Molecular, Cellular, and Tissue Characterization Unit

摘要 表征单元寻求对分子、细胞和组织变化的全面理解 在肺癌的最早期推动肺癌的发展和进展。肺癌肿瘤发生 在临床上明显的疾病发展之前很久就发生了，这提供了机会， 在这个漫长的临床前阶段进行干预。我们的多学科团队将利用最先进的多组学 解决导致肺癌前病变（PML）进展的关键决定因素的技术 到恶性肿瘤在这第一个目标中，我们将利用已建立的测定来评估分子和细胞 在回顾性肺癌队列中促进肺癌发生的改变和试点技术 癌前病变在这里，我们将讨论在已确定的癌症背景下， 肺鳞状细胞癌（LUSC）和腺癌（LUAD）的横断面分析， 以前是从外科标本中提取的最大的挑战是确定 将在目标2中利用肺的分子和细胞表型来解决进展或消退 通过采用已建立的检测方法并结合新兴的更高分辨率（单细胞）技术， 以及在前瞻性队列中Aim 1的成功试点试验。在这里，纵向前瞻性研究将允许 癌前病变时空分析。精确的临床注释将有助于确定关键的 翻译成果。因为癌前微环境（PME）可能促进或抑制 在浸润性肺癌的发展过程中，表征单元将通过广泛的 免疫分析这项研究将有助于随后分析突变负荷之间的相互作用， 癌前细胞的基因表达状态和免疫识别，包括鉴定 新抗原和免疫编辑，贯穿癌前病变的演变。使用采购的生物标本 生物标本股，表征股将利用技术，产生多维，大规模的 可由数据分析单元分析以发现与疾病相关的关系的数据 进展用于评估肺癌前病变的技术平台和相应的 微环境包括：整个组织（散装）和单细胞DNA和RNA测序，单核RNA， 测序、RNA原位（SNAIL）、高度多重（40 - 50个标记/板）成像技术，包括 多路离子束成像（MIBI）和通过indEXing（CODEX）进行CO检测（包括Ce3D 技术）以及通过多重免疫荧光（MIF）验证。该股最终将提供 这些数据使我们了解肺癌的发病机制， 癌前病变到浸润性疾病。这项研究将提供一个机会， 从晚期疾病干预到早期拦截，以防止肺癌前病变的进展。

ABSTRACT The Characterization Unit seeks a comprehensive understanding of molecular, cellular, and tissue changes that drive lung cancer development and progression during its very earliest stages. Lung cancer tumorigenesis occurs long before the development of clinically apparent disease, which affords the opportunity for intervention in this extended preclinical phase. Our multidisciplinary team will utilize state-of-the-art multi-omic technologies to address the key determinants that cause a pulmonary premalignant lesion (PML) to progress to invasive malignancy. In this first aim, we will utilize established assays to evaluate molecular and cellular alterations that contribute to lung carcinogenesis and pilot technologies in retrospective cohorts of lung premalignancy. Here we will address the evolution of premalignancy in the context of established cancers in cross-sectional analysis of both lung squamous (LUSC) and adenocarcinoma (LUAD) that have been previously banked from surgical specimens. The paramount challenge of delineating the determinants of progression or regression will be addressed in Aim 2 utilizing the molecular and cellular phenotyping of lung PMLs by employing established assays, and incorporating emerging higher resolution (single cell) technologies and successful pilot assays from Aim 1 in prospective cohorts. Here longitudinal prospective studies will allow temporal and spatial analysis of premalignancy. Precise clinical annotation will facilitate determination of critical translational outcomes. Because the premalignant microenvironment (PME) may either promote or constrain the development of invasive lung cancer, the Characterization Unit will evaluate the PME through extensive immune profiling. This investigation will facilitate subsequent analysis of the interplay between mutational load and gene expression status of premalignant cells and immune recognition, including identification of neoantigens and immunoediting, throughout the evolution of premalignancy. Using biospecimens procured by the Biospecimen Unit, the Characterization Unit will utilize technologies that yield multidimensional, large-scale data that can be analyzed by the Data Analysis Unit to discover relationships associated with disease progression. Technology platforms to be utilized to assess lung premalignancy and the corresponding microenvironment include: whole tissue (bulk) and single cell DNA- and RNA-sequencing, single nuclei RNA- sequencing, RNA in situ (SNAIL), highly multiplexed (40–50 markers/panel) imaging technologies including multiplexed ion beam imaging (MIBI), and CO-Detection by indEXing (CODEX) (including with Ce3D technology) in addition to validation by multiplex immunofluorescence (MIF). This Unit will ultimately provide the data that informs our understanding of the pathogenesis of lung cancer from its earliest appearance as premalignancy to invasive disease. This research will afford the opportunity to shift the paradigm from advanced disease intervention to early interception that prevents the progression of pulmonary premalignancy.