Dissecting neoepitope-specific clonal T cell populations in advanced melanoma patients vaccinated with personal neoantigen peptides partnered with local and systemic immune checkpoint Inhibition

项目摘要 我们的长期目标是为黑色素瘤患者提供安全、有效和 持久的肿瘤控制。抗PD-1和抗CTLA-4抗体的免疫检查点阻断(ICB) 被批准用于治疗黑色素瘤，然而，有很大一部分患者是原发或继发的 对这些药物的抗药性。癌症疫苗提供了产生新的和扩大现有的机会 抗原特异性T细胞反应集中免疫反应对抗肿瘤细胞和潜在的 与免疫检查点封锁协同作用。新抗原是一种很有前途的新型癌症 通过在每个患者的肿瘤中发现的个人突变创建疫苗靶点，因为它们是 对肿瘤具有精致的特异性，不受中枢耐受的影响。最近，在高危患者中 黑色素瘤，我们展示了个人的安全性、可行性和免疫原性的概念证明。 利用合成长肽和TLR3激动剂PolyICLC(称为NeoVax)的新抗原疫苗。 我们现在建议对晚期黑色素瘤患者进行一期临床试验，旨在提高 NeoVax在肿瘤免疫反应的3个关键节点的疗效：i)将NeoVax与 矿物油免疫佐剂Montanide(改良配方)，II)注射抗CTLA-4 与疫苗注射部位相邻的抗体Ipiimumab(增强引爆)，以及iii)与 使用PD-1导向抗体Nivolumab(重新激活肿瘤中的T细胞)的疫苗。我们 提出创新的免疫学分析，以了解改良疫苗的活性和 尼伏卢单抗利用连续采集的血液和肿瘤活检。除了T的标准批量分析之外 细胞，我们将通过对单个T细胞受体进行测序来表征T细胞受体(TCR)谱系 外周和肿瘤浸润性T细胞克隆配对TcRα和TcRβ链及配对筛选 针对疫苗表位的TCR，以识别每个TCR的同源新抗原。最后，我们将使用Single 对同一肿瘤浸润性T细胞进行细胞RNA测序以确定其激活状态和 确定肿瘤反应性T细胞是否采用独特的状态，并监测在 在治疗之后。我们的研究将有助于确定关键的肿瘤抗原、T细胞受体、T细胞激活 在临床试验中，对肿瘤免疫的基础状态和免疫亚群。因此，我们将 确定尼伏卢单抗与新抗原疫苗相比对抗肿瘤T细胞诱导的影响 细胞，确定选定的新抗原的免疫原性，并为改善 未来新抗原疫苗试验的设计和分析。

Project Summary Our long-term goal is to provide melanoma patients with therapies that produce safe, effective, and durable tumor control. Immune checkpoint blockade (ICB) with anti-PD-1 and anti-CTLA-4 antibodies is approved for the treatment of melanoma, however a large subset of patients has primary or secondary resistance to these agents. Cancer Vaccines provide an opportunity to generate new and amplify existing antigen-specific T cell responses focusing the immune response against tumor cells and potentially synergizing with immune checkpoint blockade. Neoantigens are a promising novel class of cancer vaccine targets created by the personal mutations found in each patient's tumor because they are exquisitely specific to the tumor and not subject to central tolerance. Recently, in patients with high-risk melanoma, we demonstrated proof-of-concept of the safety, feasibility, and immunogenicity of a personal neoantigen vaccine utilizing synthetic long peptides and the TLR3 agonist poly-ICLC (called NeoVax). We now propose a phase 1 clinical trial in patients with advanced melanoma that seeks to enhance the efficacy of NeoVax at 3 critical nodes of the tumor immune response by i) admixing NeoVax with the mineral oil-based immune adjuvant Montanide (improved formulation), ii) administering the anti-CTLA-4 antibody Ipilimumab adjacent to the vaccine injection site (enhanced priming), and iii) partnering the vaccine with the PD-1 directed antibody Nivolumab (re-invigorating T-cells infiltrating the tumor). We propose innovative immunological analyses to understand the activity of the modified vaccine and Nivolumab utilizing serially collected blood and tumor biopsies. In addition to standard bulk profiling of T cells, we will characterize T cell receptor (TCR) repertoires by sequencing T cell receptors in single peripheral and tumor infiltrating T cells for clone-paired TCRα and TCRβ chains, and screening of paired TCRs against vaccine epitopes to identify cognate neoantigens of each TCR. Finally, we will use single cell RNA-sequencing of the same tumor infiltrating T cells to determine their activation state and determine if tumor-reactive T cells adopt unique states, and to monitor changes in activation before and after therapy. Our studies will help identify the critical neoantigens, T cell receptors, T cell activation states and immune subpopulations that underlie immunity against tumors in the clinical trial. We will thus determine the impact of Nivolumab relative to neoantigen vaccination on the induction of anti-tumor T cells, determine the immunogenicity of the selected neoantigens and provide insights for improving the design and analysis of future neoantigen vaccine trials.