Integrative Single-Cell Atlas of Host and Microenvironment in Colorectal Neoplastic Transformation

项目总结：总体而言，结直肠癌（CRC）是美国三大最常见的癌症之一， 全球发病率和死亡率。这些癌症大多数是从癌前腺瘤发展而来的。结肠镜检查是 目前最有效的CRC预防策略。然而，结肠镜检查可能无法预防癌症， 多达24%的病例在预防近端CRC方面效果较差，对卫生保健系统来说是昂贵的 实施，为患者带来经济和心理负担，并可能因出血而复杂化， 穿孔和其他不良事件。制定新的预防战略和风险管理措施的需求尚未得到满足。 分层模型来解决这些和其他问题。通过对整个人体组织的分析， Bert Vogelstein及其同事证明，CRC是由遗传事件的积累发展而来的， 肿瘤从小腺瘤发展到大腺瘤，并最终发展为癌症。最近，我们的小组报告说， 第一个全面的CRC蛋白基因组学特征，这也是从整体分析， 尽管有大量关于CRC的数据，但我们认为，提供最有效的精确性的能力， 诊断和预防策略只能通过单细胞分析来实现。通过这样一个单细胞 分析，我们建议映射正常结肠，早期息肉和晚期息肉频谱的空间关系， 腺瘤，包括其独特的基质和微生物微环境。目的1：构建癌前病变 描述肿瘤生态系统空间景观的结直肠腺瘤进展图谱，包括 基质和生物膜相关微生物组，使用单细胞（sc）RNA-seq，全外显子组测序， 多重免疫荧光（MxIF）和种特异性细菌荧光原位杂交（FISH）。 目标2：整合生物标本、组织表征和数据分析的活动和数据 用于前瞻性标准化收集和分析结直肠组织、相关生物标本的单位， 以及来自1,800名接受结肠镜检查或外科手术的参与者的相关临床和流行病学数据 切除术目标3：传播癌前图谱、相关生物标本、原始数据集和分析 工具，以人类肿瘤图谱网络（HTAN），更广泛的科学界，和外行公众。到 为了实现这些目标，我们组建了一个高度互动和成熟的调查团队， 补充专业知识（流行病学家，胃肠病学家，病理学家，外科医生，系统生物学家， 生物信息学家、癌症生物学家、免疫学家和生物膜/传染病专家）。进一步 优化我们的新方法，以应用于从1,800个图谱中前瞻性收集的样本 参与者，我们将利用我们现有的大型结肠直肠腺瘤库和支持 生物标本，通过一个正在进行的流行病学项目，通过3个周期的 范德比尔特GI卓越研究特别计划（SPORE）。我们相信，我们的应用程序，在 总的来说，它大于其部分的总和，我们期待着与HTAN进行强大的双向互动。

PROJECT SUMMARY: Overall Colorectal cancer (CRC) is among the top three most prevalent cancers in global incidence and mortality. Most of these cancers develop from pre-cancerous adenomas. Colonoscopy is currently the most effective CRC prevention strategy. However, colonoscopy may fail to prevent carcinoma in as many as 24% of cases, is less effective at preventing proximal CRCs, is expensive for health care systems to implement, carries economic and psychosocial burdens for patients, and can be complicated by bleeding, perforation, and other adverse events. There is an unmet need to develop new preventive strategies and risk stratification models to address these and other issues. By analysis of whole human tissue, seminal work from Bert Vogelstein and co-workers demonstrated that CRC develops from an accumulation of genetic events as tumors evolve from small to large adenomas and, eventually, to cancers. More recently, our group reported the first comprehensive proteogenomic characterization of CRC, which also was from a bulk analysis of whole tissue Despite this wealth of data on CRC, we believe that the ability to provide the most effective precision diagnostics and preventive strategies can only be achieved with single-cell analysis. Through such a single-cell analysis, we propose to map spatial relationships across the spectrum of normal colon, early polyps, and late adenomas, including their unique stromal and microbial microenvironments. Aim 1: To construct a pre-cancer atlas of colorectal adenoma progression that depicts the spatial landscape of the tumor ecosystem, including the stroma and biofilm-associated microbiome, using single-cell (sc)RNA-seq, whole exome sequencing, multiplex immunofluorescence (MxIF), and species-specific bacterial fluorescence in situ hybridization (FISH). Aim 2: To integrate the activities and data from the Biospecimen, Tissue Characterization and Data Analysis Units for the prospective standardized collection and analysis of colorectal tissue, associated biospecimens, and related clinical and epidemiological data from 1,800 participants undergoing colonoscopy or surgical resection. Aim 3: To disseminate the pre-cancer atlas, related biospecimens, primary data sets and analytical tools to the Human Tumor Atlas Network (HTAN), the broader scientific community, and the lay public. To accomplish these aims, we have assembled a highly interactive and established team of investigators with complementary expertise (epidemiologists, gastroenterologists, pathologists, surgeons, systems biologists, bioinformaticians, cancer biologists, immunologists, and biofilms/infectious disease experts). To further optimize our novel methodologies for application to the prospectively collected samples from 1,800 atlas participants, we will leverage our existing large repository of colorectal adenomas and supporting biospecimens, generated and curated through an ongoing epidemiological project through 3 cycles of the Vanderbilt GI Special Programs of Research Excellence (SPORE). We are confident that our application, in toto, is greater than the sum of its parts, and we look forward to robust bi-directional interactions with HTAN.