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中癌症死亡的主要原因，也是世界上癌症死亡的主要原因。 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“拦截”奠定基础，这是一种寻求阻止肺癌的策略。 癌前病变进展为浸润性癌。在我们的初步研究中，我们已经开始评估 肺癌前病变和相关癌前微环境的突变景观 外显子组DNA测序和免疫组织化学。值得注意的是，我们发现免疫效应细胞 浸润以及肺癌前病变中免疫抑制的证据。这些发现使我们 假设癌前相关新抗原（PAN）被识别并在 肺腺癌发生的最早时间点。这项研究将确定新表位， 在侵袭性肺癌发展之前就有针对性，从而改变了疾病拦截的方法 通过免疫预防和治疗疾病的最早阶段。 具体目标是：1）利用全外显子组DNA测序（WES）来确定计算定义的 原发性肿瘤、癌前病变和相邻组织学正常肺的匹配组中的新抗原 组织中2)鉴定与肿瘤进展相关的功能相关新表位：T细胞的两种来源 细胞，一个来自TIL，另一个来自外周血PD 1 + T细胞，将用于鉴定新表位特异性 CD 8 + 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性肿瘤。将进行功能试验， 验证所鉴定的新表位。这将为未来的疫苗或过继细胞提供患者定制的新表位 非小细胞肺癌（NSCLC）的治疗。3)为了将免疫结构与WES定义的突变相关联， 我们将：3A）进行定量多路复用， 免疫荧光染色的相同标本中使用的前两个目的是评估调节细胞- 介导的免疫，并将其与癌前病变的突变景观和新表位联系起来 3B）利用770个免疫相关基因的Nanostring组评估基因表达，以及3C） 整合WES、基因表达和组织免疫染色的发现来定义 肺腺癌癌前病变这项研究旨在改变方法， 通过发现功能性新表位预防和治疗肺腺癌 开发疫苗和过继疗法，以便在最早阶段阻断疾病。来临 在筛查中，许多患者的影像学检查结果与局灶性或多灶性 癌前病变随着我们对该疾病的分子发病机制和自然史的了解的增加， 关键新表位的发现将促进疫苗的开发，用于那些疾病进展风险最高的人。 到侵袭性肺癌。

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.