A Genome Wide RNAi Vulnerability Map for Myeloma

骨髓瘤全​​基因组 RNAi 漏洞图谱

• 批准号: 8298645
• 负责人: ALEXANDER KEITH STEWART
• 金额: $ 24.68万
• 依托单位: MAYO CLINIC ARIZONA
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8298645
• 关键词: Affect; Animal Model; Bioinformatics; Biological Markers; Bortezomib; Candidate Disease Gene; Cell Line; Cells; Clinical; Data Set; Databases; Disease; Drug Delivery Systems; Future; Gene Expression; Gene Family; Gene Targeting; Genes; Genome; Genomics; Goals; Growth; Health; Human; Individual; Light; Maps; Molecular; Molecular Biology; Multiple Myeloma; New Agents; Pathway interactions; Patients; Pharmaceutical Preparations; Pharmacogenomics; Pharmacologic Substance; Phenotype; Phosphotransferases; Process; RNA Interference; Research; Role; Sampling; Screening procedure; Small Interfering RNA; Specificity; Technology; Thalidomide; Therapeutic; Time; Tissues; United States; Validation; Work; cell growth; clinically relevant; comparative genomic hybridization; cytotoxic; data mining; functional genomics; genome-wide; improved; inhibitor/antagonist; lenalidomide; neoplastic cell; novel; response; small hairpin RNA; small molecule

DESCRIPTION (provided by applicant): The central hypothesis for the proposed research is that genome wide RNAi inhibition of specific gene targets will identify previously unrecognized critical molecular pathways which modulate the growth of Myeloma cells in either direction and that such information can be positively exploited clinically. While newer agents such as bortezomib, thalidomide and lenalidomide have profound clinical activity in myeloma the exact point of molecular action is unknown. Furthermore, none of these drugs is curative and the identification of novel vulnerability targets which can be exploited, together with the identification of existing pharmaceutical agents which may have unrecognized activity in MM is a critical goal for future progress. Since the critical targets of MM cells remain elusive further genomic scale analysis and the creation of a vulnerability map of MM, is in our opinion, required to further our global understanding of this disease and how treatments may be both personalized and optimized. Our objective in this proposal is therefore to apply advanced functional genomic strategies to identify and rapidly validate the critical role of candidate genes in MM growth and survival and advance this information clinically. In that light we have recently conducted high throughput, kinome wide, RNAi lethality screening in MM cell lines to identify kinases essential to the survival of human MM. In addition, we have identified kinase targets that sensitize tumor cells to bortezomib therapy by RNAi screening in the presence of this drug. Finally, we have now completed a preliminary screen of the druggable genome (7000 genes) in a single MM cell line with and without bortezomib and lenalidomide. Through other previous efforts we have an extensive panel of 60 MM cell lines, a large database of both gene expression and comparative genomic hybridization in cell lines and primary patient samples and ready access to patient tissues. We propose here to extend these findings to explore a more globally representative 17,000 gene high throughput, synthetic lethal RNAi screen in MM cell lines and to validate these findings using secondary screening, target validation in primary patient cells, and bioinformatic processing which brings together our disparate genomic datasets. Specifically, we will determine the extent to which silencing gene expression, by parallel RNAi, will modify cytotoxic sensitivity in either direction in cultured Myeloma cell lines. We will then apply pharmacogenomics and classical molecular biology to cell lines, animal models and patient samples to validate the clinical relevance of these putative drug targets and determine the extent to which they can be used as biomarkers of therapeutic response. PUBLIC HEALTH RELEVANCE: Multiple Myeloma affects 50,000 people in the United States at any given time. Major advances have been made in the treatment and newer agents such as bortezomib, thalidomide and lenalidomide have profound clinical activity. However, none of these drugs is curative and the means by which they work opaque. Thus identification of novel vulnerability targets which can be exploited, together with the identification of existing pharmaceutical agents which may have unrecognized activity in MM is a critical goal for future progress. To achieve this we will screen 17,000 genes for there ability to control myeloma cell growth. This genomic scale analysis and the creation of a vulnerability map of Myeloma, is a prerequisite to further our global understanding of this disease and how treatments may be both personalized and optimized.

描述（由申请人提供）：拟议研究的中心假设是，对特定基因靶标的全基因组 RNAi 抑制将识别以前未识别的关键分子途径，这些途径可在任一方向上调节骨髓瘤细胞的生长，并且这些信息可以在临床上积极利用。虽然硼替佐米、沙利度胺和来那度胺等新型药物在骨髓瘤中具有深远的临床活性，但分子作用的确切点尚不清楚。此外，这些药物都没有治愈性，识别可利用的新的脆弱性目标，以及识别可能在多发性骨髓瘤中具有未被识别的活性的现有药物制剂是未来进展的关键目标。由于 MM 细胞的关键靶点仍然难以捉摸，我们认为，需要进一步的基因组规模分析和创建 MM 的脆弱性图谱，以进一步加深我们对这种疾病的全球了解以及如何个性化和优化治疗。因此，我们本提案的目标是应用先进的功能基因组策略来识别和快速验证候选基因在 MM 生长和生存中的关键作用，并在临床上推进这一信息。鉴于此，我们最近在 MM 细胞系中进行了高通量、全激酶组范围的 RNAi 致死性筛选，以确定对人类 MM 生存至关重要的激酶。此外，我们还通过在药物存在的情况下进行 RNAi 筛选，确定了使肿瘤细胞对硼替佐米治疗敏感的激酶靶点。最后，我们现已完成了对使用或不使用硼替佐米和来那度胺的单个 MM 细胞系中的可药物基因组（7000 个基因）的初步筛选。通过之前的其他努力，我们拥有 60 个 MM 细胞系的广泛面板、细胞系和原代患者样本中基因表达和比较基因组杂交的大型数据库，并可随时获取患者组织。我们在此建议扩展这些发现，以探索更具全球代表性的 17,000 个基因高通量、MM 细胞系中的合成致死性 RNAi 筛选，并使用二次筛选、原代患者细胞中的目标验证以及汇集我们不同基因组数据集的生物信息学处理来验证这些发现。具体来说，我们将确定通过平行 RNAi 沉默基因表达将在多大程度上改变培养的骨髓瘤细胞系中任一方向的细胞毒性敏感性。然后，我们将药物基因组学和经典分子生物学应用于细胞系、动物模型和患者样本，以验证这些假定药物靶标的临床相关性，并确定它们在多大程度上可以用作治疗反应的生物标志物。公共卫生相关性：多发性骨髓瘤在任何特定时间都会影响美国 50,000 人。治疗方面已取得重大进展，硼替佐米、沙利度胺和来那度胺等新型药物具有深远的临床活性。然而，这些药物都没有疗效，而且它们的作用方式也不透明。因此，识别可利用的新的脆弱性目标，以及识别可能在多发性骨髓瘤中具有未被识别的活性的现有药剂是未来进展的关键目标。为了实现这一目标，我们将筛选 17,000 个基因，以确定它们是否具有控制骨髓瘤细胞生长的能力。这种基因组规模分析和骨髓瘤脆弱性图的创建是进一步我们对这种疾病以及如何个性化和优化治疗的全球了解的先决条件。

项目成果

Mechanism of action of immunomodulatory drugs (IMiDS) in multiple myeloma.

• DOI: 10.1038/leu.2009.236
• 发表时间: 2010-01
• 期刊: LEUKEMIA
• 影响因子: 11.4
• 作者: Quach, H.;Ritchie, D.;Stewart, A. K.;Neeson, P.;Harrison, S.;Smyth, M. J.;Prince, H. M.
• 通讯作者: Prince, H. M.

Carfilzomib: a novel second-generation proteasome inhibitor.

• DOI: 10.2217/fon.11.42
• 发表时间: 2011-05
• 期刊: Future oncology (London, England)
• 作者: Khan ML;Stewart AK
• 通讯作者: Stewart AK

What is the functional role of the thalidomide binding protein cereblon?

沙利度胺结合蛋白 cereblon 的功能是什么？

• 发表时间: 2011
• 期刊: International journal of biochemistry and molecular biology
• 作者: Chang,Xiu-Bao;Stewart,AKeith
• 通讯作者: Stewart,AKeith

Molecular mechanism of action of immune-modulatory drugs thalidomide, lenalidomide and pomalidomide in multiple myeloma.

• DOI: 10.3109/10428194.2012.728597
• 发表时间: 2013-04
• 期刊: Leukemia & lymphoma
• 影响因子: 2.6
• 作者: Zhu YX;Kortuem KM;Stewart AK
• 通讯作者: Stewart AK

Xbp1s-negative tumor B cells and pre-plasmablasts mediate therapeutic proteasome inhibitor resistance in multiple myeloma.

• DOI: 10.1016/j.ccr.2013.08.009
• 发表时间: 2013-09-09
• 期刊: Cancer cell
• 影响因子: 50.3
• 作者: Leung-Hagesteijn C;Erdmann N;Cheung G;Keats JJ;Stewart AK;Reece DE;Chung KC;Tiedemann RE
• 通讯作者: Tiedemann RE