ShEEP Request for NanoString GeoMx Digital Spatial Profiling System

ShEEP 请求 NanoString GeoMx 数字空间剖析系统

• 批准号: 10741001
• 负责人: Wenhan Chang
• 金额: --
• 依托单位: VETERANS AFFAIRS MED CTR SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-03-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10741001
• 关键词: Adherence; Adopted; Animal Model; Animals; Antibodies; Applications Grants; Atlases; Award; Bar Codes; Basic Science; Biological; Biological Assay; Biology; Biomechanics; Biomedical Research; Biopsy; Bone Diseases; Brain; Brain Diseases; Brain Stem; Cardiovascular Diseases; Cell Separation; Cell physiology; Cells; Collaborations; Communities; Consumption; Core Facility; Data; Dedications; Dermatology; Detection; Disease; Disease Progression; Endocrine System Diseases; Endocrinology; Equipment; Fluorescence; Formalin; Fracture; Freezing; Funding; Future; Gene Expression; Genes; Glass; Goals; Histologic; Human; Immunology; In Situ; Infrastructure; Institution; Islets of Langerhans; Kidney; Kidney Diseases; Lung; Lung diseases; Medical center; Medicine; Molecular; Mus; Musculoskeletal; Nature; Nephrology; Neurobiology; Nucleotides; Operative Surgical Procedures; Orthopedic Surgery; Paraffin Embedding; Parathyroid gland; Pathologic; Pathway interactions; Patients; Performance; Pharmacotherapy; Population; Program Reviews; Proteins; Proteomics; Protocols documentation; Pulmonology; RNA; Radiology Specialty; Reagent; Research; Research Personnel; Resolution; Resources; Sampling; San Francisco; Services; Sheep; Skeleton; Slide; Specimen; System; Techniques; Technology; Teleconferences; Testing; Time; Tissues; Training; Transcript; Transcriptional Regulation; Translational Regulation; Translational Research; United States National Institutes of Health; bone; cDNA Probes; cell growth regulation; cell type; cost; data submission; digital; experimental study; falls; genetic manipulation; interest; liquid chromatography mass spectroscopy; manufacturing systems; meter; nano-string; next generation sequencing; programs; protein expression; protein profiling; protocol development; response; sequencing platform; single-cell RNA sequencing; skeletal; skin disorder; success; therapy development; tool; transcriptomic profiling; transcriptomics; translational study; virtual laboratory

This application is to acquire a GeoMx™ Digital Spatial Profiler System (NanoString Technology, Inc.) on behalf of the BLRD/CSRD FRACTURE CURB Collaborative Merit Review Program (CMRP) and the San Francisco VA Medical Center (SFVAMC) Skeletal Biology and Biomechanics (SBB) Core facility, which was originally established in 2003 through funding of BLRD Research Enhancement Award Program and later a BLRD Program Project. This core is also one of 3 core facilities in the NIH (P30) Core Center for Musculoskeletal Biology and Medicine (CCMBM). This self-reliant Core had supported basic and translational research for more than 100 VA, NIH, and DoD-funded projects in endocrinology, orthopedics surgery, neurobiology, nephrology, radiology, pulmonology, dermatology, immunology, and cardiothoracic surgery, and enabled numerous new collaborative projects within the greater UCSF research community and more recently nationwide VA stations. This Core has been designated in 2022 as the Molecular and Histological Core for the newly awarded FRACTURE CURB CMRP, which includes 5 independent skeleton-centric Merit Review projects across 4 VA stations. Comprehensive transcriptomic and proteomic profiling techniques are essential for understanding of changes in transcriptional and translational regulation, respectively, in tissues subjected to diseases, drug treatments, or genetical manipulations. Advances in high-throughput ensemble or single-cell RNA sequencing and liquid chromatography Mass Spectroscopy (LC-MS) for tissues or isolated cells have filled some of these technical gaps. However, latter technologies lack resolution to delineate spatial effects and cell-specific actions on gene expression that have been proven critical in regulations of cellular functions at cellular and/or molecular levels. To overcome the latter pitfalls, the SFVAMC-SBB core successfully installed a state-of-the- art GeoMx™ DSP System in 2021 to permit high-throughput in situ proteomic and transcriptomic profiling in tissue sections in a spatially-defined and cell type-specific manner. After several months of intensive protocol development and testing, the DSP proteomic and whole transcriptomic assay (WTA) profiling service were sequentially rolled out to local VA and UCSF community in late 2021. Initial responses to the soft opening of these new services have been overwhelming. In the past 12 months, we have successfully completed 60 DSP assays. Some of the results have been used as preliminary data for grant applications, including 5 awarded Merit Reviews under the FRACTURE CURB CMRP and 3 NIH applications which have recently received fundable scores (based on 2022 institutional paylines). Given the initial successes, requests for the DSP services have substantially increased in the Fall of 2022 as such that the service backlog has been extended to 6-8 weeks for the current projects in the queue. We anticipate the project turnaround time will be further lengthened when the studies proposed in the 5 FRACTURE CURB projects and the 3 to-be-awarded NIH projects are in full swing. Given the labor-intense and time-consuming natures of equipment setup and protocol development, we intend to make these technologies available to other nationwide VA researchers who do not have access to this technology to further fulfill the spirit of ShEEP. We will, therefore, request another unit of the GeoMx™ DSP System to double the current spatial transcriptomic and proteomic profiling capacity at SFVAMC-SBB Core for 3 specific goals. Frist, we will reduce the turnaround time of DSP service to less than 3 weeks for ongoing projects. Second, we will dedicate 25% of machine time to develop protocols for RNA and protein profiling in bone and provide the needed services to the 5 active and future additional FRACTURE CURB CMRP projects. Third, we will develop workflow and infrastructure to enable DSP profiling services to nationwide VA researchers who do not have access to this technology. We believe, by fulfilling these 3 goals, our core DSP services will greatly enhance the VA research resources as a whole.

此应用程序将收购GeoMx™数字空间剖面仪系统(纳米弦技术公司)在……上面 代表BLRD/CSRD裂缝遏制协作功绩审查计划(CMRP)和SAN 旧金山退伍军人医学中心(SFVAMC)骨骼生物学和生物力学(SBB)核心设施， 最初成立于2003年，通过资助BLRD研究促进奖计划和后来的 BLRD计划项目。该核心设施也是美国国立卫生研究院(P30)核心中心的3个核心设施之一 肌肉骨骼生物学与医学(CCMBM)。这个自力更生的核心支持基本和翻译 为退伍军人事务部、美国国立卫生研究院和国防部资助的100多个内分泌学、整形外科、 神经生物学、肾病学、放射学、肺病学、皮肤科、免疫学和心胸外科， 并在加州大学旧金山分校的研究社区内促成了许多新的合作项目，以及更多 最近在全国各地的退伍军人事务部。这一核心已于2022年被指定为分子和组织学 新授予的骨折遏制cMRP的核心，包括5个独立的以骨骼为中心的优点 审查4个退伍军人管理局的项目。 全面的转录和蛋白质组学分析技术对于理解 在受疾病、药物影响的组织中，转录和翻译调控的变化 治疗，或者说基因操作。高通量集成或单细胞RNA测序研究进展 而组织或分离细胞的液质联用(LC-MS)已经填充了其中的一些 技术差距。然而，后一种技术缺乏描述空间效应和特定细胞的分辨率 已被证明在细胞和/或细胞功能调节中起关键作用的基因表达的作用 分子水平。为了克服后一种缺陷，SFVAMC-SBB核心成功安装了最新的 ART GeoMx™数字信号处理器系统将在2021年实现高通量的原位蛋白质组和转录图谱分析 以空间定义和细胞类型特定的方式进行组织切片。经过几个月的密集礼仪 开发和测试，数字信号处理器蛋白质组和整体转录分割分析(WTA)分析服务 于2021年底在当地退伍军人事务部和加州大学旧金山分校社区相继推出。对软开放的初步反应 这些新服务令人应接不暇。在过去的12个月里，我们成功地完成了60 数字信号处理器分析。其中一些成果已用作赠款申请的初步数据，包括5项 根据裂缝控制cMRP和最近获得的3项NIH申请获得了功绩审查 获得可资助的分数(基于2022年的机构支付线)。鉴于最初的成功，对 数字信号处理器服务在2022年秋季大幅增加，因此服务积压 目前正在排队的项目延长到6-8周。我们预计项目的周转时间将是 进一步延长了5个裂缝遏制项目和3个待授予项目中提出的研究 美国国立卫生研究院的项目正在如火如荼地进行。鉴于设备设置和安装的劳动强度和耗时特性 协议开发，我们打算将这些技术提供给其他全国性的退伍军人管理局研究人员 那些没有获得这项技术的人，进一步履行了绵羊的精神。因此，我们将要求 GeoMx™数字信号处理系统的另一个单位，将把目前的空间转录和蛋白质组图谱增加一倍 SFVAMC-SBB核心的3个特定目标的容量。首先，我们将减少DSP服务的周转时间 对于正在进行的项目，可以在3周内完成。其次，我们将花费25%的机器时间来开发协议 对骨骼中的RNA和蛋白质进行分析，并为5个现役和未来的其他 裂解遏制cmrp项目。第三，我们将开发工作流和基础架构以启用DSP分析 为无法使用这项技术的全国退伍军人管理局研究人员提供服务。我们相信，通过履行 这3个目标，我们的核心DSP服务将极大地提升整个退伍军人管理局的研究资源。