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.

此应用程序旨在获取 GeoMx™ 数字空间分析系统 (NanoString Technology, Inc.) 代表 BLRD/CSRD FRACTURE CURB 协作绩效审查计划 (CMRP) 和 San 弗朗西斯科退伍军人医疗中心 (SFVAMC) 骨骼生物学和生物力学 (SBB) 核心设施， 最初于 2003 年通过 BLRD 研究增强奖计划的资助成立，后来又成立了 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础和转化。 为 100 多个 VA、NIH 和 DoD 资助的内分泌学、骨科手术、 神经生物学、肾病学、放射学、肺病学、皮肤病学、免疫学和心胸外科， 并在更大的加州大学旧金山分校研究社区等范围内启用了许多新的合作项目 最近，该核心已在 2022 年被指定为全国 VA 站。 新获得的 FRACTURE CURB CMRP 的核心，其中包括 5 个以骨骼为中心的独立优点 审查 4 个 VA 站点的项目。 全面的转录组学和蛋白质组学分析技术对于理解 遭受疾病、药物影响的组织中转录和翻译调节的变化 治疗或基因操作的进展。 组织或分离细胞的液相色谱质谱 (LC-MS) 已填补了其中一些 然而，后者的技术缺乏描绘空间效应和细胞特异性的分辨率。 对基因表达的作用已被证明对细胞和/或细胞功能的调节至关重要 为了克服后者的缺陷，SFVAMC-SBB 核心成功地安装了最先进的- art GeoMx™ DSP 系统将于 2021 年实现高通量原位蛋白质组学和转录组学分析 经过几个月的强化方案后，以空间定义和细胞类型特异性的方式进行组织切片。 开发和测试后，DSP 蛋白质组和全转录组分析 (WTA) 分析服务 于 2021 年底陆续向当地 VA 和 UCSF 社区推出。对试营业的初步反应 在过去的 12 个月里，我们已经成功完成了 60 项新服务。 一些 DSP 分析结果已被用作拨款申请的初步数据，其中包括 5 项。 根据 FRACTURE CURB CMRP 和最近 3 项 NIH 申请获得优异评审 收到了可资助的分数（基于 2022 年机构支付线）。 DSP 服务在 2022 年秋季大幅增加，因此服务积压已 我们预计当前队列中的项目周转时间将延长至 6-8 周。 当 5 个 FRACTURE CURB 项目和 3 个即将授予的项目中提出的研究进一步延长时 鉴于设备安装和安装的劳动密集型和耗时性，NIH 项目正在如火如荼地进行。 协议开发后，我们打算将这些技术提供给其他全国 VA 研究人员 因此，我们将要求那些无法获得这项技术以进一步履行 ShEEP 精神的人。 GeoMx™ DSP 系统的另一个单元，可将当前的空间转录组和蛋白质组分析提高一倍 SFVAMC-SBB 核心的容量可实现 3 个具体目标。首先，我们将缩短 DSP 服务的周转时间。 其次，我们将投入 25% 的机器时间来开发协议。 用于骨骼中的 RNA 和蛋白质分析，并为 5 个活跃的和未来的额外项目提供所需的服务 第三，我们将开发工作流程和基础设施以实现 DSP 分析。 我们相信，通过实现这一目标，可以为无法获得这项技术的全国 VA 研究人员提供服务。 这3个目标，我们的核心DSP服务将大大增强VA整体研究资源。