Improvement and standardization of a bioinformatic software suite for multiplexed imaging

用于多重成像的生物信息学软件套件的改进和标准化

• 批准号: 10609313
• 负责人: Helen M Blau
• 金额: $ 21.87万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-15 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10609313
• 关键词: Adhesions; Affect; Aged, 80 and over; Aging; Algorithms; Applications Grants; Architecture; Bioinformatics; Biological Process; Biology of Aging; Catabolism; Cell Communication; Cell Cycle Proteins; Cell Therapy; Cell surface; Cells; Cessation of life; Clinical; Collaborations; Communities; Computer software; Data; Databases; Detection; Development; Diffusion; Dinoprostone; Disease; Documentation; Elderly; Environment; Enzymes; Extracellular Matrix Proteins; Funding; Gene Expression; Goals; Grant; Growth Factor; Histology; Homeostasis; Human; Image; Imaging technology; Inflammatory; Injury; Intervention; Knowledge; Label; Ligands; Link; Lipids; Location; Longevity; Machine Learning; Maintenance; Methodology; Methods; Microscope; Modality; Modeling; Molecular; Morbidity - disease rate; Mus; Muscle; Muscle function; Muscular Atrophy; Oxidoreductase; Periodicity; Persons; Pharmacology; Phenotype; Physical activity; Play; Process; Property; Prostaglandin D2; Prostaglandins; Proteins; Pythons; Quality of life; Research; Resolution; Role; Running; Services; Signal Transduction; Signaling Molecule; Sister; Skeletal Muscle; Source; Spatial Distribution; Standardization; Talents; Techniques; Therapeutic; Time; Tissue imaging; Tissues; Visualization; age related; aged; analysis pipeline; base; cell type; connectome; data format; data quality; data standards; experience; experimental study; graphical user interface; high resolution imaging; image registration; imaging modality; improved; in silico; indexing; intercellular communication; mortality; multiplexed imaging; muscle aging; muscle form; muscle regeneration; muscle strength; novel; nutrition; overexpression; parent grant; physically handicapped; programs; receptor; sarcopenia; senescence; single-cell RNA sequencing; skeletal muscle wasting; software development; spatial relationship; terabyte; therapeutic target; tool; transcription factor; transcriptome; usability; user-friendly

PROJECT SUMMARY Sarcopenia, or age-related muscle atrophy, afflicts 15% of the elderly, severely diminishing quality of life and increasing morbidity and mortality. Our overarching goal is to elucidate novel causal mechanisms of sarcopenia and use this knowledge to improve aged muscle function. We propose to capitalize on our discovery that a reduction in the prostaglandins PGE2 and PGD2 in aged muscle results from catabolism by 15-hydroxyprosta- glandin dehydrogenase (15-PGDH), the prostaglandin degrading enzyme, the subject of the parent grant of this application. As described in the grant, we made the unexpected finding that 15-PGDH expression is significantly increased in aged mouse and human muscles. Additionally, our data show that overexpressing 15-PGDH in young muscles induces an aging phenotype accompanied by a marked decrease in muscle mass and function, mimicking sarcopenia. The central hypothesis of the parent grant is that during aging, senescent and inflamma- tory cells accumulate in the muscle microenvironment and express 15-PGDH, which degrades PGE2 and PGD2, and causes muscle wasting. Therefore, inhibition of 15-PGDH in aged muscles will increase PGE2 and PGD2 lipid metabolites and augment muscle mass and strength. Our aims are to (i) elucidate the roles of PGE2 and PGD2 in skeletal muscle homeostasis, (ii) identify the cell source of 15-PGDH and prostaglandin dysregulation in aged muscle, and (iii) restore aged muscle function and mass by inhibiting 15-PGDH. Parent grant Aim 2 employs a cutting-edge single cell multiplexed imaging technology called CODEX (CO-Detection by indEXing). CODEX allows us to resolve up to 60 markers simultaneously in single tissue sections. This breakthrough meth- odology will enable a determination of whether senescent cells comprise a cell source of 15-PGDH and allow us to resolve the spatial relationships among the diverse cell types present in aged muscles. Each CODEX experi- ment produces terabytes of high-resolution images that must be deconvolved and stitched together. We have developed 3 software packages (CRISP, HFCluster, and SpaCE) to deconvolve, stitch, cluster, and annotate our CODEX data and computationally identify signaling among cell types. Our goal for this supplement is to fund a skilled and dedicated lab associate for the continued improvement and maintenance of this software, specifi- cally to improve user interface, standardize data input formats, and provide compatibility for a range of multi- plexed imaging workflows. These improvements will not only help us achieve the second aim of our grant, but they will also make the software we develop far more user-friendly and readily accessible to the muscle biology and aging communities, as well as to all users of CODEX and other multiplexed imaging modalities.

项目概要 肌肉减少症，或与年龄相关的肌肉萎缩，困扰着 15% 的老年人，严重降低了生活质量和 发病率和死亡率增加。我们的首要目标是阐明肌肉减少症的新因果机制 并利用这些知识来改善衰老的肌肉功能。我们建议利用我们的发现 老化肌肉中前列腺素 PGE2 和 PGD2 的减少是由于 15-羟基前列腺素的分解代谢所致。 腺素脱氢酶 (15-PGDH)，前列腺素降解酶，本专利授权的主题 应用。正如资助中所描述的，我们意外地发现 15-PGDH 表达显着 老年小鼠和人类肌肉的增加。此外，我们的数据表明，15-PGDH 在 年轻的肌肉会导致衰老表型，并伴随着肌肉质量和功能的显着下降， 模仿肌肉减少症。父母资助的中心假设是，在衰老、衰老和炎症过程中， 保守细胞在肌肉微环境中积聚并表达 15-PGDH，从而降解 PGE2 和 PGD2， 并导致肌肉萎缩。因此，抑制衰老肌肉中的15-PGDH会增加PGE2和PGD2 脂质代谢并增强肌肉质量和力量。我们的目标是 (i) 阐明 PGE2 的作用和 PGD​​2 在骨骼肌稳态中的作用，(ii) 识别 15-PGDH 和前列腺素失调的细胞来源 (iii) 通过抑制 15-PGDH 恢复老化肌肉的功能和质量。家长资助目标 2 采用尖端的单细胞多重成像技术，称为 CODEX（CO-Detection by indEXing）。 CODEX 使我们能够在单个组织切片中同时解析多达 60 个标记。这一突破性的方法 odology 将能够确定衰老细胞是否包含 15-PGDH 的细胞来源，并允许我们 解决衰老肌肉中不同细胞类型之间的空间关系。每个 CODEX 经验 ment 会产生数 TB 的高分辨率图像，必须对这些图像进行去卷积并拼接在一起。我们有 开发了 3 个软件包（CRISP、HFCluster 和 SpaCE）来进行反卷积、缝合、聚类和注释 我们的 CODEX 数据并通过计算识别细胞类型之间的信号传导。我们提供此补助的目标是资助 一个熟练且专注的实验室助理，用于持续改进和维护该软件，具体来说 旨在改进用户界面，标准化数据输入格式，并提供对一系列多系统的兼容性 复杂的成像工作流程。这些改进不仅有助于我们实现赠款的第二个目标，而且 它们还将使我们开发的软件更加用户友好，并且易于肌肉生物学人士使用 和老龄化社区，以及 CODEX 和其他多重成像模式的所有用户。