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

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. 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.

本研究从既往未接受治疗的晚期滤泡性淋巴瘤（follicular lymphoma, FL）患者的受累淋巴结获取切除活检标本，用于制备异源杂交瘤与独特型疫苗以开展一项临床试验（PubMed编号：21632504）。解离后的细胞经活体冻存的剩余悬液通过阴性选择磁分选，被分为名义B细胞组分（去除CD3+细胞）与非B细胞组分（NB；去除CD19+及CD20+细胞）。从每个组分中提取总RNA，以分别开展基因表达谱（GEP）分析。43例患者的两个细胞组分均获得了符合技术标准的GEP分析结果。研究人员借助相关矩阵分析（CMA）技术，利用NB组分的GEP数据鉴定该组分中免疫细胞类型与生物学过程的特征标签。同时通过CMA及其他方法对B细胞组分与NB组分的数据进行交叉关联分析，以明确参与滤泡性淋巴瘤肿瘤B细胞与免疫微环境相互作用的免疫细胞类型、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细胞样本；其中7位数字为唯一患者标识符，若存在后缀数字，则代表同一患者的重复阵列芯片之一。