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.

项目摘要 肌肉减少症或与年龄相关的肌肉萎缩，折磨了老年人的15％，严重降低了生活质量和 发病率和死亡率提高。我们的总体目标是阐明肌肉减少症的新型因果机制 并利用这些知识来改善老化的肌肉功能。我们建议利用我们的发现 老年肌肉中前列腺素PGE2和PGD2的降低是由15-羟基刺激的分解代谢引起的 Glandin脱氢酶（15-PGDH），Prostaglandin降解酶，这是父母授予的主题 应用。如赠款中所述，我们提出了一个意外的发现，即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，在 年轻的肌肉诱导衰老表型，伴随着肌肉质量和功能明显降低， 模仿肌肉减少症。父母赠款的核心假设是，在衰老，衰老和炎症期间 托里细胞积聚在肌肉微环境中，并表达15-PGDH，降低了PGE2和PGD2， 并导致肌肉浪费。因此，抑制15-PGDH的老年肌肉将增加PGE2和PGD2 脂质代谢产物和增强肌肉质量和力量。我们的目的是（i）阐明PGE2和 骨骼肌稳态中的PGD2，（ii）识别15-PGDH和前列腺素失调的细胞来源 在老年肌肉中，（iii）通过抑制15-PGDH来恢复老化的肌肉功能和质量。父母赠款目标2 采用一种称为codex的尖端的单个单元多路复用成像技术（通过索引进行共检测）。 Codex允许我们在单组织部分同时解决多达60个标记。这次突破 那言将确定衰老细胞是否包含15-PGDH的细胞来源，并允许我们 解决老年肌肉中存在的各种细胞类型之间的空间关系。每个法典经验 MENT产生的高分辨率图像必须进行反应和缝合在一起。我们有 开发了3个软件包（清晰，HFCLUSTER和SPACE），以切换，针迹，群集和注释 我们的法典数据和计算在细胞类型之间识别信号传导。我们的这项补充的目标是资助 熟练而专用的实验室助理，以继续改进和维护该软件，指定 cally以改善用户界面，标准化数据输入格式，并为一系列多种多样提供兼容性 悬式成像工作流程。这些改进不仅将帮助我们实现赠款的第二个目标，而且还可以 他们还将使我们开发的软件更加用户友好，很容易访问肌肉生物学 以及老化的社区，以及所有Codex和其他多重成像方式的用户。