Identification of C/EBPβ Target Genes in ALK+ Anaplastic Large Cell Lymphoma (ALCL) by Gene Expression Profiling and Chromatin Immunoprecipitation

C/EBPβ (CCAAT enhancer binding protein) is a transcription factor that plays a crucial role in survival and transformation of ALK+ anaplastic large cell lymphoma (ALCL). The aim of this study was to identify the downstream targets of C/EBPβ responsible for ALK-mediated oncogenesis. C/EBPβ was knocked down in ALK+ ALCL cell lines with a C/EBPβ-shRNA, followed by gene expression profiling (GEP). GEP analysis revealed a reproducible signature of genes that were significantly regulated by C/EBPβ. Classification into biological categories revealed overrepresentation of genes involved in the immune response, apoptosis and cell proliferation. Transcriptional regulation by C/EBPβ was found in 6 of 11 (BCL2A1, G0S2, TRIB1, S100A9, DDX21 and DDIT4) genes investigated by chromatin immunoprecipitation. We demonstrated that BCL2A1, G0S2 and DDX21 play a crucial role in survival and proliferation of ALK+ ALCL cells. DDX21, a gene involved in rRNA biogenesis, was found differentially overexpressed in primary ALK+ ALCL cases. All three candidate genes were validated in primary ALCL cases by either immunohistochemistry or RT-qPCR. In conclusion, we identified and validated several key C/EBPβ-regulated genes with major impact on survival and cell growth in ALK+ ALCL, supporting the central role of C/EBPβ in ALK-mediated oncogenesis.

C/EBPβ（CCAAT增强子结合蛋白）是一类转录因子，在ALK阳性间变性大细胞淋巴瘤（ALK+ anaplastic large cell lymphoma, ALCL）的细胞存活与恶性转化过程中发挥关键作用。本研究旨在鉴定参与ALK介导致癌过程的C/EBPβ下游靶基因。研究人员采用C/EBPβ短发夹RNA（shRNA）在ALK+ ALCL细胞系中敲低C/EBPβ，随后开展基因表达谱分析（GEP）。GEP分析结果显示，存在一组可重复的、受C/EBPβ显著调控的基因表达特征。对基因进行生物学功能分类后发现，免疫应答、细胞凋亡及细胞增殖相关基因显著富集。通过染色质免疫沉淀（ChIP）验证的11个候选基因中，6个基因（BCL2A1、G0S2、TRIB1、S100A9、DDX21与DDIT4）受C/EBPβ转录调控。本研究证实，BCL2A1、G0S2及DDX21在ALK+ ALCL细胞的存活与增殖中发挥关键作用。其中DDX21作为参与核糖体RNA（rRNA）生物发生的基因，在原发性ALK+ ALCL临床病例中被检测到差异高表达。最后，研究通过免疫组织化学或实时定量逆转录聚合酶链反应（RT-qPCR）验证了这三个候选基因在原发性ALCL病例中的表达情况。综上，本研究鉴定并验证了多个受C/EBPβ调控的关键基因，这些基因对ALK+ ALCL细胞的存活与生长具有显著影响，从而支持了C/EBPβ在ALK介导的致癌过程中的核心作用。