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

项目总结/摘要： 基于细胞毒性T淋巴细胞（CTL）的免疫疗法已经在治疗恶性肿瘤方面显示出巨大的成功。 患有几种不同类型癌症的患者。CTL识别肿瘤细胞上呈递的肽抗原 表面的HLA I类分子，触发特定的肿瘤细胞裂解。定义这种肿瘤的性质- 相关抗原（TAA）可以通过多种途径直接促进治疗性肿瘤靶向， 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，只有少数的人TAA可以确信地使用常规方法鉴定。 蛋白质组学方法最近的证据表明，这可能是由于大多数人 免疫肽组由来源于“非规范”来源的肽组成， 来自翻译的内含子、RNA编辑、蛋白酶体剪接或含有翻译后修饰。 虽然这些代表了潜在的高价值肿瘤靶点，但其中很少有被证实为bona 真正的TAA。然而，克服非规范TAA鉴定中固有的挑战， 有望显著扩大癌症患者的靶向抗原的前景。 该项目的具体目标是识别和评估非典型TAAs作为潜在的 黑色素瘤的治疗靶点，作为产生有效CTL的必要前提和基础， 免疫疗法来治疗这种疾病。我们的核心假设是，独特的，非- 典型的TAAs可以构成共享的免疫细胞CTL靶点，并且那些TAAs诱导的CTL靶点可以被认为是特异性的。 致癌驱动突变如BRAF（V600 E）的下游将显示更大的肿瘤特异性， 对抗原丧失的不应性。我们根据初步数据提出了这一假设，这些数据表明， 潜在的可靶向的非典型TAA肽可以使用高度敏感的 质谱（MS）结合基因测序分析和一种新的内部生物信息学 渠道.我们还表明，组成性致癌MAPK途径激活导致了戏剧性的全球性的 肿瘤免疫肽组的变化似乎可能涉及数千个非典型的TAA。有 这一抗原发现工作的强有力的临床理由，因为它将直接促进 新的，基于CTL的疗法，有可能使大量癌症患者受益。 拟议的工作是创新的，因为它将探讨不同类别的非规范TAAs 并评估其免疫原性和作为共同癌症靶点的潜在治疗价值。它将 也揭示了转录组和蛋白质组的变化，发生在致癌介导的MAPK 通路激活，以及这如何影响肿瘤免疫肽组。最后，完成概述的 目标将产生重要的积极临床影响，因为它们将促进下一个目标的开发 产生用于黑素瘤患者的新的抗原特异性基于CTL的免疫疗法，并且还可能 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.