The genetic markers of ipilimumab response in patients with metastatic melanoma

描述（由申请人提供）：与黑色素瘤相关的稳定高死亡率主要是由于晚期或转移性疾病患者现有治疗的局限性。免疫疗法是为数不多的为转移性患者提供更持久生存益处的替代方案之一。在转移性黑色素瘤治疗中的新型免疫抑制剂是伊匹单抗，其通过阻断CTLA-4（一种负责负免疫原性信号传导的抗原）来刺激T细胞介导的免疫应答。尽管与其他免疫疗法相比有希望的反应，但目前只有约30%的患者受益于ipilimumab治疗。这表明存在影响该机制的其他潜在宿主相关因素，在该机制下，伊匹单抗阻断CTLA 4介导的免疫抑制。然而，虽然分子医学将从这些知识中受益匪浅，但迄今为止还没有鉴定出CTLA-4阻断的“靶向”分子调节剂。在我们的研究中，我们假设ipilimumab/CTLA 4抑制的功效是由活化T细胞中影响调节CTLA 4免疫检查点的途径的未知遗传（生殖系）遗传变异或体细胞遗传改变调节的。我们研究的总体目标是发现新的药物基因组学靶点（种系和/或体细胞），这些靶点调节对易普利姆玛的敏感性/耐药性，最终导致改进免疫疗法和其他靶向治疗的药物设计。为了鉴定影响易普利姆玛/CTLA阻断的分子机制的生殖系遗传变异，在本研究中，我们提出了一项利用CTLA 4信号通路中涉及的396个基因的深度测序的初步研究，比较了两个“极端”临床子集：50名伊匹单抗完全应答者和50名伊匹单抗无应答者，随后是在另外n>300名伊匹单抗治疗的患者中的验证阶段（具体目标1）。同时，将对同一组396个基因进行转录组测序，以鉴定循环CD 4 +/CD 8 + T细胞中CTLA 4信号传导途径的体细胞获得性遗传改变（特定目标2）。具有成本效益的设计和新颖的分析平台将允许综合分析，结合种系和体细胞数据以鉴定易普利姆玛/CTLA 4阻断的调节机制的遗传替代物。我们认为，在这项研究中发现的新的“可操作的”遗传改变（体细胞和生殖细胞），影响伊匹单抗在刺激免疫应答中的功效，不仅将提供在改进的药物设计和治疗决策中的利用，而且将可能指向触发应用于治疗转移性黑色素瘤的其他联合治疗方法的新的分子机制。CTLA 4调节的免疫检查点的遗传改变的初步检查，如所提出的，也将显着扩大我们对其他影响T细胞介导的免疫应答的潜在关键分子机制的知识。

DESCRIPTION (provided by applicant): The steadily high mortality rates associated with melanoma are mainly due to the limitations of current therapies available for patients with advanced or metastatic disease. Immunotherapy is one of the few alternatives that provide more durable survival benefits for metastatic patients. Among the novel immunotherapeutic agents in metastatic melanoma treatment is ipilimumab, which stimulates T-cell mediated immune response by blocking CTLA-4, an antigen responsible for negative immunogenic signaling. Despite promising response compared to other immunotherapies, only ~ 30% of patients currently benefit from ipilimumab treatment. This indicates that there are other underlying host-related factors impacting the mechanism, under which ipilimumab blocks CTLA4-mediated immune inhibition. However, while molecular medicine would strongly benefit from such knowledge, no "targetable" molecular modulators of CTLA-4 blockade have been identified so far. In our study we hypothesize that the efficacy of ipilimumab/CTLA4 inhibition is modulated by yet unknown inherited (germline) genetic variation or somatic genetic alterations in activated T-cells affecting the pathways that regulate CTLA4 immune checkpoints. The overall goal of our study is to discover novel pharmacogenomic targets (germline and/or somatic) that modulate sensitivity/resistance to ipilimumab, eventually leading to modified drug designs in improved immunotherapies and other targeted treatments. To identify germline genetic variants that affect the molecular mechanisms of ipilimumab/CTLA-blockade, in this study we propose a pilot investigation utilizing deep sequencing of 396 genes involved in CTLA4 signaling pathway comparing two "extreme" clinical subsets: 50 ipilimumab-complete responders and 50 ipilimumab non-responders, followed by the validation stage in additional n>300 ipilimumab treated patients (Specific Aim 1). In parallel, the transcriptome sequencing of the same set of 396 genes will be performed to identify somatically acquired genetic alterations in CTLA4 signaling pathways in circulating CD4+/CD8+ T-cells (Specific Aim 2). The cost efficient design and novel analytical platform will allow for the integrative analysis, combining te germline and somatic data to identify genetic surrogates underlying the modulatory mechanisms of ipilimumab/CTLA4-blockade. We suggest that the novel "actionable" genetic alterations discovered in this study (somatic and germline), impacting efficacy of ipilimumab in stimulation of immune response, will not only offer utilization in improved drug designs and therapeutic decisions, but will likely point to novel molecular mechanisms triggering the application to other combined therapy approaches in treatment of metastatic melanoma. The pilot examination of genetic alterations in CTLA4-regulated immune checkpoint, as proposed, will also significantly widen our knowledge on other potentially critical molecular mechanisms that impact T-cell mediated immune response in general.