Elucidating the mechanisms of CDK inhibitor resistance in cancer using chemical proteomics

项目摘要 精确治疗的发展-靶向致癌驱动蛋白的选择性药物- 彻底改变了癌症的治疗;但这些药物中的大多数都受到快速出现的癌症的困扰。 阻力一些耐药机制可以通过基因组测序容易地推断（例如，药物- 致癌驱动因素本身的耐药突变），但其他耐药状态缺乏明确的基因特征 因此可能反映了降低药物作用敏感性的蛋白质组学改变。CDK4/6-Cyclin D1- 视网膜母细胞瘤蛋白（Rb）轴在特定癌症中经常失调，包括雌激素受体- 阳性（ER+）乳腺癌虽然CDK 4/6抑制剂，如palbociclib和ribociclib，已经出现， 令人信服的药物治疗ER+乳腺癌患者，耐药性已经在临床上出现， 设置.值得注意的是，这些耐药机制仍然知之甚少，通常不涉及 CDK突变或Rb缺失，其直接位于CDK 4/6-CyclinD 1复合物的下游， 负调控E2 F转录。该应用的总体目标是利用先进的化学蛋白质组学 细胞周期蛋白依赖激酶获得性耐药的分子机制 在ER+乳腺癌细胞中的CDKi抑制剂，并提供新的治疗靶点，以克服对 CDKi's。根据蛋白质活性确定癌症中的蛋白质靶点是推进癌症研究的不可避免的下一步 靶向癌症治疗。我们的实验室已经建立了一套化学探针，可以共同评估 在> 5，000种人类蛋白质中，> 10，000个半胱氨酸、赖氨酸和丝氨酸/苏氨酸残基的反应性和可药用性。 因此，我们已经表明，我们可以使用基于活性的蛋白质谱（ABPP）平台来发现 基因定义的癌症中的新的可药物化的脆弱性，包括表现出差异的半胱氨酸， KEAP 1突变型癌细胞与活化的NRF 2通路的配体能力。这些发现表明， 潜在的ABPP作为一种方法，以寻找不同的配体和反应性在特定的疾病状态。在 在这方面，我假设CDKi抗性状态含有具有差异反应性的蛋白质和/或 配位性支持对CDKi敏感性的丧失。为了验证这一假设，我提出了两个具体目标：1） 鉴定和表征具有CDKi抗性状态特有的差异反应性和配体性的蛋白质 和2）表征MGLL和其他具有不同反应性和/或配体能力的蛋白质在以下中的作用： 对CDKi的获得性抵抗。我将使用ABPP方法检查CDKi抗性细胞系，以了解 CDKi抗性的分子基础，并确定新的潜在治疗方法，这是关键的下一步 在个体化医疗时代对抗耐药性的重要性。

PROJECT SUMMARY The development of precision therapeutics – selective drugs that target oncogenic driver proteins – has revolutionized the treatment of cancer; but most of these drugs are plagued by the rapid emergence of resistance. Some drug resistance mechanisms can be readily deduced by genome sequencing (e.g., drug- resistant mutations in the oncogenic driver itself), but other drug-resistant states lack a clear genetic signature and therefore likely reflect proteomic alterations that reduce sensitivity to drug action. The CDK4/6-Cyclin D1- Retinoblastoma protein (Rb) axis is frequently dysregulated in specific cancers, including estrogen receptor- positive (ER+) breast cancers. Though CDK4/6 inhibitors, such as palbociclib and ribociclib, have emerged as compelling drugs to treat patients with ER+ breast cancer, resistance has already presented itself in clinical settings. Notably, these resistance mechanisms remain poorly understood and do not commonly involve mutations in CDKs or loss of the Rb, which is directly downstream of the CDK4/6-CyclinD1 complex and negatively regulates E2F transcription. The overall goal of this application is to utilize advanced chemoproteomic approaches to understand the molecular mechanisms of acquired resistance to cyclin dependent kinase inhibitors (CDKi’s) in ER+ breast cancer cells and provide novel therapeutic targets to overcome resistance to CDKi’s. Identifying protein targets in cancer based on their protein activity is an inevitable next step in advancing target cancer therapeutics. Our lab has established a suite of chemical probes that can collectively assess the reactivity and druggability of > 10,000 cysteine, lysine, and serine/threonine residues in > 5,000 human proteins. We have accordingly shown that we can use the activity-based protein profiling (ABPP) platform to discover novel druggable vulnerabilities in genetically defined cancers, including cysteines that show differential ligandability in KEAP1-mutant cancer cells with an activated NRF2 pathway. These findings point to the broader potential for ABPP as a method to search for differential ligandability and reactivity in specific disease states. In this respect, I hypothesize that the CDKi-resistant state harbors proteins with differential reactivity and/or ligandability that support loss of sensitivity to CDKi’s. To test this hypothesis, I propose two specific aims: 1) to identify and characterize proteins with differential reactivity and ligandability unique to the CDKi resistant state and 2) to characterize the role of MGLL and other proteins with differential reactivity and/or ligandability in acquired resistance to CDKi’s. I will examine CDKi resistant cell lines using the ABPP approach to understand the molecular underpinnings of CDKi resistance and to identify novel potential therapeutics, a crucial next step in combating drug resistance in the era of personalized medicine.