ShEEP Request for NanoString GeoMx Digital Spatial Profiling System

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.