Determining the role of DNMT-interacting RNAs in myeloid disorders

确定 DNMT 相互作用 RNA 在骨髓疾病中的作用

• 批准号: 9532339
• 负责人: Annalisa Di Ruscio
• 金额: $ 24.9万
• 依托单位: BETH ISRAEL DEACONESS MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-07-01 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9532339
• 关键词: Aberrant DNA Methylation; Acute Myelocytic Leukemia; Affinity; Azacitidine; Biological; Biological Assay; Biology; Bone Marrow; CEBPA gene; Categories; Cell Proliferation; Cells; Clinic; Code; Collaborations; Computer Analysis; DNA; DNA Methylation; DNA Modification Methylases; Databases; Decitabine; Development; Diagnosis; Disease; Down-Regulation; Drug usage; Dysmyelopoietic Syndromes; Epigenetic Process; Evolution; Gene Expression; Gene Expression Profile; Gene Silencing; Genes; Genetic Transcription; Genomic Segment; Genomics; Hematopoietic; Human; Hypermethylation; In Vitro; Letters; Link; Malignant - descriptor; Malignant Neoplasms; Mediating; Mentors; Methods; Methylation; Molecular; Molecular Profiling; Mononuclear; Mus; Myelogenous; Nature; Oncogenes; Ontology; Pharmaceutical Preparations; Phase; Play; Process; RNA; RNA Binding; RNA immunoprecipitation sequencing; Research; Role; Sampling; Specificity; Symptoms; System; Testing; The Cancer Genome Atlas; Therapeutic; Tissues; Toxic effect; Transcript; Transgenic Mice; Transplantation; Universities; Validation; Variant; alpha-Thalassemia; base; bisulfite sequencing; cancer cell; cancer therapy; candidate validation; cell transformation; cytotoxic; deep sequencing; demethylation; differential expression; genome-wide; histone modification; in vivo; leukemogenesis; medical schools; methylation pattern; mouse model; novel; novel strategies; novel therapeutics; overexpression; prevent; promoter; public health relevance; targeted treatment; tool; transcriptome sequencing; tumor

DESCRIPTION (provided by applicant): DNA methylation is a key epigenetic signature playing mediating role in gene expression. Numerous studies have established a link between aberrant genomic methylation and cancers. In Myelodysplastic Syndromes (MDS), a heterogeneous group of malignant hematopoietic disorders, DNA methylation abnormalities play a pivotal role during the progression to Acute Myeloid Leukemia (AML) occurring in 30 percent of the cases. To date the cause of a deleterious genomic methylation remains elusive. Recently we identified a novel class of RNAs able to interact with DNA methyltransferase 1 (DNMT1), DNMT1-interacting RNAs (DiRs) and inhibit DNMT1 enzymatic activity thus regulating genomic methylation patterns and expression of the corresponding genes. We have shown that DiR originating within the locus of the methylation sensitive gene CEBPA - the extra-coding CEBPA (ecCEBPA) - regulates CEBPA expression by preventing CEBPA gene locus methylation through its interaction with DNMT1. Furthermore, by deep sequencing of the transcripts associated with DNMT1, combined with genome-scale methylation and expression profiling we have extended the generality of this finding to numerous gene loci. Here, we hypothesize that dysregulation of transcriptional profile triggers DNA methylation changes promoting secondary leukemogenesis. The two aims of this project are: 1) to identify DiRs involved in the establishment of aberrant DNA methylation patterns in MDS evolution to AML: and 2) to validate their potential as a tool to reset aberrant genomic methylation. Aim 1 will be accomplished during the K99 mentored phase, under the guidance of Prof. Daniel G Tenen (Harvard Medical School) and Prof. John L. Rinn (Harvard University), world-leading experts in the field of leukemogenesis and RNA biology, respectively. By correlating DiRs and DiRs-regulated genes' transcription profiles of primary paired MDS (diagnosis)/AML (progression) bone marrow mononuclear cells with DNA methylation status of the correspondent genomic regions, DNA methylation and gene expression profiles will be linked to the presence or absence of RNA-DNMT association. This will lead to the identification of DiRs associated with aberrant DNA methylation patterns in MDS-AML transformation (Aim 1). Chosen candidates will be functionally validated during the R00 phase, in vitro and in vivo systems (Aim 2). This approach will allow correcting gene-specific aberrant DNA methylation using RNA molecules. Currently, the only demethylating agents approved for therapeutic applications are Azacitidine and Decitabine. However major downsides for using these drugs include cytotoxic effects and global non-specific demethylation. This study holds promise for a genuine, rather than nominal, targeted therapy. While in the short terms this research will lead to the identification of novel ky regulators contributing to leukemogenesis; in the long terms it will pave the way for the development of a long-awaited gene-specific demethylating tool for the treatment of cancer and other diseases triggered by DNA methylation abnormalities.

描述（由申请人提供）：DNA甲基化是在基因表达中扮演中介作用的关键表观遗传学特征。许多研究已经建立了异常基因组甲基化与癌症之间的联系。在骨髓增生综合征（MDS）中，在30％的病例中出现的急性髓样白血病（AML）的过程中，DNA甲基化异常在进展为急性髓样白血病（AML）期间起着关键作用。迄今为止，有害基因组甲基化的原因仍然难以捉摸。最近，我们确定了一类能够与DNA甲基转移酶1（DNMT1），DNMT1相互作用RNA（DIRS）（DIRS）和抑制DNMT1酶促活性相互作用的新型RNA。我们已经表明，DIR源自甲基化敏感基因CEBPA的基因座 - 外编码CEBPA（ECCEBPA） - 通过与DNMT1的相互作用防止CEBPA基因甲基化来调节CEBPA的表达。此外，通过对与DNMT1相关的转录本的深层测序，结合了基因组级甲基化和表达分析，我们将该发现的一般性扩展到了许多基因基因座。在这里，我们假设转录谱的失调会触发DNA甲基化变化，促进了次生白血病。该项目的两个目的是：1）确定在MDS进化为AML中建立异常DNA甲基化模式的DIR：和2）验证其作为重置异常基因组甲基化的工具的潜力。在K99指导阶段，AIM 1将在Daniel G Tenen教授（哈佛医学院）和John L. Rinn教授（哈佛大学）的指导下，分别是白血病和RNA生物学领域的世界领先专家。通过将原代配对MD的DIRS和DIRS调节的基因转录谱相关联（诊断）/AML（进展）骨髓单核细胞与相应基因组区域的DNA甲基化状态，DNA甲基化和基因表达谱将与RNA-DNMT联合的存在或不存在有关。这将导致鉴定与MDS-AML转化中异常DNA甲基化模式相关的DIR（AIM 1）。选定的候选者将在R00阶段，体外和体内系统上进行功能验证（AIM 2）。这种方法将允许使用RNA分子校正基因特异性异常DNA甲基化。目前，唯一被批准用于治疗应用的脱甲基剂是阿扎西替丁和切替滨。但是使用这些药物的主要缺点包括细胞毒性作用和全球非特异性脱甲基化。这项研究有望实现真正的，而不是标称有针对性的治疗。简而言之，这项研究将导致鉴定出促成白血病的新型KY调节剂。从长远来看，它将为期待已久的基因特异性去甲基化工具的开发铺平道路，用于治疗由DNA甲基化异常触发的癌症和其他疾病。