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， 持久的肿瘤控制。使用抗PD-1和抗CTLA-4抗体的免疫检查点阻断（ICB）是 批准用于治疗黑色素瘤，然而，大部分患者患有原发性或继发性黑色素瘤。 对这些药物的抵抗。癌症疫苗提供了一个机会，以产生新的和放大现有的 抗原特异性T细胞应答集中于针对肿瘤细胞的免疫应答， 与免疫检查点阻断协同作用。新抗原是一类有前途的新型癌症 在每个患者的肿瘤中发现的个人突变产生的疫苗靶点， 对肿瘤有特异性，不受中枢耐受性的影响。最近，在高风险患者中， 黑色素瘤，我们证明了概念的安全性，可行性和免疫原性的个人 利用合成长肽和TLR 3激动剂聚-ICLC（称为NeoVax）的新抗原疫苗。 我们现在提出了一项在晚期黑色素瘤患者中进行的1期临床试验， i）将NeoVax与肿瘤免疫应答的3个关键节点混合， 基于矿物油的免疫佐剂Montanide（改进的制剂），ii）施用抗CTLA-4 i i）将抗体伊匹单抗与疫苗注射部位相邻（增强的引发），和 使用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， 使用连续收集的血液和肿瘤活检的纳武单抗。除了T的标准批量分析外， 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）库。 外周和肿瘤浸润T细胞的克隆配对TCRα和TCRβ链，以及配对TCR α和TCRβ链的筛选。 针对疫苗表位的TCR，以鉴定每个TCR的同源新抗原。最后，我们将使用单个 对相同肿瘤浸润性T细胞进行细胞RNA测序以确定其活化状态， 确定肿瘤反应性T细胞是否采取独特的状态，并监测活化前和活化后的变化。 在治疗后。我们的研究将有助于确定关键的新抗原，T细胞受体，T细胞活化 状态和免疫亚群，其是临床试验中抗肿瘤免疫的基础。因此我们将 确定纳武单抗相对于新抗原疫苗接种对诱导抗肿瘤T细胞的影响 细胞，确定所选新抗原的免疫原性，并提供改善免疫原性的见解。 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.