Spatially Resolved Metagenomics to Explore Tumor-Microbiome Interactions in Human Colorectal Cancer

空间分辨宏基因组学探索人类结直肠癌中肿瘤-微生物组的相互作用

• 批准号: 10005220
• 负责人: Ilana Lauren Brito
• 金额: $ 38.13万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10005220
• 关键词: Address; Affect; Architecture; Atlases; Automated Annotation; Bacteria; Bacteroides; Bar Codes; Bioinformatics; Biopsy; Catalogs; Cells; Cessation of life; Colon Carcinoma; Colonic Adenoma; Colonic Neoplasms; Colorectal Cancer; Complex; Computer software; Consequentialism; Custom; DNA; DNA sequencing; Data; Development; Disease; Disease Progression; Distal; Epithelial; Epithelium; Event; Fluorescence Microscopy; Foundations; Fusobacterium nucleatum; Gene Expression; Genes; Genetic Transcription; Human; Image; Image Analysis; Imaging Techniques; Immune response; Inflammation; Investigation; Knowledge; Location; Malignant Neoplasms; Maps; Metagenomics; Methodology; Methods; Microbe; Microbial Biofilms; Microscope; Molecular Analysis; Molecular Biology; Mucous Membrane; Mucous body substance; Natural Killer Cells; Neoplasm Metastasis; Optics; Organism; Patients; Phylogenetic Analysis; Play; Prevotella; Procedures; RNA, Ribosomal, 16S; Resolution; Role; Selenomonas; Shotguns; Speed; Surface; Surveys; System; T-Lymphocyte; Technology; Testing; Time; Tissues; Validation; bacterial community; base; carcinogenesis; chemotherapy; colon microbiota; colorectal cancer progression; design; design and construction; dysbiosis; experimental study; flexibility; fluorophore; gut microbiome; host microbiome; hybrid gene; imaging software; improved; innovation; innovative technologies; instrument; microbial; microbial community; microbiome; microbiome research; microbiota; microorganism interaction; novel; quantitative imaging; rRNA Genes; response; spectrograph; tool; tumor; tumor growth; tumor initiation; tumor microbiome; tumor microenvironment; tumor progression; validation studies

PROJECT SUMMARY Microbes are increasingly recognized as a critical component of the tumor microenvironment of cancers that arise at epithelial barrier surfaces, such as human colorectal cancer (CRC). Spatial interactions between microbes and between microbes and host tissues, are fundamental to the mechanisms by which microbiota drive carcinogenesis in CRC, yet these interactions remain poorly studied. This lack of knowledge is in large part due to fundamental limitations of the tools available to study microbes and microbiomes. Microbiome studies primarily rely on shotgun DNA sequencing, which destroys all information about the spatial context of microbes and their functional interactions, or imaging methodologies that are limited to identifying a small number of organisms using general species marker tags. In this project, we will invent and apply spatially resolved metagenomics (SRM), a revolutionary molecular analysis technology that enables to create micro-scale maps of the locations of thousands of different bacterial species in dense microbial communities. SRM takes advantage of optical barcoding and spectral imaging-based barcode decoding, enabling the identification of bacterial species by their unique 16S ribosomal RNAs, and even quantification of host gene expression. SRM is a flexible and inexpensive technology that increases the number of unique microbial species that can be identified over existing methods by at least two orders of magnitude and is well supported by pilot data. We will investigate three aims. First, we will refine a host of innovative technologies that together lay the foundation for SRM, including but not limited to software for the automated design of hybridization probes, spectral imaging procedures and software for the automated annotation of images. Second, we will design and construct a custom broad-wavelength confocal microscope, that will improve the multiplexity, and speed of SRM by an additional order of magnitude, which in turn will improve the range of possible applications of SRM. Third, we will perform rigorous validation of SRM in experiments that address highly timely questions in human CRC. The functional roles of cancer-promoting microbes in CRC, the role for biofilm formation as a consequential, early event in CRC development, and the presence of a persistent microbiome in CRC tumors, are all very recent landmark discoveries, that we will be able to study with unprecedented spatial and phylogenetic resolution by taking advantage of the features SRM. SRM enables to survey not only who is there, but also who is next to who and who is next to what, and therefore provide a powerful, novel means to study the functional role of microbiota in the initiation and progression of CRC, a disease that accounts for more than 50,000 deaths annually in the US.

项目概要 微生物越来越被认为是癌症肿瘤微环境的关键组成部分， 出现在上皮屏障表面，例如人类结直肠癌（CRC）。之间的空间相互作用 微生物之间以及微生物与宿主组织之间的关系是微生物群驱动机制的基础 结直肠癌的致癌作用，但这些相互作用的研究仍然很少。这种知识的缺乏很大程度上是由于 用于研究微生物和微生物组的工具的基本局限性。主要研究微生物组 依赖鸟枪法 DNA 测序，这会破坏有关微生物及其空间背景的所有信息 功能相互作用或仅限于识别少数生物体的成像方法 使用通用物种标记标签。 在这个项目中，我们将发明并应用空间分辨宏基因组学（SRM），这是一种革命性的技术 分子分析技术能够创建数千个位置的微尺度地图 密集微生物群落中的不同细菌种类。 SRM 利用光学条形码和 基于光谱成像的条形码解码，能够通过其独特的 16S 识别细菌种类 核糖体 RNA，甚至宿主基因表达的定量。 SRM 是一种灵活且廉价的技术 与现有方法相比，至少增加了可识别的独特微生物物种的数量 两个数量级，并且得到了试点数据的良好支持。我们将研究三个目标。首先我们要细化 一系列创新技术共同奠定了 SRM 的基础，包括但不限于软件 用于杂交探针、光谱成像程序和自动化软件的自动化设计 图像注释。其次，我们将设计和构建定制的宽波长共焦显微镜， 这将把 SRM 的多路复用性和速度提高一个额外的数量级，进而将 扩大 SRM 的可能应用范围。第三，我们将对SRM进行严格的验证 解决人类 CRC 中非常及时的问题的实验。促癌的功能作用 结直肠癌中的微生物、生物膜形成作为结直肠癌发展中一个重要的早期事件的作用，以及 结直肠癌肿瘤中存在持久微生物组，都是最近的里程碑式发现，我们将 能够利用 SRM 功能以前所未有的空间和系统发育分辨率进行研究。 SRM 不仅可以调查谁在那儿，还可以调查谁在谁旁边以及谁在什么旁边，因此 提供了一种强大的、新颖的方法来研究微生物群在疾病发生和进展中的功能作用 结直肠癌是一种在美国每年导致 50,000 多人死亡的疾病。