Clinically Actionable Neoantigens in Non-Small Cell Lung Cancer

非小细胞肺癌中临床可操作的新抗原 肺癌是美国退伍军人癌症死亡的主要原因，也是世界上最主要的癌症死亡原因 癌症死亡。退伍军人的环境暴露和烟草使用共同增加了风险。 释放针对肺部癌前病变的免疫反应可以改变治疗和结果。 在这里，我们建议为肺癌“癌症拦截”奠定基础，这是一种试图阻止 癌前病变向浸润性癌的进展。在我们的初步研究中，我们已经开始评估 肺癌前病变的变异景观及其相关的癌前微环境 外显子组DNA测序和免疫组织化学。值得注意的是，我们发现频繁的免疫效应细胞 肺部癌前病变中的浸润和免疫抑制的证据。这些发现引导我们 假设癌前相关新抗原(PAN)被识别并在 肺腺癌发生发展的最早点。这项研究将确定可以被 在发展为浸润性肺癌之前有针对性，从而改变疾病拦截的方法 通过免疫预防和治疗疾病的最早阶段。 其具体目的是：1)利用整个外显子组DNA测序(WES)来确定计算定义的 配对的原发肿瘤、癌前病变和邻近正常肺组织中的新抗原 纸巾。2)确定与肿瘤进展相关的功能相关的新表位：T的两个来源 细胞，一个来自TIL，另一个来自外周血PD1+T细胞，将被用来识别新的表位特异性 CD8+T细胞。为了提高筛查效率，我们将重点关注癌前病变之间共享的新抗原。 可能与进展相关的病变和原发肿瘤。将进行功能分析以 验证已鉴定的新表位。这将导致为患者量身定做未来疫苗或采用细胞的新表位 治疗非小细胞肺癌(NSCLC)。3)将免疫环境与WES定义的突变联系起来 癌前病变和相关肿瘤中的景观我们将：3A)执行定量多路传输 对前两个样本进行免疫荧光染色的目的是评估细胞- 介导性免疫及其与癌前病变的突变景观和新表位的关系 和肿瘤，3B)利用由770个免疫相关基因和，3C)组成的纳米串小组评估基因表达 结合WES、基因表达和组织免疫染色的结果来定义 肺腺癌、癌前病变。这项研究试图将方法转变为既 通过发现可用于治疗的功能性新表位预防和治疗肺腺癌 疫苗和过继疗法的发展，以在最早的阶段拦截疾病。随着时代的到来 在筛查中，许多患者的影像表现与局灶性或多灶性一致。 癌症前疾病。随着我们对这种疾病的分子发病机制和自然病史的了解不断增加， 关键新表位的发现将促进那些进展风险最高的人的疫苗开发 到浸润性肺癌。

Clinically actionable neoantigens in non-small cell lung cancer Lung cancer is the leading cause of cancer death among US Veterans as well as the world's leading cause of cancer death. Environmental exposure and tobacco use among Veterans operate together to increase risk. Unleashing the immune response against pulmonary premalignancy could transform therapy and outcomes. Here, we propose to lay the ground work for lung “cancer interception,” a strategy that seeks to block the progression of premalignancy to invasive cancer. In our preliminary studies we have begun to evaluate the mutational landscape of pulmonary premalignancy and the associated premalignant microenvironment by whole exome DNA sequencing and immunohistochemistry. Remarkably, we find frequent immune-effector cell infiltration as well as evidence of immune suppression in pulmonary premalignancy. These findings lead us to hypothesize that premalignant-associated neoantigens (PANs) are recognized and elicit immune responses at the earliest points of lung adenocarcinoma development. This research will identify neoepitopes that can be targeted before the development of invasive lung cancer, thus shifting the approach to disease interception through immunoprevention and treatment of the very earliest phase of the disease. The specific aims are: 1) To utilize whole exome DNA sequencing (WES) to determine computationally-defined neoantigens in matched sets of primary tumor, premalignant lesions and adjacent histologically normal lung tissues. 2) To identify functionally relevant neoepitopes associated with tumor progression: Two sources of T cells, one from TIL, the other from peripheral blood PD1+ T cells, will be used to identify neoepitope-specific CD8+ T cells. To improve screening efficiency, we will focus on neoantigens shared between pre-malignant lesions and primary tumors that are potentially progression-relevant. Functional assays will be performed to verify the identified neoepitopes. This will lead to patient-tailored neoepitopes for future vaccine or adoptive cell therapies for non-small cell lung cancer (NSCLC). 3) To relate the immune contexture to WES-defined mutational landscapes in premalignancy and the associated tumor we will: 3A) Perform quantitative multiplexed immunofluorescent staining of the same specimens utilized in the first two aims to assess the regulators of cell- mediated immunity and to relate this to the mutational landscapes and neoepitopes of the premalignant lesions and tumors, 3B) Evaluate gene expression utilizing a Nanostring panel of 770 immune-related genes and, 3C) Integrate findings from WES, gene expression and tissue immunostaining to define the landscape of adenocarcinoma pulmonary premalignancy. This research seeks to transform the approach to both the prevention and treatment of lung adenocarcinoma by discovery of functional neoepitopes that can be utilized in the development of vaccines and adoptive therapies to intercept disease at the earliest phases. With the advent of screening, many patients are presenting with imaging studies consistent with focal or multifocal premalignancy. As we increase our knowledge of the molecular pathogenesis and natural history of the disease, discovery of critical neoepitopes will facilitate vaccine development for those at the highest risk for progression to invasive lung cancer.