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

项目概要 我们的长期目标是为黑色素瘤患者提供安全、有效和可靠的治疗方法 持久的肿瘤控制。使用抗 PD-1 和抗 CTLA-4 抗体进行免疫检查点阻断 (ICB) 批准用于治疗黑色素瘤，但是很大一部分患者患有原发性或继发性黑色素瘤 对这些药剂的抵抗力。癌症疫苗提供了产生新疫苗和扩大现有疫苗的机会 抗原特异性 T 细胞反应集中针对肿瘤细胞的免疫反应，并可能 与免疫检查点阻断协同作用。新抗原是一种有前途的新型癌症 疫苗靶点是由每个患者肿瘤中发现的个体突变产生的，因为它们是 对肿瘤具有精确的特异性，并且不受中枢耐受的影响。近期，高危患者 黑色素瘤，我们展示了个人治疗的安全性、可行性和免疫原性的概念验证 利用合成长肽和 TLR3 激动剂聚 ICLC（称为 NeoVax）的新抗原疫苗。 我们现在提议对晚期黑色素瘤患者进行一期临床试验，旨在增强 NeoVax 在肿瘤免疫反应的 3 个关键节点上的功效 i) 将 NeoVax 与 基于矿物油的免疫佐剂 Montanide（改进配方），ii) 施用抗 CTLA-4 抗体 Ipilimumab 靠近疫苗注射部位（增强启动），以及 iii) 与 含有 PD-1 定向抗体 Nivolumab（重新激活浸润肿瘤的 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，并 纳武单抗利用连续收集的血液和肿瘤活检。除了 T 的标准批量分析外 细胞，我们将通过对 T 细胞受体进行单次测序来表征 T 细胞受体 (TCR) 库。 外周和肿瘤浸润 T 细胞克隆配对 TCRα 和 TCRβ 链，并筛选配对 针对疫苗表位的 TCR 可以识别每个 TCR 的同源新抗原。最后，我们将使用单 对同一肿瘤浸润 T 细胞进行细胞 RNA 测序以确定其激活状态 确定肿瘤反应性 T 细胞是否采用独特的状态，并监测激活前后的变化 治疗后。我们的研究将有助于识别关键的新抗原、T 细胞受体、T 细胞激活 临床试验中构成肿瘤免疫基础的状态和免疫亚群。我们将因此 确定纳武单抗相对于新抗原疫苗接种对诱导抗肿瘤 T 的影响 细胞，确定所选新抗原的免疫原性，并为改善免疫原性提供见解 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.