Synthetic Lethal Targeting of SETD2 in Renal Cell Carcinoma

SETD2 在肾细胞癌中的合成致死靶向

• 批准号: 10607320
• 负责人: Thai Huu Ho
• 金额: $ 55.49万
• 依托单位: MAYO CLINIC ROCHESTER
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-02-01 至 2028-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10607320
• 关键词: Affect; Automobile Driving; Biological; Biological Assay; CRISPR interference; CRISPR screen; Cancer Etiology; Cell Line; Cell Survival; Cells; Cessation of life; ChIP-seq; Chromatin; Clear cell renal cell carcinoma; Clinical Treatment; Compensation; DNA; DNA Methylation; Defect; Disease; Drug Targeting; Enhancers; Epigenetic Process; Exhibits; FDA approved; Family; Frequencies; Gene Expression; Gene Mutation; Genes; Genetic; Genetic Epistasis; Genotype; Health; Histone H3; Histones; Homeostasis; Human; Immune checkpoint inhibitor; Individual; Injections; Link; Lysine; Malignant Epithelial Cell; Malignant Neoplasms; Malignant neoplasm of lung; Malignant neoplasm of pancreas; Malignant neoplasm of prostate; Mediating; Methylation; Modeling; Mus; Mutate; Mutation; Neoplasm Metastasis; Organoids; Outcome; Pathway interactions; Patients; Phenocopy; Phenotype; Primary Neoplasm; Proteins; RNA; Regulator Genes; Renal Cell Carcinoma; Renal carcinoma; Repression; Role; Scheme; Signal Pathway; Signal Transduction; Solid Neoplasm; Specificity; TP53 gene; Tail; Testing; The Cancer Genome Atlas; Therapeutic; Tumor Tissue; Tumorigenicity; United States; Veins; Writing; actionable mutation; bevacizumab; cell growth; clinically actionable; combinatorial; efficacy validation; epigenome; genome-wide; in vivo; individualized medicine; inhibitor; loss of function; loss of function mutation; molecular phenotype; mouse model; mutant; novel; novel strategies; novel therapeutics; personalized approach; pharmacologic; pre-clinical; response; side effect; small molecule inhibitor; standard of care; targeted treatment; therapeutic target; transcriptome; tumor; tumor growth; virtual

ABSTRACT Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers and is the 8th leading cause of cancer death in the United States. After completion of The Cancer Genome Atlas (TCGA) Project, clinically actionable mutations were identified in virtually every solid tumor. One major exception, however, is RCC, where the current standard of care, checkpoint inhibitor and anti-VEGF therapy, does not take into account that ~50% of RCCs have mutations in chromatin regulators. After first-line therapy, response rates are 20% and there are no FDA-approved therapies that target chromatin regulators, highlighting the need to identify how loss-of-function genotypes can be therapeutically targeted. The epigenome is profoundly disrupted in cancers including ccRCC. Aside from the near ubiquitous loss of VHL, the mutational landscape of ccRCC is dominated by loss-of-function mutations in epigenetic regulators, including SETD2, BAP1, and PBRM1. SETD2 loss has now been firmly linked to poor outcome and metastasis. The molecular phenotype of H3K36me3 deregulation in SETD2-mutant ccRCC makes this an ideal scenario to study from the angle of synthetic lethality because it induces global epigenetic changes that must be compensated for, creating unique vulnerabilities. Targeting factors that exhibit genetic epistasis with known cancer mutations to drive a synthetic lethal phenotype is a proven therapeutic approach. We performed an unbiased CRISPR/Cas9 screen to identify factors that exhibit synthetic lethality with SETD2 loss-of-function. The epigenetic factor NSD1, a writer of H3K36me1/2 acting through the H3K36 pathway, was identified. Based on these findings, we hypothesize that suppression of the H3K36 axis in the form of its epigenetic writers (NSD1 in a SETD2 loss context) drives a synthetic lethal phenotype mediated by distinct enhancer remodeling accompanied by expression defects incompatible with cell viability. Identification of NSD1, which is part of a larger family of three related proteins (NSD1/2/3) within the H3K36 signaling axis in turn, will lead to novel approaches for individualized therapeutics to target SETD2 loss-of-function, classically defined as ‘undruggable’. We will address this hypothesis with three aims. In aim 1 we functionally characterize the synthetic lethal phenotypes associated with H3K36 writers NSD1, NSD2, and NSD3 in isogenic SETD2 ccRCC cell lines. In aim 2 we demonstrate the utility of pharmacologic inhibitors of H3K36 signaling in driving synthetic lethality in SETD2-mutant cells and elucidate their biological underpinnings. Finally, in aim 3 we validate the efficacy and specificity of genetic and pharmacologic targeting of the H3K36 signaling axis to induce SETD2-mutant synthetic lethality in vivo using mouse models. Our studies will shed new light on how epigenetic regulators and the H3K36 axis specifically, drive cancer and metastasis when deregulated. This is expected to positively affect human health by generating preclinical evidence for new ways to treat SETD2-mutant ccRCC that will minimize off-target side effects, and enhance survival for patients with ccRCC, particularly those with more aggressive/metastatic disease.

摘要 透明细胞肾细胞癌（ccRCC）占肾癌的约75%，是肾癌的第8大主要原因。 美国的癌症死亡率。在完成癌症基因组图谱（TCGA）项目后， 实际上在每种实体瘤中都鉴定出了可行的突变。然而，一个主要的例外是RCC， 当前的标准治疗、检查点抑制剂和抗VEGF治疗没有考虑到 约50%的RCC在染色质调节因子中存在突变。一线治疗后，有效率为20%， 目前还没有FDA批准的针对染色质调节因子的治疗方法，这突出了确定如何 功能丧失基因型可以作为治疗靶点。表观基因组在癌症中被严重破坏 包括ccRCC。除了几乎普遍存在的VHL丢失外，ccRCC的突变景观占主导地位， 表观遗传调节因子（包括SETD 2、BAP 1和PBRM 1）的功能缺失突变。SETD 2损失 现在已经与预后差和转移密切相关。H3 K36 me 3失调的分子表型 在SETD 2突变型ccRCC中，这是从合成致死率角度研究的理想场景，因为它 导致全球表观遗传变化，必须得到补偿，创造独特的脆弱性。靶向 与已知的癌症突变表现出遗传上位性以驱动合成致死表型的因子是一种 经过验证的治疗方法。我们进行了无偏的CRISPR/Cas9筛选，以确定表现出 具有SETD 2功能丧失的合成致死性。表观遗传因子NSD 1是H3 K36 me 1/2的一个转录因子， 通过H3 K36途径，被鉴定。基于这些发现，我们假设， H3 K36轴以其表观遗传书写者的形式（在SETD 2缺失背景下的NSD 1）驱动合成致死性转录因子。 表型由不同的增强子重塑介导，伴随着与 细胞活力NSD 1的鉴定，它是一个更大的三个相关蛋白质家族（NSD 1/2/3）的一部分， 反过来，H3 K36信号传导轴将导致针对SETD 2的个体化治疗的新方法 功能丧失，传统上定义为“不坚固”。我们将以三个目标来讨论这个假设。在aim 1中 我们在功能上表征了与H3 K36编写者NSD 1、NSD 2和NSD 3相关的合成致死表型。 在同基因SETD 2 ccRCC细胞系中的NSD 3。在目标2中，我们证明了药物抑制剂的效用， H3 K36信号转导在驱动SETD 2突变细胞中的合成致死性中的作用并阐明其生物学特性 基础最后，在目标3中，我们验证了遗传和药理靶向的有效性和特异性 的H3 K36信号传导轴，以使用小鼠模型在体内诱导SETD 2突变体的合成致死性。我们 研究将揭示表观遗传调节因子和H3 K36轴如何具体驱动癌症， 当解除管制时转移。预计这将通过产生临床前 有证据表明，治疗SETD 2突变型ccRCC的新方法将最大限度地减少脱靶副作用， ccRCC患者的生存率，尤其是那些侵袭性/转移性疾病更严重的患者。