The changing neoantigen landscape and associated immune response during immune checkpoint blockade in recurrent glioblastoma: a pathway to personalized tumor immunotherapy

每年有成千上万的胶质母细胞瘤（GBM）患者被诊断出来，尽管目前 最大手术切除、放疗和化疗的标准治疗，中位生存期小于 超过15个月。虽然免疫检查点抑制剂（ICI）已经导致了生存的显着改善， 尽管它们在许多全身性癌症中的作用不显著，但它们在GBM中的作用不太显著。预测指标， 确定哪些患者将更好地响应ICI，并且GBM中缺乏有效的免疫治疗靶点。 本申请的总体目标是鉴定对ICI应答的免疫基因组决定因素， 以确定最有可能从这些治疗中受益的患者。核心假设是， GBM新抗原的免疫原性，以及在GBM过程中新抗原特异性免疫应答的时间变化。 ICI治疗与临床反应相关。该项目的理由是，更好地确定 对ICI有反应的患者将提高靶向免疫治疗的疗效， 开发新的个性化疗法。该提案将利用肿瘤和匹配的血液标本 来自NIH资助的一项研究联合ICI在GBM中的疗效的试验，以实现以下具体目标： 1)鉴定引发新抗原特异性T细胞克隆扩增的新抗原，并确定 IC阻断期间丢失或获得新抗原的免疫原性，（2）鉴定共享的新抗原特异性T细胞 - 在血液和肿瘤之间的克隆，并且用IC阻断来量化这些克隆的时间变化，以及 (3)确定这些共享克隆的多样性和增殖与对ICI的响应的关联。 推定的新抗原将通过全外显子组测序和新抗原的应用来鉴定 将通过评估治疗前肿瘤的预测平台及其免疫原性， 使用TCR-Vβ CDR 3区的下一代测序扩增新抗原特异性T细胞克隆 在体外肽刺激后。利用这种新的检测方法和生物信息学平台， 区域将被用作条形码，以鉴定血液和淋巴细胞之间共享的新抗原特异性T细胞克隆。 肿瘤，跟踪和定量这些克隆的增殖或消耗与IC阻断，并确定 这些克隆的多样性和增殖与对ICI的反应的关联。该研究在 本申请是创新性的，因为它使用了一种新颖的、定量的、灵敏的和特异性的技术来确定 在一些实施方案中，免疫原性以常规测定法检测不到的频率增加。拟议的研究是 这是重要的，因为它将鉴定哪些新抗原与T细胞增殖最强相关， 鉴定ICI应答免疫基因组学生物标志物。这样的知识将允许选择患者最 可能受益于ICI疗法，并为新型个性化免疫疗法提供新的靶点。通过 执行这项研究，杰克逊博士将接受严格的培训，在研究设计，方法， 成为一名熟练的外科医生科学家和神经外科肿瘤学的领导者所必需的研究计划。

There are thousands of patients with glioblastoma (GBM) being diagnosed each year and despite current standard therapy of maximal surgical resection, radiation, and chemotherapy, have a median survival of less than 15 months. While immune checkpoint inhibitors (ICIs) have led to significant improvements in survival in a number of systemic cancers, their effectiveness has been less dramatic in GBM. Predictive metrics to determine which patients will better respond to ICIs, and effective immunotherapy targets are lacking in GBM. The overall objective of this application is to identify immunogenomic determinants of response to ICIs in order to identify patients who are most likely to benefit from these therapies. The central hypothesis is that the immunogenicity of GBM neoantigens, and temporal changes in neoantigen-specific immune responses during ICI therapy are correlated with clinical response. The rationale for this project is that better identification of patients who will respond to ICIs will improve the efficacy of targeted immunotherapy and allow for development of novel personalized therapies. This proposal will leverage tumor and matched blood specimens from a NIH-funded trial studying the efficacy of combination ICIs in GBM to pursue the following specific aims: 1) identify neoantigens that elicit expansion of neoantigen-specific T cell clones and determine the immunogenicity of lost or gained neoantigens during IC blockade, (2) identify shared neoantigen-specific T cell clones between the blood and tumor and quantify the temporal changes of these clones with IC blockade, and (3) determine the association of the diversity and proliferation of these shared clones with response to ICIs. Putative neoantigens will be identified through whole exome sequencing and application of a neoantigen prediction platform of pre-treatment tumors and their immunogenicity will be assessed by evaluating the expansion of neoantigen-specific T cell clones using next-generation sequencing of the TCR-Vβ CDR3 region following in vitro peptide stimulation. Utilizing this novel assay and bioinformatics platform, the TCR-Vβ CDR3 region will be used as a barcode to identify shared neoantigen-specific T cell clones between the blood and tumor, track and quantify the proliferation or depletion of these clones with IC blockade, and determine the association of the diversity and proliferation of these clones with response to ICIs. The research proposed in this application is innovative in that it uses a novel, quantitative, sensitive, and specific technique to determine immunogenicity of neoantigens at a frequency undetectable by conventional assays. The proposed research is significant because it will identify which neoantigens are most strongly associated with T cell proliferation and identify immunogenomic biomarkers of ICI response. Such knowledge will allow for selection of patients most likely to benefit from ICI therapy and offer new targets for novel personalized immune-based therapies. By performing this research, Dr. Jackson will receive the rigorous training in study design, methodology, and research planning necessary to become a skilled surgeon-scientist and a leader in neurosurgical oncology.