Mixed-species RNAseq analysis of human lymphoma cell adhesion to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of MCL and CLL patients.

Background:A subset of hematological cancer patients is refractory to treatment or suffer relapse, due in part to minimal residual disease, whereby some cancer cells survive treatment via microenvironment interaction. Cell-adhesion mediated drug resistance is an important mechanism, whereby cancer cells receive survival signals via interaction with e.g. stromal cells. No genome-wide studies of in vitro systems have yet been performed to compare gene expression in different cell subsets within a co-culture and cells grown separately. Results: Using RNAseq and species-specific read mapping, we compared transcript levels in human Jeko-1 mantle cell lymphoma (MCL) cells stably adhered to stromal cells or in suspension within a co-culture and in separate culture as well as mouse MS-5 stromal cells in co-culture or in separate culture. 1050 differentially expressed transcripts in adherent MCL cells identified 24 functional categories that together represent four main functional themes, anti-apoptosis, B-cell signaling, cell adhesion/migration and early mitosis. Comparison with previous MCL and chronic lymphocytic leukemia (CLL) patient data identified 116 genes that are differentially regulated in all three studies. From these genes we suggest a gene signature (CCL3, CCL4, DUSP4, ETV5, ICAM1, IL15RA, IL21R, IL4I1, MFSD2A, NFKB1, NFKBIE, SEMA7A, TMEM2) characteristic of cells undergoing cell-adhesion mediated microenvironment signaling in MCL/ CLL cells. Conclusions: The model system developed and characterized here together with suggested signature genes can be used in future studies of pathways that mediate increased cancer cell survival and drug resistance mechanisms. Overall design: RNA-seq; four conditions in quadruplicates, 16 samples in total.

背景：部分血液系统癌症患者会出现治疗难治或复发的情况，这在一定程度上源于微小残留病（minimal residual disease）——部分癌细胞通过与肿瘤微环境的相互作用得以在治疗后存活。细胞黏附介导的药物抗性（cell-adhesion mediated drug resistance）是重要的耐药机制之一，癌细胞可通过与基质细胞等的相互作用获取生存信号。目前尚无针对体外培养体系的全基因组研究，用于比较共培养体系中不同细胞亚群与单独培养细胞的基因表达差异。
结果：本研究借助RNA测序（RNAseq）与物种特异性读段映射技术，比较了以下各组的转录本水平：稳定黏附于基质细胞的、共培养体系中处于悬浮状态的人源Jeko-1套细胞淋巴瘤（mantle cell lymphoma, MCL）细胞，以及单独培养的该类细胞；同时还比较了共培养或单独培养的小鼠MS-5基质细胞。在黏附状态的MCL细胞中，共鉴定出1050个差异表达转录本，这些转录本可归为24个功能类别，涵盖四大核心功能主题：抗凋亡、B细胞信号通路、细胞黏附/迁移以及早期有丝分裂。将本研究结果与既往MCL及慢性淋巴细胞白血病（chronic lymphocytic leukemia, CLL）患者的相关数据进行比对后，共鉴定出116个在三项研究中均存在差异调控的基因。基于这些基因，我们提出了一套基因特征标签（包含CCL3、CCL4、DUSP4、ETV5、ICAM1、IL15RA、IL21R、IL4I1、MFSD2A、NFKB1、NFKBIE、SEMA7A、TMEM2），可用于表征MCL/CLL细胞中经历细胞黏附介导的微环境信号转导的细胞群体。
结论：本研究构建并表征的体外培养模型，结合本次提出的特征基因标签，可用于后续介导癌细胞存活增强及耐药机制相关通路的研究。
整体实验设计：RNA测序（RNAseq）；共设置4种实验条件，每组4个生物学重复，总计16个样本。