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.

项目摘要 微生物越来越被认为是癌症肿瘤微环境的关键成分， 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 微生物以及微生物和宿主组织之间是微生物驱动的机制的基础 CRC中的致癌作用，但这些相互作用的研究仍然很差。缺乏知识在很大程度上是由于 用于研究微生物和微生物组的工具的基本局限性。微生物组研究主要是 依靠shot弹枪DNA测序，它破坏了有关微生物及其空间上下文的所有信息 功能相互作用或限于识别少量生物的成像方法 使用一般物种标记标签。 在这个项目中，我们将发明和应用空间解决的元基因组学（SRM），这是革命性的 分子分析技术，该技术能够创建数千个位置的微尺度地图 密集的微生物群落中的不同细菌物种。 SRM利用光条形码和 基于光谱成像的条形码解码，使细菌物种独特的16s鉴定 核糖体RNA，甚至定量宿主基因表达。 SRM是一种灵活且廉价的技术 这增加了可以在现有方法上识别的独特微生物物种的数量 两个数量级，并由Pilot数据得到很好的支持。我们将调查三个目标。首先，我们将完善 许多创新技术共同为SRM奠定了基础，包括但不限于软件 为了自动设计杂交探针，光谱成像程序和自动化的软件 图像的注释。其次，我们将设计和构建一个自定义的宽波长共聚焦显微镜， 这将提高多重性和SRM的速度，而额外的数量级，进而将 改善SRM可能应用的范围。第三，我们将对SRM进行严格验证 在人类CRC中提出高度及时问题的实验。促进癌症的功能作用 CRC中的微生物，生物膜形成的作用是CRC发育中的早期事件，并且 CRC肿瘤中存在持续的微生物组，都是最近的地标发现，我们将成为 能够利用SRM的功能，以前所未有的空间和系统发育分辨率进行研究。 SRM使不仅可以调查谁在那里，还可以调查谁在谁和谁​​旁边的人身边，因此 提供了一种强大的新颖手段来研究微生物群在启动和发展中的功能作用 CRC，每年在美国每年有50,000多人死亡的疾病。