Connecting Genomic Alterations in Liposarcomas with Drug Responses and Identification of New Therapeutic Approaches

将脂肪肉瘤的基因组改变与药物反应联系起来并确定新的治疗方法

• 批准号: 9919544
• 负责人: Harold Phillip Koeffler
• 金额: $ 36.31万
• 依托单位: CEDARS-SINAI MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9919544
• 关键词: Address; Adult; Affect; Animal Model; Biological Markers; CRISPR screen; CRISPR/Cas technology; Cancer cell line; Cell Line; Cells; Clinical; Clinical Trials; Clone Cells; Collaborations; Collection; DNA Sequence Alteration; Data; Databases; Dependence; Development; Diagnosis; Disease; Drug Addiction; Drug Combinations; Drug Interactions; Drug resistance; Engineering; Evaluation; FDA approved; Family; Gene Mutation; Genes; Genetic; Genetic Determinism; Genetic Engineering; Genetic Predisposition to Disease; Genome; Genomics; Genotype; Histologic; Individual; Institutes; Investigation; Lentivirus Vector; Libraries; Link; Malignant Neoplasms; Manuscripts; Medical; Mesenchymal; Mesenchymal Stem Cells; Modeling; Modification; Morbidity - disease rate; Mutation; Neoplasm Metastasis; Neoplasms; Oregon; Pathway Analysis; Patients; Pharmaceutical Preparations; Phosphotransferases; Recurrence; Resistance; Sampling; Series; Small Interfering RNA; Soft tissue sarcoma; System; Therapeutic; Universities; Unresectable; base; cancer cell; cell transformation; chemotherapy; clinical implementation; clinical investigation; clinically relevant; cohort; drug candidate; drug development; drug discovery; drug market; drug sensitivity; experimental study; genome-wide; high throughput screening; high-throughput drug screening; innovation; insight; liposarcoma; loss of function; mortality; novel; novel strategies; novel therapeutic intervention; novel therapeutics; outcome forecast; overexpression; personalized medicine; resistance mechanism; response; screening; small molecule; small molecule libraries; stem; targeted treatment; therapeutic target; tumor

PROJECT SUMMARY Approximately 12,000 individuals in the USA will develop soft tissue sarcoma in 2015. In adults, liposarcoma (LPS) is one of the most common types of soft tissue sarcoma. Though rare, LPS tumors are often very aggressive with high morbidity and mortality rates. Resistance to conventional chemotherapeutics and lack of effective targeted therapies create a critical need to develop novel treatment options for patients with this devastating disease. Recent large-scale analyses by us and other groups have provided a comprehensive view of the genomic landscape of LPS. Despite the new insights, these studies, for the most part have not translated into definitive therapeutic strategies. One challenge is determining how individual gene -drug relationships affect drug responses ; a second challenge is that many of the genetic alterations identified in LPS have not been paired to a suitable targeted therapy. Synthetic lethality is an attractive approach for selective therapeutic targeting of cancer cells lacking otherwise obvious actionable genetic vulnerabilities. Large-scale cancer cell line screens helped uncover synthetic lethal interactions that link genetic determinants to drug responses; yet due to the complexity of most cancer cell lines, distinguishing the relevance of single mutations to the impact of a drug remains difficult. In the current proposal we will use an innovative approach to address these challenges. Our aim is to link specific LPS associated genetic alterations with sensitivities to multiple clinically relevant compounds. Thus, our study will begin to bridge the gap between the plethora of genetic alterations that we and others identified in LPS genomes and clinical implementation. We will use a novel screening strategy based on partly transformed mesenchymal stem cells (MSC) which we will genetically engineer to express a series of specific, recurrent LPS genotypic alterations. The resulting panel of isogenic clones and parental control cells will be subjected to high-throughput small molecule and siRNA screens (Collaboration with Dr. J. Tyner, Oregon University, Portland, and Sanford Burnham, La Jolla). Results will be validated and functionally investigated in LPS cell lines and animal models. In addition, we will perform a cutting-edge, genome-wide CRISPR screen to identify drugs that synergize with a leading compound that we will identify in our initial screens. Impact: We will conduct an integrative analysis of drug sensitivities p athway alterations and genotype-specific dependencies in a panel of isogenic MSC clones; results are likely to uncover previously unexpected gene-drug interactions that will allow us to nominate actionable therapeutic targets and suggest combinational treatments to mitigate drug resistance. Ultimately, our study will help guide new clinical trials for various investigational and help develop new genotype- , FDA-approved and drugs, directed therapies for subsets of LPS patients currently lacking satisfactory therapeutic options.

项目总结 2015年，美国将有大约12,000人患上软组织肉瘤。成人脂肪肉瘤 脂多糖(LP)是最常见的软组织肉瘤之一。虽然罕见，但内毒素肿瘤通常非常 攻击性强，发病率和死亡率高。对传统化疗药物的抗药性和缺乏 有效的靶向治疗产生了为患有这种疾病的患者开发新的治疗方案的迫切需要 毁灭性的疾病。我们和其他组织最近进行的大规模分析提供了一个 全面 内毒素的基因组图景。尽管有新的见解，但这些研究在很大程度上并没有 翻译成 明确的治疗策略。其中一个挑战是确定单个基因如何 -毒品 关系 影响药物反应 第二个挑战是，在脂多糖中发现的许多基因变化 尚未配对进行合适的靶向治疗。合成致命性是一种有吸引力的方法 治疗靶向缺乏其他明显的可操作的遗传脆弱性的癌细胞。大规模 癌症细胞系筛查有助于揭示将遗传决定因素与药物联系起来的合成致死相互作用 反应；然而，由于大多数癌细胞系的复杂性，区分单个突变的相关性 对一种药物的影响仍然很难。在目前的提案中，我们将使用创新的方法来解决 这些挑战。我们的目标是将特定的内毒素相关基因改变与敏感性联系起来 多种临床相关化合物。因此，我们的研究将开始弥合过剩的 我们和其他人在脂多糖基因组中识别的基因改变和临床应用。我们将使用 基于部分转化间充质干细胞(MSC)的新筛选策略 工程师表达一系列特定的、反复发生的内毒素基因改变。由此产生的同源基因的面板 克隆和亲本对照细胞将接受高通量小分子和siRNA筛选 (与俄勒冈大学波特兰J·泰纳博士和拉霍亚桑福德·伯纳姆博士合作)。结果将是 在脂多糖细胞系和动物模型中进行了验证和功能研究。此外，我们还将执行一项 先进的全基因组CRISPR屏幕，用于识别与我们发现的领先化合物协同作用的药物 将在我们的初始屏幕中识别。影响：我们将进行药物敏感性的综合分析 一组等基因MSC克隆中的基因改变和特定于基因的依赖关系；结果可能是 揭示以前意想不到的基因-药物相互作用，使我们能够提名可行的治疗方法 目标和建议的联合治疗，以减轻耐药性。最终，我们的研究将有助于指导 用于各种研究的新临床试验，并有助于开发新的基因型- ， FDA批准的药品， 针对目前缺乏令人满意的治疗选择的内毒素患者亚群的定向治疗。

项目成果

MNK1 and MNK2 enforce expression of E2F1, FOXM1, and WEE1 to drive soft tissue sarcoma.

• DOI: 10.1038/s41388-021-01661-4
• 发表时间: 2021-03
• 期刊: Oncogene
• 影响因子: 8
• 作者: Ke XY;Chen Y;Tham VY;Lin RY;Dakle P;Nacro K;Puhaindran ME;Houghton P;Pang A;Lee VK;Ding LW;Gery S;Hill J;Chen L;Xu L;Koeffler HP
• 通讯作者: Koeffler HP

Signalling inhibition by ponatinib disrupts productive alternative lengthening of telomeres (ALT).

• DOI: 10.1038/s41467-023-37633-3
• 发表时间: 2023-04-06
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Kusuma, Frances Karla;Prabhu, Aishvaryaa;Tieo, Galen;Ahmed, Syed Moiz;Dakle, Pushkar;Yong, Wai Khang;Pathak, Elina;Madan, Vikas;Jiang, Yan Yi;Tam, Wai Leong;Kappei, Dennis;Droge, Peter;Koeffler, H. Phillip;Jeitany, Maya
• 通讯作者: Jeitany, Maya

Novel carfilzomib-based combinations as potential therapeutic strategies for liposarcomas.

• DOI: 10.1007/s00018-020-03620-w
• 发表时间: 2021-03
• 期刊: Cellular and molecular life sciences : CMLS
• 作者: Jeitany M;Prabhu A;Dakle P;Pathak E;Madan V;Kanojia D;Mukundan V;Jiang YY;Landesman Y;Tam WL;Kappei D;Koeffler HP
• 通讯作者: Koeffler HP

Treatment for ovarian clear cell carcinoma with combined inhibition of WEE1 and ATR.

• DOI: 10.1186/s13048-023-01160-y
• 发表时间: 2023-04-22
• 期刊: JOURNAL OF OVARIAN RESEARCH
• 影响因子: 4
• 作者: Chien, Wenwen;Tyner, Jeffrey W. W.;Gery, Sigal;Zheng, Yueyuan;Li, Li-Yan;Pillai, Mohan Shankar Gopinatha;Nam, Chehyun;Bhowmick, Neil A. A.;Lin, De-Chen;Koeffler, H. Phillip
• 通讯作者: Koeffler, H. Phillip

Topography of transcriptionally active chromatin in glioblastoma.

• DOI: 10.1126/sciadv.abd4676
• 发表时间: 2021-04
• 期刊: Science advances
• 影响因子: 13.6
• 作者: Xu L;Chen Y;Huang Y;Sandanaraj E;Yu JS;Lin RY;Dakle P;Ke XY;Chong YK;Koh L;Mayakonda A;Nacro K;Hill J;Huang ML;Gery S;Lim SW;Huang Z;Xu Y;Chen J;Bai L;Wang S;Wakimoto H;Yeo TT;Ang BT;Müschen M;Tang C;Tan TZ;Koeffler HP
• 通讯作者: Koeffler HP