Targeting the non-coding stem cell signature in childhood acute myeloid leukemia

尽管对来自基因组非蛋白质编码区的过多转录本的研究有所增加，但我们对非编码RNA的知识仍远未应用于临床。这一不足与儿童急性髓系白血病(AML)尤其相关，30年来，这种疾病的治疗几乎没有改善，针对这种疾病，有针对性的战略将极大地改善与治疗相关的长期毒性和年轻患者的生活质量。了解非编码RNA(NcRNA)介导的干细胞维持机制以及这些过程在恶性转化过程中是如何被劫持的，对于了解白血病的发病机制至关重要，并将为开发新的靶向癌症特异性治疗以根除自我更新的白血病干细胞奠定基础。我们最近建立了一个定义人类造血系统ncRNA图景的综合资源(www.lncScape.de)1，并确定了正常造血干细胞(HSCs)和儿童白血病母细胞所共有的核心ncRNA干细胞特征。由于长非编码RNA(LncRNAs)已被证明调节表观遗传和转录途径，我们假设来自核心干细胞信号的lncRNAs塑造细胞染色质和转录格局，从而协调正常和恶性干细胞的自我更新、增殖和分化。为了确定该信号中功能相关的干细胞特异性LncRNAs，我们在体外和体内应用了两种基于CRISPRi的互补筛选策略。17个lncRNA基因的敲除有效且显著地干扰了白血病在两个或更多细胞环境中的生长。因此，在这个项目中，我们将(1)鉴定5个对白血病进展至关重要的高置信度干细胞特异性lncRNA，(2)解决它们的功能和机制特征。此外，我们还将评估临床前以RNA为中心的治疗干预措施，目的是克服目前儿童AML治疗中的障碍。针对这种恶性肿瘤的核心可能会导致癌症治疗的范式转变-将重点转移到诱发和维持癌症的潜在遗传程序，而不是致癌打击本身。

Despite increased research on the plethora of transcripts that arise from non-protein-coding regions of the genome, our knowledge of non-coding RNAs is still far from being applied in a clinical context. This shortfall is particularly relevant to pediatric acute myeloid leukemia (AML), the treatment of which has hardly improved in three decades, and for which targeted strategies stand to greatly ameliorate long-term treatment-related toxicities and quality of life for young patients. Understanding noncoding RNA (ncRNA)-mediated mechanisms of stem cell maintenance and how these processes are hijacked during malignant transformation is crucial for understanding the pathogenesis of leukemia, and will lay a foundation for developing novel targeted cancer-specific therapies that eradicate self-renewing leukemic stem cells.We recently built a comprehensive resource defining the ncRNA landscape of the human hematopoietic system (www.lncScape.de)1 and identified a core ncRNA stem cell signature shared by normal hematopoietic stem cells (HSCs) and pediatric leukemia blasts. Since long non-coding RNAs (lncRNAs) have been shown to regulate epigenetic and transcriptional pathways, we hypothesize that lncRNAs from the core stem cell signature shape the cellular chromatin and transcriptional landscape and thereby coordinate self-renewal, proliferation and differentiation in normal and malignant stem cells. To identify functionally relevant stem cell-specific lncRNAs within this signature, we applied two complementary CRISPRi-based screening strategies in vitro and in vivo. Knockdown of 17 lncRNA genes efficiently and significantly perturbed leukemic growth in two or more cellular contexts. In this project we will therefore (1) characterize 5 high confidence stem cell-specific lncRNAs that are essential for leukemia progression and (2) resolve their functional and mechanistic features. We will additionally (3) evaluate pre-clinical RNA-centered therapeutic interventions, with the aim of overcoming current obstacles in the treatment of pediatric AML. Targeting this malignancy at its core could lead to a paradigm shift in cancer treatment – shifting the focus to the underlying genetic programs that induce and sustain cancer, rather than the oncogenic hit itself.