Structural modeling of neoantigen presentation for rational design of heteroclitic neoepitope vaccines

项目摘要 胰腺导管腺癌（PDAC）对一线手术切除具有高度抵抗性， 化疗许多耐药癌症类型受益于免疫疗法， 活化细胞毒性抗肿瘤T细胞对抗癌细胞中表达的体细胞突变或新抗原。 针对PDAC的新抗原靶向免疫疗法的发展的一个主要挑战是低免疫原性。 鉴定的新抗原的数量和弱免疫原性谱。新抗原特异性T细胞的有效活化 细胞依赖于对人类白细胞抗原（HLA）上展示的8-至11-mer新表位的识别 I类分子。这种认识是生物物理和立体化学之间的联系的顶点 肽、HLA和T细胞受体（TCR）分子。改善新表位的一种机制 免疫原性是通过修饰肽氨基酸残基以增强HLA结合或TCR识别， 从而增强同源T细胞活化，同时保留对亲本表位的反应性。这些改性 表位被称为不规则表位。然而，不规则表位的立体化学特征， 增强HLA结合或TCR识别的研究不足。此外，已经发现了异型表位。 在HLA亚型数量有限的情况下进行探索，限制了它们的发展和应用 在患者中。我们假设，通过结构上的改变， 建模将改善针对PDAC新抗原的T细胞应答。为了解决这个问题，我们将定义 共享和私有PDAC不规则新表位的结构结合和空间展示动力学 不同的HLA。在PDAC中表达的共有新抗原中，KRAS中密码子12处的激活突变是 存在于高达80%的PDAC肿瘤中。在具体目标1中，我们将询问结构力学， 一组18个全球代表性HLA中异型KRAS G12 D/V/C表位免疫原性谱 亚型在具体目标2中，我们将开发一个计算管道来识别，优先考虑和优化患者- 基于结构表位特征的特异性不规则新抗原疫苗候选物。我们将使用HLA 结合测量和T细胞反应性测定，以验证我们的计算免疫原性特征， 模拟的不规则表位。总之，这些目标将定义免疫原性的结构特征， 不同HLA中的新抗原，产生用于共享和私有PDAC的异型表位疫苗候选物， 抗原，并提高癌症疫苗对难以治疗的癌症如PDAC的治疗潜力。

Project Summary Pancreatic ductal adenocarcinoma cancer (PDAC) is highly resistant to frontline surgical resection and chemotherapy treatments. Many treatment-resistant cancer types have benefited from immunotherapies that activate cytotoxic anti-tumor T cells against the somatic mutations, or neoantigens, expressed in cancer cells. One major challenge to the development of neoantigen-targeted immunotherapy for PDAC has been the low number and weakly immunogenic profile of identified neoantigens. Efficient activation of neoantigen-specific T cells is dependent on the recognition of 8- to 11-mer neoepitopes displayed on human leukocyte antigen (HLA) class I molecules. This recognition is the culmination of the biophysical and stereochemical contacts between the peptide, HLA, and T cell receptor (TCR) molecules. One mechanism to improve neoepitope immunogenicity is by modifying the peptide amino acid residues to enhance HLA binding or TCR recognition, thereby enhancing cognate T cell activation, while conserving reactivity to the parental epitope. These modified epitopes are termed heteroclitic epitopes. However, the stereochemical features of heteroclitic epitopes that enhance HLA binding or TCR recognition are understudied. Additionally, heteroclitic epitopes have been explored in the context of a limited number of HLA subtypes, restricting their development and application across patients. We hypothesize that rational design of heteroclitic neoepitope vaccines through structural modelling will improve T cell responses against PDAC neoantigens. To address this hypothesis, we will define the structural binding and spatial display dynamics of both shared and private PDAC heteroclitic neoepitopes in diverse HLAs. Among shared neoantigens expressed in PDAC, activating mutations in KRAS at codon 12 are present in up to 80% of PDAC tumors. In Specific Aim 1, we will interrogate the structural mechanics and immunogenic profile of heteroclitic KRAS G12D/V/C epitopes in a panel of 18, globally representative HLA subtypes. In Specific Aim 2, we will develop a computational pipeline to identify, prioritize and optimize patient- specific heteroclitic neoantigen vaccine candidates based on structural epitope features. We will use HLA binding measurements and T cell reactivity assays to validate immunogenic features of our computationally modelled heteroclitic epitopes. Together, these aims will define the structural features of immunogenic neoantigens in diverse HLAs, generate heteroclitic epitope vaccine candidates for shared and private PDAC antigens, and improve the therapeutic potential of cancer vaccines for hard-to-treat cancers such as PDAC.