNA was extracted from each fraction for separate gene expression profiling (GEP). Technically-satisfactory GEP results were obtained from both fractions for 43 patients. Overall design: GEP data from the NB fraction were used to identify signatures of immune cell types and biological processes in the NB fraction, through the technique of correlation matrix analysis (CMA). B and NB fraction data were also cross-correlated, by CMA and other means, to implicate immune cell types, genes, and biological processes involved in interactions between tumor B cells and the immune microenvironment in FL. Negatively-enriched B or non-B cells, as indicated, from untreated follicular lymphoma. 7-digit number is the unique patient identifier. Suffix number, when present, indicates which one of the duplicate arrays that were used for the same patient.

本数据集的样本取自既往未接受治疗的晚期滤泡性淋巴瘤（follicular lymphoma, FL）受累淋巴结的切除活检组织，用于为一项临床试验生成异源杂交瘤及独特型疫苗（PMID: 21632504）。将剩余的经活力保存的低温冷冻解离细胞悬液通过阴性选择磁分选，分为名义B细胞组分（CD3缺失）与非B细胞组分（NB；CD19及CD20缺失）。从每个组分中提取总RNA，以开展独立的基因表达谱分析（gene expression profiling, GEP）。最终43例患者的两个组分均获得了符合技术标准的GEP结果。整体实验设计：通过相关矩阵分析（correlation matrix analysis, CMA）技术，利用NB组分的GEP数据鉴定该组分中的免疫细胞类型及生物学过程特征；同时通过CMA及其他方法对B细胞组分与NB组分的数据进行互相关分析，以揭示滤泡性淋巴瘤中肿瘤B细胞与免疫微环境相互作用所涉及的免疫细胞类型、基因及生物学过程。本数据集包含来自未经治疗的滤泡性淋巴瘤患者的阴性富集B细胞或非B细胞，如标注所示。其中7位数字为患者唯一标识符，若存在后缀数字则代表同一患者所用重复芯片的编号。