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.

该应用程序是在ON上获取Geomx™数字空间剖面系统（Nanostring Technology，Inc。） 代表BLRD/CSRD断裂遏制协作功绩审查计划（CMRP）和SAN Francisco VA医疗中心（SFVAMC）骨骼生物学和生物力学（SBB）核心设施 最初是通过BLRD Research Enhancement奖计划的资助于2003年建立的，然后是 BLRD计划项目。该核心也是NIH（P30）核心中心的3个核心设施之一 肌肉骨骼生物学和医学（CCMBM）。这个自力更生的核心支持基本和翻译 在内分泌，骨科手术中进行100多个VA，NIH和DOD资助的项目的研究， 神经生物学，肾脏学，放射学，肺病学，皮肤病学，免疫学和心胸外科手术， 并在更大的UCSF研究社区中启用了许多新的合作项目等等 最近在全国范围内的VA车站。该核心在2022年被指定为分子和组织学 新授予的断裂路缘CMRP的核心，其中包括5个以骨架为中心的功绩 在4个VA站进行审查项目。 全面的转录组和蛋白质组学分析技术对于理解 在疾病，药物的组织中分别转录和翻译调节的变化 治疗或遗传操作。高通量合奏或单细胞RNA测序的进步 以及用于组织或孤立细胞的液相色谱质谱（LC-MS）填充了其中一些 技术空白。但是，后来的技术缺乏划定空间效应和细胞特异性的解决方案 对基因表达的作用，已被证明在细胞和/或细胞功能的法规中至关重要 分子水平。为了克服后者的陷阱，SFVAMC-SBB核心成功安装了最新的 2021年的Art Geomx™DSP系统允许在原位蛋白质组学和转录组中进行高通量 组织切片以空间定义和细胞类型特异性方式。经过几个月的密集协议 开发和测试，DSP蛋白质组学和整个转录组分析（WTA）分析服务是 在2021年底依次推出了当地的VA和UCSF社区。 这些新服务令人压倒。在过去的12个月中，我们成功完成了60个 DSP测定。一些结果已用作赠款应用程序的初步数据，包括5个 根据裂缝遏制CMRP和3个NIH申请的授予优异评论 获得了基本分数（基于2022机构的收费线）。鉴于最初的成功，请求 DSP服务在2022年秋天已经大大增加了 队列中当前项目的延长至6-8周。我们预计项目周转时间将会 当在5个断裂遏制项目中提出的研究和3个授予的研究时，进一步延长了 NIH项目如火如荼。考虑到设备设置的劳动力强度和耗时的本质 协议开发，我们打算使这些技术可用于其他弗吉尼亚州的研究人员 谁无法使用这项技术来进一步实现绵羊的精神。因此，我们将要求 GEOMX™DSP系统的另一个单元是当前空间转录组和蛋白质组学分析的一倍 SFVAMC-SBB核心的能力3个特定目标。弗里斯特，我们将减少DSP服务的周转时间 正在进行的项目不到3周。其次，我们将花费25％的机器时间来制定协议 用于骨骼中的RNA和蛋白质分析，并为5个活跃和未来的额外提供所需的服务 断裂遏制CMRP项目。第三，我们将开发工作流程和基础架构以启用DSP分析 为无法访问这项技术的全国VA研究人员提供服务。我们相信，通过实现 这三个目标，我们的核心DSP服务将大大增强整个VA研究资源。