Identification and assessment of unconventional tumor-associated antigens as potential targets for cytotoxic T-cell based immunotherapy of cancer

项目摘要/摘要： 以细胞毒性T淋巴细胞(CTL)为基础的免疫疗法在治疗恶性黑色素瘤方面取得了巨大的成功 患有几种不同癌症类型的患者。CTL识别出现在肿瘤细胞中的多肽抗原 表面受人类白细胞抗原I类分子影响，触发特异性肿瘤细胞溶解。定义了这种肿瘤的性质- 相关抗原(TAAs)可通过多种途径直接促进肿瘤靶向治疗 干预措施，包括个性化疫苗、内源性T细胞输注或TCR工程 免疫疗法。然而，只有一小部分人类TAA可以用常规方法确定 蛋白质组学方法。最近的证据表明，这可能是因为大多数 免疫球蛋白是由来自“非规范”来源的多肽组成，例如那些 从翻译的内含子、RNA编辑、蛋白酶体剪接或包含翻译后修饰。 尽管这些都是潜在的高价值肿瘤靶点，但几乎没有几个已经被证实是良药。 真正的助教。然而，克服非规范TAA识别所固有的挑战 承诺显著扩大癌症患者的靶向抗原的范围。 该项目的具体目标是确定和评估潜在的非规范交通协议。 黑色素瘤的治疗靶点，作为产生有效CTL的必要前提和基础- 基于免疫疗法的治疗这种疾病的患者。这是我们的中心假设，独特的，非 规范的TAA可以构成共享的免疫治疗性CTL靶点，并且这些TAA诱导 致癌驱动基因突变的下游，如BRAF(V600E)将显示出更强的肿瘤特异性和 对抗原丢失不耐药。我们根据初步数据提出了这一假设，这些数据表明 可以使用高度敏感的整合来识别潜在靶向的非正则TAA肽 结合遗传测序的质谱学和一种新的内部生物信息学 输油管道。我们还表明，结构性致癌MAPK通路的激活导致戏剧性的全局 肿瘤免疫表位移位可能涉及数千个非典型性TAA。的确有 这项抗原发现工作有很强的临床基础，因为它将直接促进 新的、基于CTL的治疗方法，有可能使大量癌症患者受益。 拟议的工作是创新的，因为它将探索不同类别的非规范TA 作为共同的癌症靶点，评估它们的免疫原性和潜在的治疗价值。会的 还阐明了发生在癌基因介导的MAPK上的转录和蛋白质组变化 途径激活，以及这是如何影响肿瘤免疫多肽的。最后，落实纲要 目标将产生重要的积极临床影响，因为它们将促进下一步的发展 为黑色素瘤患者产生新的抗原特异性CTL免疫疗法，并可能 其他癌症类型的患者。

PROJECT SUMMARY / ABSTRACT: Cytotoxic T lymphocyte (CTL)-based immunotherapies have shown great success in the treatment of patients with several different cancer types. CTLs recognize peptide antigens presented at the tumor cell surface by HLA class I molecules, triggering specific tumor cell lysis. Defining the nature of such tumor- associated antigens (TAAs) can directly facilitate therapeutic tumor targeting through a number of interventions, including personalized vaccines, endogenous T cell infusion, or TCR-engineered immunotherapies. However, only a minority of human TAAs can be confidently identified using conventional proteomic methodologies. Recent evidence suggests this may be due to the fact that most of the immunopeptidome is comprised of peptides derived from ‘non-canonical’ sources such as those derived from translated introns, RNA editing, proteasome splicing, or containing post-translational modifications. Although these represent potentially high value tumor targets, few of these have yet been validated as bona fide TAAs. However, overcoming the challenges inherent in non-canonical TAA identification holds the promise of significantly expanding the landscape of targetable antigens for cancer patients. The specific objective of this project is to identify and assess non-canonical TAAs as potential therapeutic targets for melanoma, as a necessary prerequisite and foundation for generating effective CTL- based immunotherapies for treating patients with this disease. It is our central hypothesis that unique, non- canonical TAAs can constitute shared immunotherapeutic CTL targets, and that those TAAs induced downstream of oncogenic driver mutations such as BRAF(V600E) will show greater tumor specificity and refractoriness to antigen loss. We have formulated this hypothesis based on preliminary data showing that potentially targetable non-canonical TAA peptides can be identified using an integration of highly sensitive mass spectrometry (MS) combined with genetic sequencing analysis and a novel, in-house bioinformatics pipeline. We have also shown that constitutive oncogenic MAPK pathway activation leads to dramatic global tumor immunopeptidome shifts that appear to potentially involve thousands of non-canonical TAAs. There is a strong clinical rationale for this antigen discovery work since it will directly facilitate the development of novel, CTL-based therapies with the potential to benefit large numbers of cancer patients. The proposed work is innovative, because it will explore different categories of non-canonical TAAs in cancer and assess their immunogenicity and potential therapeutic value as shared cancer targets. It will also shed light on the transcriptomic and proteomic changes that occur upon oncogenic-mediated MAPK pathway activation, and how this influences the tumor immunopeptidome. Lastly, fulfilling the outlined objectives will have an important positive clinical impact, because they will facilitate development of the next generation of novel antigen-specific CTL-based immunotherapies for melanoma patients, and possibly also patients with other cancer types.