A druggable dependency in low-MITF/high-AXL melanoma: preclinical efficacy and mechanism of action in a key treatment-resistant subclass.

低 MITF/高 AXL 黑色素瘤的药物依赖性：关键耐药亚类的临床前疗效和作用机制。

• 批准号: 10331800
• 负责人: DAVID E FISHER
• 金额: $ 36.61万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10331800
• 关键词: Ablation; BRAF gene; Behavior; Binding; Binding Sites; Biological Markers; Biopsy; C57BL/6 Mouse; Cell Death; Cell Line; Cell Nucleus; Cells; ChIP-seq; Complex; Computer Analysis; DNA; Databases; Dependence; Development; Elements; Engineering; Enzyme Tests; Enzymes; Exhibits; Failure; Genes; Genetic; Genetic Databases; Genetic Engineering; Genetic Transcription; Genomic approach; Histone H3; Histones; Human; Immunotherapy; In Vitro; KDM1A gene; Lysine; MEKs; Malignant Neoplasms; Mediating; Mediator of activation protein; Melanoma Cell; Messenger RNA; Modeling; Monitor; Mus; Mutation; NDRG1 gene; Oncogenic; PTEN gene; Pancreas; Patients; Pattern; Pharmacology; Phenocopy; Physiological; Population; Process; Protein Tyrosine Kinase; Publishing; Relapse; Reporting; Repression; Repressor Proteins; Resistance; Resistance development; Role; Small Interfering RNA; Systemic Therapy; Testing; The Cancer Genome Atlas; Therapeutic; Tumor Suppressor Genes; Undifferentiated; Work; Xenograft procedure; anti-PD-1; base; cancer cell; checkpoint inhibition; checkpoint therapy; clinical development; demethylation; drug candidate; experience; genetic corepressor; genome-wide; global run on sequencing; histone demethylase; in vitro testing; in vivo; inhibitor; insight; knock-down; loss of function; melanocyte; melanoma; mutant; overexpression; patient derived xenograft model; patient subsets; pharmacodynamic biomarker; pre-clinical; preclinical efficacy; response; single-cell RNA sequencing; small hairpin RNA; targeted treatment; therapeutic target; therapy resistant; transcriptome sequencing; triple-negative invasive breast carcinoma; tumor; tumorigenic

PROJECT SUMMARY Despite major advances in targeted and immune therapies for melanoma, most patients experience relapses or do not respond adequately. Acquired and intrinsic resistance to these therapies in both patient biopsies and cell lines have been associated with a unique undifferentiated cell state characterized by low levels of MITF, the master regulator of melanocyte development, and high levels of the AXL tyrosine kinase. This cell state is reported in a high fraction of melanomas exhibiting de novo resistance to BRAF inhibition and in 50-100% with acquired resistance. It is also a prominent feature of anti-PD1 resistant melanomas. Single-cell RNA-seq demonstrated that all melanomas, even high-MITF ones, contain low-MITF subpopulations that are positively selected by targeted therapy. To eradicate this population, AXL itself is not a therapeutic target, based on published tests of multiple inhibitors and shRNAs. We therefore interrogated genetic dependencies using Project Achilles—an unbiased genome-scale loss-of-function screen—and found that low-MITF/high-AXL melanomas exhibit a striking dependency, not on AXL, but on LSD1, a lysine-specific histone demethylase that has been implicated in oncogenic processes. We validated LSD1 dependence in multiple melanoma lines using both genetic and pharmacologic inhibition. Analysis of melanomas in the TCGA and CCLE databases for candidate LSD1 target genes mediating its dependency revealed three candidates that LSD1 selectively modulates in low-MITF melanomas. The first of these, NDRG1, was shown to be required for LSD1-targeted lethality. Concordance of these LSD1-target expression patterns is seen across both cell lines and tumors (TCGA). We also show that SP2509, an LSD1 inhibitor related to a compound in clinical development, is highly lethal to multiple low-MITF melanomas, an effect that is dependent upon (and modulated by) the low-MITF state. Deeper analysis of the Achilles database identified multiple subunits of CoREST (known LSD1 co- repressive complex) as strong dependency factors, phenocopying selective lethality of low-MITF/high-AXL melanomas and suggesting a mechanistic connection to LSD1-dependency. In Aim 1, we will test the hypothesis that therapeutic resistance of low-MITF melanomas can be mitigated by combining targeted or immune therapies with LSD inhibition in early passage melanoma cell lines and PDX. Our preliminary results demonstrate profound cooperative lethality by combining genetic or pharmacologic LSD1 inhibition with BRAF inhibitor in vitro and in xenografts. We will test the ability of LSD1 inhibition to antagonize the emergence of resistance in high-MITF melanoma, as well as to cooperate with agents that actively suppress MITF expression. In Aim 2, we will mechanistically examine functional roles of four candidate mediators of LSD1 dependency and use genomic approaches to systematically scrutinize the low-MITF state, identifying potential pharmacodynamic markers and mediators of LSD1 dependency. These findings provide a unique opportunity to reveal mechanistic insights and therapeutic opportunities for important treatment-resistant patient subsets.

项目摘要 尽管黑色素瘤的靶向和免疫疗法取得了重大进展，但大多数患者都会经历接力赛 或不做出适当的反应。在患者活检和 细胞系与独特的未分化细胞状态有关，其特征是MITF水平低， 黑素细胞发育的主要调节剂和高水平的AXL酪氨酸激酶。这个细胞状态是 报道了大量的黑色素瘤对BRAF抑制作用，在50-100％中报道 获得的阻力。它也是抗PD1抗性黑色素瘤的重要特征。单细胞RNA-seq 证明所有梅洛马斯（甚至高MITF）都包含低MITF亚群 通过靶向治疗选择。为了使该人群放射，AXL本身不是基于治疗靶标的 发表了多种抑制剂和shRNA的测试。因此，我们使用 阿喀琉斯项目 - 公正的基因组规模的功能丧失屏幕 - 发现低MITF/High-axl 黑色素瘤暴露了惊人的依赖性，而不是在AXL上，而是在LSD1上，是一种赖氨酸特异性组蛋白脱甲基酶 在致癌过程中已隐含。我们验证了多种黑色素瘤线中的LSD1依赖性 同时使用遗传和药物结肠抑制。 TCGA和CCLE数据库中黑色素瘤的分析 介导其依赖性的候选LSD1靶基因揭示了三个候选者，其中LSD1有选择地 在低MITF黑色素瘤中调节。其中的第一个是NDRG1，被证明是LSD1靶向的 致死性。在细胞系和肿瘤中都可以看到这些LSD1靶向表达模式的一致性 （TCGA）。我们还表明，SP2509是与临床开发中化合物有关的LSD1抑制剂，非常高 致命对多个低MITF黑色素瘤，这种作用取决于（并调节）低MITF 状态。对阿基里斯数据库的更深入分析确定了Corest的多个亚基（已知的LSD1共同 抑制性复合物）作为强依赖性因素，低MITF/高轴的选择性杀伤力 黑色素瘤并提出了与LSD1依赖性的机械联系。在AIM 1中，我们将测试 假设低MITF黑色素瘤的治疗性可以通过结合靶向或 早期传入黑色素瘤细胞系和PDX中LSD抑制的免疫疗法。我们的初步结果 通过将遗传或药物LSD1抑制与BRAF相结合，表现出深刻的合作致死性 抑制剂在体外和异种移植物中。我们将测试LSD1抑制与拮抗出现的能力 高MITF黑色素瘤的抗性，以及与积极抑制MITF的剂 表达。在AIM 2中，我们将机械检查LSD1四个候选者的功能作用 依赖性和使用基因组方法系统地仔细检查低MITF状态，确定潜力 LSD1依赖性的药学标记和介体。这些发现提供了独特的机会 揭示机械洞察力和治疗机会，以避免重要的治疗患者子集。

项目成果

Targeting TBK1 to overcome resistance to cancer immunotherapy.

• DOI: 10.1038/s41586-023-05704-6
• 发表时间: 2023-03
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Sun, Yi;Revach, Or-yam;Anderson, Seth;Kessler, Emily A. A.;Wolfe, Clara H. H.;Jenney, Anne;Mills, Caitlin E. E.;Robitschek, Emily J. J.;Davis, Thomas G. R.;Kim, Sarah;Fu, Amina;Ma, Xiang;Gwee, Jia;Tiwari, Payal;Du, Peter P. P.;Sindurakar, Princy;Tian, Jun;Mehta, Arnav;Schneider, Alexis M. M.;Yizhak, Keren;Sade-Feldman, Moshe;LaSalle, Thomas;Sharova, Tatyana;Xie, Hongyan;Liu, Shuming;Michaud, William A. A.;Saad-Beretta, Rodrigo;Yates, Kathleen B. B.;Iracheta-Vellve, Arvin;Spetz, Johan K. E.;Qin, Xingping;Sarosiek, Kristopher A. A.;Zhang, Gao;Kim, Jong Wook;Su, Mack Y. Y.;Cicerchia, Angelina M. M.;Rasmussen, Martin Q. Q.;Klempner, Samuel J. J.;Juric, Dejan;Pai, Sara I. I.;Miller, David M. M.;Giobbie-Hurder, Anita;Chen, Jonathan H. H.;Pelka, Karin;Frederick, Dennie T. T.;Stinson, Susanna;Ivanova, Elena;Aref, Amir R. R.;Paweletz, Cloud P. P.;Barbie, David A. A.;Sen, Debattama R. R.;Fisher, David E. E.;Corcoran, Ryan B. B.;Hacohen, Nir;Sorger, Peter K. K.;Flaherty, Keith T. T.;Boland, Genevieve M. M.;Manguso, Robert T. T.;Jenkins, Russell W. W.
• 通讯作者: Jenkins, Russell W. W.