RNAseq analysis of AML cells upon lncRNA knockdown

It is well understood how proteins regulate cell fate, both in normal development and disease. However, a substantial fraction of the genome is transcribed in a cell type- specific manner, producing long non-coding RNAs (lncRNA) rather than protein- coding transcripts. Here we systematically characterize transcriptional dynamics (both mRNA and lncRNA) during hematopoiesis and in hematological malignancies. We present de novo assembled transcriptome models and expression values for hematopoietic lncRNAs. We found lncRNAs to be regulated during differentiation and misregulated in disease. We assessed lncRNA function via an in vivo RNAi screen in a model of acute myeloid leukemia. With this approach, we identified several lncRNAs essential for leukemia maintenance, and found that a number act by promoting leukemia stem cell signatures. Leukemia blasts show a myeloid differentiation phenotype when these lncRNAs were depleted, and our data indicates that this effect is mediated via effects on the c-MYC oncogene.

目前学界已明确蛋白质在正常发育与疾病进程中如何调控细胞命运。然而，仍有相当比例的基因组以细胞特异性方式转录，生成长链非编码RNA（long non-coding RNAs, lncRNA）而非编码蛋白质的转录本。本研究系统性表征了造血过程及血液系统恶性肿瘤中的转录动态变化（涵盖信使RNA [messenger RNA, mRNA] 与长链非编码RNA [lncRNA]）。本研究提供了造血相关lncRNA的从头转录组组装模型与表达量数据。研究发现，lncRNA在细胞分化过程中受到调控，且在疾病状态下存在表达失调。本研究借助急性髓系白血病模型的体内RNA干扰（RNA interference, RNAi）筛选实验，对lncRNA的功能进行了评估。通过该方法，我们鉴定出多个对白血病维持至关重要的lncRNA，并发现其中部分通过调控白血病干细胞特征发挥作用。当这些lncRNA被敲低后，白血病母细胞会呈现髓系分化表型；本研究数据表明，该效应通过影响c-MYC癌基因实现。