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

基本信息

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
项目类别：
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

项目摘要

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发挥介导作用的关键表观遗传特征。许多研究已经确定了异常基因组甲基化与癌症之间的联系。骨髓增生异常综合征 (MDS) 是一组异质性恶性造血系统疾病，其中 30% 的病例中 DNA 甲基化异常在进展为急性髓系白血病 (AML) 的过程中发挥着关键作用。迄今为止，有害基因组甲基化的原因仍然难以捉摸。最近，我们发现了一类新的RNA，能够与DNA甲基转移酶1（DNMT1）、DNMT1相互作用RNA（DiR）相互作用并抑制DNMT1酶活性，从而调节基因组甲基化模式和相应基因的表达。我们已经证明，源自甲基化敏感基因CEBPA基因座的DiR——额外编码CEBPA (ecCEBPA)——通过与DNMT1相互作用阻止CEBPA基因位点甲基化来调节CEBPA表达。此外，通过对与 DNMT1 相关的转录本进行深度测序，结合基因组规模的甲基化和表达谱分析，我们已将这一发现的普遍性扩展到许多基因位点。在这里，我们假设转录谱的失调会触发 DNA 甲基化变化，从而促进继发性白血病的发生。该项目的两个目标是：1) 识别在 MDS 进化为 AML 过程中参与异常 DNA 甲基化模式建立的 DiR；2) 验证它们作为重置异常基因组甲基化工具的潜力。目标1将在K99指导阶段完成，在白血病发生和RNA生物学领域的世界领先专家Daniel G Tenen教授（哈佛大学医学院）和John L. Rinn教授（哈佛大学）的指导下，分别。通过将初级配对 MDS（诊断）/AML（进展）骨髓单核细胞的 DiR 和 DiRs 调节基因的转录谱与相应基因组区域的 DNA 甲基化状态相关联，DNA 甲基化和基因表达谱将与存在或不存在 RNA-DNMT 关联。这将导致识别与 MDS-AML 转化中异常 DNA 甲基化模式相关的 DiR（目标 1）。选定的候选者将在 R00 阶段的体外和体内系统中进行功能验证（目标 2）。这种方法将允许使用 RNA 分子纠正基因特异性的异常 DNA 甲基化。目前，唯一批准用于治疗应用的去甲基化药物是阿扎胞苷和地西他滨。然而，使用这些药物的主要缺点包括细胞毒性作用和整体非特异性去甲基化。这项研究有望实现真正的而非名义上的靶向治疗。虽然从短期来看，这项研究将导致识别出有助于白血病发生的新型 ky 调节因子；从长远来看，它将为开发期待已久的基因特异性去甲基化工具铺平道路，该工具用于治疗癌症和其他由 DNA 甲基化异常引发的疾病。