Alternative splicing analysis of pediatric B-cell acute lymphoblastic leukemia compared to normal bone marrow derived pro-B cells

Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. hnRNPA1. hnRNPA1 3’UTR was most pervasively misspliced, yielding the transcript subject to nonsense-mediated decay. Thus, we knocked it down in B-lymphoblastoid cells, identified 213 hnRNPA1-dependent splicing events, and defined the hnRNPA1 splicing signature in pediatric leukemias. One of its elements was DICER1, a known tumor suppressor gene; its LSVs involved the 5’ UTR, suggestive of splicing as a mechanism of translational deregulation. Additionally, we searched for LSVs in other leukemia and lymphoma drivers and discovered 81 LSVs in 41 genes. 77 LSVs were confirmed using two large independent B-ALL RNA-seq datasets. In fact, the twenty most common B-ALL drivers showed higher prevalence of aberrant splicing than of somatic mutations. Thus, post-transcriptional deregulation of SF can drive widespread changes in B-ALL splicing and likely contribute to disease pathogenesis. Refer to individual Series

剪接异常是携带剪接因子（splicing factor, SF）编码基因突变的白血病的标志性特征。本研究针对剪接因子未发生突变的儿童B细胞急性淋巴细胞白血病（B-cell acute lymphoblastic leukemias, B-ALL），探究了异常剪接的发生频率。通过将样本与正常前B细胞进行比对，我们在每个样本中检测到数千个异常局部剪接变异（aberrant local splice variations, LSVs）；其中241个基因共携带279个在所有比对组中均存在的LSVs。上述基因显著富集于RNA加工通路，且编码约100种剪接因子，例如异质性核核糖核蛋白A1（heterogeneous nuclear ribonucleoprotein A1, hnRNPA1）。其中，hnRNPA1的3'非翻译区（3' untranslated region, 3'UTR）出现了最为广泛的错剪接，所产生的转录本会受到无义介导的降解（nonsense-mediated decay）调控。据此，我们在B淋巴母细胞系中敲低了hnRNPA1的表达，鉴定出213个依赖于hnRNPA1的剪接事件，并明确了儿童白血病中hnRNPA1的剪接特征。该特征的靶点之一为已知抑癌基因DICER1，其LSVs涉及5'非翻译区（5' untranslated region, 5'UTR），提示剪接可能作为翻译调控失调的潜在机制。此外，我们在其他白血病及淋巴瘤驱动基因中检索LSVs，在41个基因中发现了81个LSVs。其中77个LSVs通过两个独立的大型B-ALL RNA测序（RNA-seq）数据集得到了验证。事实上，20种最常见的B-ALL驱动基因的异常剪接发生率高于体细胞突变发生率。综上，剪接因子的转录后调控失调可驱动B-ALL中广泛的剪接改变，并可能在疾病发病机制中发挥关键作用。具体信息请参见各数据集系列。