C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma [Illumina BeadChip]. C99R mutation in IRF4 drives a novel gain of function binding and gene upregulation in classical Hodgkin lymphoma [Illumina BeadChip]

Disease-causing mutations in genes encoding transcription factors (TF) are frequent in hematopoietic malignancies and might affect TF-interactions with respective DNA-binding motifs. Here, we report the characterization of a recurrent somatic mutation c.295T>C in the IRF4 gene in classic Hodgkin lymphoma (cHL) leading to a C99R exchange. IRF4-C99R is located in the center of the IRF4 alpha3-recognition helix contacting the DNA 5´-GAAA-3´ IRF consensus sequence. IRF4-C99R fundamentally alters IRF4 DNA-binding, combining loss-of-binding at canonical IRF motifs and neomorph gain-of-binding at canonical and non-canonical IRF composite elements (CEs), in particular AP-1-IRF-CEs (AICEs). In line, IRF4-C99R profoundly impairs IRF4-dependent plasma cell induction, and specifically up-regulates degenerate-AICE-dependent distinct cHL disease-characteristic genes. These data document an unprecedented mutation-induced shift of TF binding specificity and its impact for lymphoma pathogenesis and TF modulation. Overall design: Illumina BeadChip HT-12 V4.0 expression data from BJAB cells with Tet-inducible control, IRF4WT and IRF4C99R cells treated with 0, 6, 24 and 48 hours doxycycline

编码转录因子（TF）的基因所携带的致病突变在造血系统恶性肿瘤中较为常见，且可能会干扰转录因子与其对应DNA结合基序的相互作用。本研究报道了经典霍奇金淋巴瘤（cHL）中IRF4基因一处复发性体细胞突变c.295T>C的鉴定结果，该突变会引发C99R氨基酸替换。IRF4-C99R位点位于IRF4的α3识别螺旋核心区域，可结合DNA 5'-GAAA-3' IRF保守序列。IRF4-C99R从根本上改变了IRF4的DNA结合特性：既会丧失对经典IRF基序的结合能力，又会在经典与非经典IRF复合元件（CEs）——尤其是AP-1-IRF复合元件（AICEs）——上获得新的结合活性。与之相符的是，IRF4-C99R会显著抑制IRF4介导的浆细胞分化诱导过程，并特异性上调依赖简并型AICE的、与cHL疾病特征相关的独特基因。上述研究结果揭示了一种前所未有的、由突变诱导的转录因子结合特异性改变，及其对淋巴瘤发病机制与转录因子调控的影响。实验设计概述：本研究的基因表达谱数据来自携带四环素诱导型对照载体、IRF4野生型（IRF4WT）及IRF4-C99R的BJAB细胞，上述细胞分别经0、6、24及48小时多西环素处理后，采用Illumina BeadChip HT-12 V4.0芯片完成检测。