Unsupervised Statistical Methods for Data-driven Analyses in Spatially Resolved Transcriptomics Data

空间分辨转录组数据中数据驱动分析的无监督统计方法

• 批准号: 10350850
• 负责人: Lukas Martin Weber
• 金额: $ 8.91万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10350850
• 关键词: Address; Adopted; Award; Awareness; Benchmarking; Biological; Cells; Classification; Communities; Complex; Computer software; Data; Data Analyses; Data Set; Data Storage and Retrieval; Development; Diagnosis; Dimensions; Disease; Evaluation; Expression Profiling; Extramural Activities; Faculty; Funding; Gene Expression; Gene Expression Profile; Generations; Genes; Genetic Transcription; Goals; Health; Heterogeneity; Human; Individual; Institution; Knowledge; Lead; Machine Learning; Measurement; Measures; Mentors; Methodology; Methods; Molecular; Nature; Outcome; Pathway interactions; Pattern; Phase; Population; Positioning Attribute; Procedures; Prognosis; Property; Quality Control; RNA; Research; Research Personnel; Resolution; Resources; Signal Transduction; Specificity; Spottings; Standardization; Statistical Methods; Systematic Bias; Techniques; Technology; Time; Tissue Microarray; Tissue Preservation; Tissues; Training; Transcript; Variant; Weight; Work; base; career; cell type; complex data; data infrastructure; data resource; data reuse; data standards; density; design; feature selection; improved; insight; novel; open source; precision medicine; single-cell RNA sequencing; statistics; tenure track; tool; transcriptome; transcriptomics; treatment response; two-dimensional

Project Summary/Abstract Recently developed spatially resolved transcriptomics (ST) technologies measure transcriptome-wide gene expression at a near-single-cell, single-cell, or sub-cellular resolution in intact tissue, preserving the spatial organization of complex tissues. These technologies build upon widely-adopted single-cell RNA sequencing (scRNA-seq) technologies by adding spatial coordinates to the transcriptome-wide gene expression measurements, thus enabling an understanding of how the spatial organization of cells in complex tissues influences function, disease initiation, progression, and therapeutic response in human health and disease. However, these technologies also present new statistical and computational challenges, which need to be addressed to accurately interpret this complex data. While initial studies applying these tools have reused data analysis methods and data storage techniques designed for scRNA-seq, unfortunately these approaches largely ignore spatial information. Furthermore, existing methodologies for ST data rely on external information such as marker genes or reference cell types, potentially leading to systematic errors and biased results during preprocessing, feature selection, classification of spatially resolved cell types, and differential discovery. There do not yet exist robust and accurate preprocessing and unsupervised statistical methodologies to investigate ST data in a data-driven manner. The overall goals of this K99/R00 Pathway to Independence Award proposal are to request support to address this fundamental gap in statistical methodology to develop spatially-aware (1) methods for preprocessing, (2) unsupervised methods for spatially resolved clustering and differential discovery between conditions, and (3) data infrastructure and benchmarking resources to standardize the storage and access of ST data. These proposed methods will lead to an improved understanding of health and disease mechanisms. This proposal will provide the training, mentoring, and professional development to accomplish my research goals and transition to a tenure track faculty position at a research institution with independent extramural funding. As the demand for ST technologies grows, in particular now that it has been highlighted as the Nature Methods 2020 Method of the Year, these urgently needed statistical methods and open-source software proposed in this project will enable ST technologies to transform precision medicine through novel biological insights relating to spatial properties of cell populations and gene expression in healthy and diseased tissues. At the completion of this award, I will become part of a new generation of researchers, proficient in spatial statistics, machine learning, and spatial transcriptomics technologies, enabling me to work closely with biomedical researchers spatially profiling the transcriptomes of complex tissues.

项目摘要/摘要 最近发展起来的空间分辨转录组学(ST)技术测量转录组范围的基因 在完整组织中以接近单细胞、单细胞或亚细胞分辨率表达，保持空间 复杂组织的组织。这些技术建立在广泛采用的单细胞RNA测序的基础上 (scRNA-seq)技术通过将空间坐标添加到转录组范围的基因表达 测量，从而使我们能够理解复杂组织中细胞的空间组织 在人类健康和疾病中影响功能、疾病的发生、进展和治疗反应。 然而，这些技术也带来了新的统计和计算挑战，需要 以准确地解释这些复杂的数据。虽然应用这些工具的初步研究已经重复使用了 为scRNA-seq设计的数据分析方法和数据存储技术，不幸的是，这些方法 在很大程度上忽略了空间信息。此外，现有的ST数据方法依赖于外部信息 例如标记基因或参考细胞类型，可能导致系统误差和在 预处理、特征选择、空间分辨细胞类型的分类和差异发现。那里 尚不存在稳健和准确的预处理和非监督统计方法可供调查 以数据驱动的方式存储数据。这项K99/R00独立之路奖提案的总体目标 将请求提供支助，以解决统计方法中的这一根本差距，以发展空间意识(1) 预处理方法，(2)空间分辨聚类和微分的非监督方法 条件之间的发现，以及(3)数据基础架构和基准资源，以标准化 ST数据的存储和访问。这些建议的方法将有助于更好地了解健康和 疾病机制。 该计划将提供培训、指导和职业发展，以完成我的 研究目标和过渡到终身教职在具有独立研究机构的研究机构 校外资金。随着对科技技术的需求增长，特别是现在它已经被强调为 《自然方法2020年度方法》，这些急需的统计方法和开源 该项目中提出的软件将使ST技术通过创新实现精准医学的变革 与健康和疾病患者细胞群体空间特性和基因表达相关的生物学研究 纸巾。在完成这个奖项后，我将成为新一代研究人员中的一员，精通 空间统计、机器学习和空间转录技术，使我能够与 生物医学研究人员在空间上描绘复杂组织的转录本。