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.

项目概要 尽管黑色素瘤的靶向和免疫疗法取得了重大进展，但大多数患者都会出现复发 或在患者活检和活检中对这些疗法没有充分反应。 细胞系与独特的未分化细胞状态相关，其特征是低水平的 MITF， 黑色素细胞发育的主要调节因子，并且 AXL 酪氨酸激酶水平高。这种细胞状态是。 据报道，大部分黑色素瘤对 BRAF 抑制表现出从头耐药性，并且 50-100% 的抑制率 这也是抗 PD1 耐药黑色素瘤的一个显着特征。 证明所有黑色素瘤，即使是高 MITF 的黑色素瘤，都包含低 MITF 亚群，这些亚群具有积极的作用 通过靶向治疗选择根除这一人群，AXL本身并不是治疗靶点，基于 因此，我们使用多种抑制剂和 shRNA 来探究遗传依赖性。 阿喀琉斯计划——一项公正的基因组规模功能丧失筛查——发现低 MITF/高 AXL 黑色素瘤表现出惊人的依赖性，不是依赖于 AXL，而是依赖于 LSD1，LSD1 是一种赖氨酸特异性组蛋白去甲基化酶， 我们验证了 LSD1 在多种黑色素瘤细胞系中的依赖性。 使用 TCGA 和 CCLE 数据库中的黑色素瘤分析进行遗传和药物抑制。 介导其依赖性的候选LSD1靶基因揭示了LSD1选择性的三个候选基因 其中第一个，NDRG1，被证明是 LSD1 靶向所必需的。 这些 LSD1 靶标表达模式在细胞系和肿瘤中均存在一致性。 (TCGA)，我们还表明 SP2509（一种与临床开发中的化合物相关的 LSD1 抑制剂）具有高度的有效性。 对多种低 MITF 黑色素瘤具有致命性，这种效应依赖于（并受其调节）低 MITF 对 Achilles 数据库的深入分析确定了 CoREST 的多个亚基（已知的 LSD1 co-）。 抑制复合体）作为强依赖性因素，低-MITF/高-AXL的表型选择性致死率 黑色素瘤并暗示与 LSD1 依赖性的机制联系在目标 1 中，我们将测试 假设低 MITF 黑色素瘤的治疗耐药性可以通过结合靶向或治疗来减轻 我们对早期传代黑色素瘤细胞系和 PDX 进行 LSD 抑制的免疫疗法。 通过将遗传或药理学 LSD1 抑制与 BRAF 相结合，证明了广泛的协同致死作用 我们将在体外和异种移植物中测试 LSD1 抑制剂拮抗出现的能力。 高 MITF 黑色素瘤的耐药性，以及与积极抑制 MITF 的药物合作 在目标 2 中，我们将机械地检查 LSD1 的四个候选介质的功能作用。 依赖并使用基因组方法系统地检查低 MITF 状态，识别潜在的 这些发现提供了一个独特的机会。 揭示重要的难治性患者亚群的机制见解和治疗机会。

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.