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

项目总结 精确疗法的发展--针对致癌驱动蛋白的选择性药物--已经 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 抵抗。一些耐药机制可以很容易地通过基因组测序来推断(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遗传特征 因此可能反映了降低对药物作用敏感性的蛋白质组变化。CDK4/6-Cyclin D1- 视网膜母细胞瘤蛋白(Rb)轴在特定的癌症中经常失调，包括雌激素受体- 阳性(ER+)乳腺癌。尽管CDK4/6抑制剂，如Palbociclib和Riociclib，已经出现为 治疗ER+乳腺癌的令人信服的药物，耐药性已经出现在临床上 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 CDKs的突变或Rb的丢失，Rb直接位于CDK4/6-CyClinD1复合体的下游， 负向调节E2F转录。这项应用的总体目标是利用先进的化学蛋白质组学 细胞周期蛋白依赖性激酶获得性耐药分子机制的研究进展 ER+乳腺癌细胞中的抑制物(CDKi‘s)并提供新的治疗靶点以克服对 CDKi的。根据蛋白质活性识别癌症中的蛋白质靶点是推进研究的必然下一步 以癌症治疗为目标。我们的实验室已经建立了一套化学探针，可以集体评估 &gt；5000人蛋白质中&gt；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性。 因此，我们已经证明，我们可以使用基于活动的蛋白质图谱(ABPP)平台来发现 基因定义的癌症中的新的可药物易感性，包括表现出差异性的半胱氨酸 激活了NRF2通路的Keap1突变癌细胞的配基能力。这些发现指向了更广泛的 ABPP作为一种方法在特定疾病状态下寻找差异配基和反应性的潜力。在……里面 在这方面，我假设CDKi耐药状态含有具有不同反应性和/或 支持对CDKi失去敏感性的配基。为了检验这一假设，我提出了两个具体目标：1) 鉴定和鉴定CDKi耐药状态特有的具有不同反应性和配基的蛋白质 2)鉴定MGLL和其他具有不同反应性和/或配基的蛋白质在 对CDKi的获得性耐药。我将使用ABPP方法检测CDKi耐药细胞株，以了解 CDKi耐药的分子基础和寻找新的潜在治疗方法是关键的下一步 在个人化用药时代抗击耐药性。

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.