The Vanderbilt Mass Spectrometry Research Center’s Imaging Mass Spectrometry Core is expanding its advanced imaging capabilities with the addition of the 10x Genomics Xenium spatial transcriptomics platform, a powerful new service that enables researchers to visualize and quantify gene expression within intact tissue at single-cell resolution. The technology will enable Vanderbilt investigators to explore biological questions that have been difficult to address using conventional transcriptomic approaches.
The Xenium platform combines highly sensitive RNA detection with preserved tissue architecture, allowing investigators to precisely map where genes are expressed while maintaining the biological context of cells and their surrounding microenvironment. The technology supports applications across cancer, immunology, neuroscience, kidney biology, diabetes, developmental biology, and many other areas of biomedical research.
“Xenium offers subcellular resolution with high sensitivity for a broad array of tissue types,” said Melissa Farrow, research associate professor of cell and developmental biology and Xenium team lead for the MSRC imaging core. “The flexibility to design custom panels or leverage commercially available options makes experimental design straightforward. The outputs are user friendly, and 10x’s software provides stunning visuals.”
Unlike traditional transcriptomic approaches that require dissociating tissue into single-cell suspensions, Xenium preserves spatial relationships between cells, making it possible to identify cell types, characterize cellular neighborhoods, and study cell-cell interactions in their native environment. Researchers can simultaneously analyze hundreds to thousands of targeted genes in various kinds of tissue samples, including formalin-fixed paraffin-embedded, fresh frozen, and optimal cutting temperature-embedded.
The technology opens new opportunities for investigators seeking to better understand complex biological systems.
“Profiling of the transcriptome in situ opens up new frontiers in biomedical research,” Farrow said. “The ability to localize transcriptional responses to specific cell types adds a layer of insight not previously attainable using other platforms. This is especially intriguing when studying heterogeneous samples containing rare cell types or immune infiltrates where their signatures would normally be lost. Now they are easily detectable.”
The addition of spatial transcriptomics further strengthens the MSRC imaging core’s growing portfolio of advanced imaging technologies.
“The MSRC imaging core is now positioned to provide high-resolution imaging of all biomolecules,” Farrow said. “With the onboarding of spatial transcriptomics, we can now offer a fully multimodal imaging pipeline to profile all analytes.”
Xenium data can also be integrated with complementary imaging modalities available through the core, including imaging mass spectrometry, multiplex immunofluorescence, and conventional stained microscopy. This multimodal approach enables investigators to generate a more comprehensive view of tissue biology by combining molecular and spatial information from multiple platforms.
The MSRC imaging core team brings extensive expertise in developing and integrating spatial transcriptomics workflows through participation in major National Institutes of Health initiatives, including the Kidney Precision Medicine Project and the Human BioMolecular Atlas Program.
“Our experience operating within large consortia has taught us invaluable lessons about visualization and integration across data types,” Farrow said. “While our platform provides robust profiling of samples, investigators often have measurements that need to be integrated to provide a comprehensive analysis. Our collaborations across groups and sample types have positioned us to effectively integrate all data types.”
Investigators are encouraged to engage with the MSRC imaging core early in the planning process whether they are developing a pilot project or designing a large-scale study. Core staff can provide guidance on experimental design, tissue selection and preparation, panel design, workflow optimization, and data analysis strategies to help ensure successful experiments.
“Our personnel are ready and willing to assist in tailoring experiments to each investigator’s needs,” Farrow said.
To learn more about Xenium spatial transcriptomics or to schedule a consultation with the imaging core, contact Melissa Farrow.