MRI: Acquisition of a digital spatial molecular profiler to advance research and training at a Hispanic-serving institution

PROJECT SUMMARY
 Interrogation of basic biological phenomena in the post-genome era relies heavily on high-throughput. sensitive technologies that provide molecular profiles of cells and tissues. High-dimensionality molecular measurements (e.g.. levels of mRNAs for many/all genes) can be readily accomplished in bulk samples and down to the single-cell level. producing comprehensive (???omics) profiles for given samples that address research needs. However. such techniques necessarily ignore the tissue localization of gene products in order to produce the high-dimensionality data. This means that a key challenge to interpreting the results of ???omics molecular profiles is understanding the spatial organization of gene product distribution in the source tissues. Currently. RNAs and proteins can be localized in situ with single-cell resolution using oligo probe and antibody-based approaches and detected with chromogen or fluorescent methods. but even under the best of circumstances are limited to relatively few detection channels (e.g.. 2-4) or involve tedious iterative detection (e.g.. 3 rounds of 4). To address this key challenge. we seek funding for NanoString???s GeoMx Digital Spatial Profiler (DSP). which affords the unique capacity for sensitive detection of >40 proteins or 96 RNAs (up to 1000-plex) in tissue sections. GeoMx DSP technology uses antibodies or RNA probes conjugated to photo-cleavable DNA oligos that are digitally quantified ex situ over a ???5 Log dynamic range in specific regions of interest (ROI) ranging in size from 700??m diameter to single cells (10??m) on tissue sections. This highly-multiplexed. spatial molecular imaging links complex tissue architecture with basic biological processes and enable experiments that cannot otherwise be pursued. This resource will be housed within the existing UTSA Genomics Core and will benefit investigators in multiple departments within two colleges at UTSA and colleagues around San Antonio.
 
 Intellectual Merit. Conventional quantitative gene expression measurements reflect bulk- and single-cell levels of mRNA or protein that ignore the tissue context of the molecular and cellular profiles. In general. these approaches fail to resolve the spatial relationships of cells with varying phenotypes within a complex tissue and necessarily disregard the biological roles of tissue architecture. It is now possible to measure levels of 10s-1000s of molecules (e.g.. RNAs. proteins) with as low as 10??m spatial resolution in tissue sections[17-22]. Emerging studies utilizing high-throughput spatial molecular analyses are amongst the most transformative in the biological sciences[23-27]. This proposal is for the GeoMx DSP which is a novel platform that leverages NanoString nCounter detection to enable spatially-resolved. digital characterization of proteins or mRNA in a highly-multiplexed assay. Consequently. up to 1000 molecules can be simultaneously and quantitatively evaluated in a single tissue section with single-cell resolution. high sensitivity and superior dynamic range. This instrument marries tissue imaging with high-throughput molecular profiling to enable novel experiments that would otherwise be essentially impossible to pursue. UTSA investigators will use this instrument to ask transformative questions in broad basic biology topic areas including germline stem cells. cerebral organoids. tissue engineering. neuronal synapses. arthropod vectors. and insect olfaction. 
 
 Broader Impacts. Acquisition of the GeoMx DSP system at UTSA as shared instrumentation will enable use of a state-of-the-art research instrument by scientists. engineers. and students at all levels (high-school. undergraduate and graduate). This will enhance the quality of research that can be performed at UTSA. which in turn. will increase competitiveness for research grants. ability to publish in high quality journals. and directly enhance opportunities for trainees to become productive researchers. It is especially important to provide underrepresented minority students with opportunities to perform research using state-of-the-art instruments. Since UTSA is a Hispanic-serving institution. with 64% of ~32.000 students hailing from underrepresented groups (~60% of STEM students). we have a unique opportunity to broaden participation of underrepresented groups at all levels. Indeed. several educational programs at UTSA are designed to attract and retain underrepresented students to scientific research and promote their interest in pursuing research careers. The GeoMx DSP system will be used by students in these programs and organized courses to afford them experience with cutting-edge technology. pique their interest in research. and maximize their marketability for careers in academic and industrial science. This resource will be integrated with existing teaching and outreach programs to promote education in a manner that uses real-world experimentation and discovery.