Epigenetic and Genetic Vulnerabilities in Synovial Sarcoma

滑膜肉瘤的表观遗传和遗传脆弱性

基本信息

批准号：
10247701
负责人：
Marc Ladanyi
金额：
$ 34.47万
依托单位：
SLOAN-KETTERING INST CAN RESEARCH
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-01 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10247701
关键词：
Affect Affinity Antisense Oligonucleotides Base Sequence Binding Proteins CRISPR/Cas technology Cell Line Cell Proliferation Cell Survival Child Childhood Chromatin Clinical Clinical Trials Clustered Regularly Interspaced Short Palindromic Repeats Dependence Disease Engineering Epigenetic Process Genes Genetic Predisposition to Disease Genetic Transcription Goals Growth Human Impairment In Vitro Investigation Knock-out Lead Libraries Malignant Neoplasms Mediating Methods Modeling Oncogenes Oncogenic Open Reading Frames Patients Pharmaceutical Preparations Phase Phosphoproteins Phosphotransferases Preclinical Drug Evaluation Proteins Proteomics Sampling Signal Transduction Soft tissue sarcoma Specimen System Therapeutic Therapeutic Uses Transcript Translating Tyrosine Kinase Inhibitor Validation Work Xenograft procedure base functional genomics gene product genome-wide in vivo in vivo Model in vivo evaluation inhibitor/antagonist kinase inhibitor knock-down novel patient derived xenograft model patient subsets preclinical evaluation research clinical testing sarcoma screening small hairpin RNA synovial sarcoma targeted treatment therapeutic candidate therapeutic target treatment strategy tumor young adult

项目摘要

ABSTRACT RP-4 focuses on synovial sarcoma, an aggressive pediatric/young adult sarcoma driven by the SS18-SSX fusion oncogene. SS18-SSX has emerged as a multi-faceted disruptor of epigenetic control that mediates genome-wide transcriptional deregulation, resulting in proliferation and aberrant or arrested differentiation. Our overall goal is to probe the basic pathobiology of synovial sarcoma so as to nominate potential therapeutic targets. We propose hypothesis-driven screening approaches, namely functional genomic screens to uncover vulnerabilities among chromatin/transcriptional regulators and among kinases, as well as targeting the oncogenic fusion itself. Based on the hypothesis that SS18-SSX causes synovial sarcoma cells to possess special “epigenetic” dependencies, we will, in Aim 1, (a) perform a broad functional genomic screen using a new CRISPR knock-out pooled library against epigenetic modulators; and (b) seek to further validate and understand mechanistically KDM2B, a dependency identified in preliminary studies, as a vulnerability in human synovial sarcoma cells. Based on the hypothesis that another effect of SS18-SSX is transcriptional deregulation of growth signaling, Aim 2 will employ three orthogonal strategies to better define targetable kinase vulnerabilities in this sarcoma. Specifically, we will (a) perform a CRISPR-based functional genomic screen against kinases in human synovial sarcoma cell lines; (b) identify activated kinases in synovial sarcoma by phospho-protein profiling of patient-derived xenografts; and (c) define the targets of pazopanib in synovial sarcoma by two complementary methods, affinity proteomics and PLATO (parallel analysis of translated ORFs). These two analyses should clarify the critical kinase targets of this multi-targeted kinase inhibitor that is active in a subset of synovial sarcoma patients. The results generated in this Aim will be integrated to form the basis for more rational targeting of critical kinases in this sarcoma. As SS18-SSX is the primary driver oncogene in synovial sarcoma, the junction point of the fusion transcript represents an rational and highly specific target for sequence-based therapeutics using new antisense oligonucleotide (ASO) approaches. Building on our promising results using gapmer ASOs to directly target other sarcoma fusions in vitro and in vivo, we will optimize and evaluate gapmer ASOs against SS18-SSX. In Aim 4, we will validate the targets identified in Aims 1-3 by confirming on-target effects and expression in human tumors, and we will perform preclinical evaluation of their potential as therapeutic targets in vitro and in vivo. The most promising targets will be validated and subjected to extensive preclinical evaluation using multiple, orthogonal, relevant in vitro and in vivo systems. The ultimate overall goal of this fundamentally translational project is to begin clinical evaluation of at least one agent based on the novel targets and strategies identified through our work in patients with this often lethal sarcoma within five years.

抽象的 RP-4专注于滑膜肉瘤，这是一种由SS18-SSX驱动的侵略性儿科/年轻成人肉瘤融合癌基因。 SS18-SSX已成为一种介导的表观遗传控制的多面颠覆者全基因组的转录放松管制，导致扩散和异常分化。我们的总体目标是探究滑膜肉瘤的基本病原体学，以提名潜在的治疗靶标。我们提出了假设驱动的筛选方法，即功能性基因组筛选以发现染色质/转录调节剂之间的脆弱性以及激酶以及靶向致癌融合本身。基于SS18-SSX原因的假设滑膜肉瘤细胞具有特殊的“表观遗传学”依赖性，我们将在AIM 1中（a）进行广泛使用新的CRISPR敲除合并图书馆针对表观遗传调节剂的功能性基因组筛选；（b）寻求进一步验证和理解机械的KDM2B，这是一种依赖性初步研究，是人类滑膜肉瘤细胞中的脆弱性。基于以下假设 SS18-SSX的另一个效果是对生长信号传导的转录放松管制，AIM 2将采用三个在此肉瘤中更好地定义有目标的激酶漏洞的正交策略。具体来说，我们会的（a）对人类滑膜细胞中的激酶进行基于CRISPR的功能基因组筛选线；（b）通过患者衍生的磷酸化蛋白分析，鉴定滑膜肉瘤中激活的激酶异种移植物；（c）通过两种完成方法定义滑膜肉瘤中pazopanib的靶标，亲和力蛋白质组学和柏拉图（翻译ORF的平行分析）。这两个分析应阐明该多靶性激酶抑制剂的关键激酶靶标，该抑制剂活跃于滑膜肉瘤的一部分患者。此目标中产生的结果将被整合为以更合理的定位为基础肉瘤中的关键激酶。由于SS18-SSX是滑膜肉瘤中的主要驱动器癌基因，融合成绩单的接线点代表了基于序列的合理且高度特定的目标使用新的反义寡核苷酸（ASO）接近治疗剂。以我们的承诺结果为基础使用Gapmer ASO在体外和体内直接靶向其他肉瘤融合，我们将优化和优化评估与SS18-SSX的Gapmer ASO。在AIM 4中，我们将验证AIMS 1-3中确定的目标确认人类肿瘤的靶向效应和表达，我们将对它们作为体外和体内治疗靶标的潜力。最有希望的目标将得到验证，并且使用多个，正交的，相关的体外和体内进行广泛的临床前评估系统。该基本翻译项目的最终总体目标是开始临床评估至少一种基于通过我们的工作确定的新目标和策略的代理这通常在五年内致命。