The 10x Xenium In Situ platform is a method of spatial transcriptomics, the study of gene activity within a tissue’s physical context. This technology allows scientists to visualize and quantify the expression of thousands of RNA molecules directly inside a preserved tissue section. By providing a high-resolution, molecular map, Xenium reveals the exact location of active genes with subcellular precision. This capability moves research beyond simply listing molecular components to understanding how they are organized and interact within their native environment.
Why Location Matters in Biology
For decades, the standard approach to studying tissue involved homogenizing it to extract molecular contents for analysis. While this bulk method accurately measured average gene activity across the entire sample, it destroyed the delicate tissue architecture, losing all information about the physical arrangement of cells. Researchers were left with a “parts list” of cells and molecules without the assembly manual, making it impossible to determine how cellular interactions governed tissue function or disease progression.
Biology is inherently three-dimensional, and cell behavior is heavily influenced by their immediate surroundings and neighbors, forming cellular neighborhoods. For instance, in a tumor, the response of a cancer cell to therapy can depend entirely on whether it is adjacent to an immune cell, a blood vessel, or a stromal cell. Understanding these complex relationships, known as the tumor microenvironment, requires preserving the tissue structure while simultaneously achieving molecular detail. Spatial transcriptomics, therefore, provides the necessary context to observe cell-to-cell communication and define the precise molecular signatures of these functional neighborhoods.
Visualizing Genes: How Xenium Works
The Xenium process begins with a preserved tissue section, typically a fresh frozen or formalin-fixed paraffin-embedded (FFPE) sample, which is placed onto a specialized slide. The sample is then prepared to make the RNA targets accessible to specialized detection reagents while maintaining the overall tissue structure. The core of the technology involves a set of fluorescently labeled molecular probes introduced to the tissue. These probes are designed to bind specifically to the RNA molecules of interest.
Once a probe successfully binds to its target RNA, it is ligated and then amplified through a process called rolling circle amplification, which creates a bright, localized signal. This localized signal functions as a unique molecular barcode that tags the exact location of the original RNA molecule. The Xenium instrument then conducts cyclical rounds of fluidic delivery and high-resolution imaging. In each cycle, a different set of fluorescent reporters is introduced, binding to and decoding a portion of the molecular barcode.
By combining the images from multiple cycles, the system computationally “reads” the complete barcode sequence at each spot, identifying the specific gene and its precise coordinates within the tissue section. This iterative imaging and decoding process allows the platform to simultaneously map the expression of up to 5,000 different genes across the entire tissue section. The final output is an image-based map where individual transcripts are pinpointed.
Transforming Medical Research
The ability to map gene activity in context has opened new avenues in various medical research fields. In oncology, Xenium is leveraged to dissect the tumor microenvironment, allowing researchers to precisely locate and profile different cell types, including cancer cells, immune cells, and stromal cells. This spatial understanding is used to investigate mechanisms of immune evasion. Pinpointing these cellular interactions is instrumental for predicting patient response to immunotherapies and developing next-generation treatments.
In neuroscience, the technology is employed to map the complex circuitry of the brain, identifying the specific cell types and states that define functional regions. By visualizing which genes are active in different neuronal populations, scientists gain insight into the molecular basis of neurological disorders. Developmental biology uses Xenium to track the intricate process of cellular differentiation in developing organs. Researchers can observe how cell fates are decided based on their location and interactions, mapping the molecular programs that drive the formation of complex tissues.
The Leap in Resolution
Xenium represents a major advance in spatial biology due to its high level of detail and throughput. Earlier spatial methods were often limited to profiling a smaller number of genes or provided only single-cell resolution, meaning they could identify which cell expressed a gene but not where within the cell the RNA was located. In contrast, Xenium provides subcellular resolution, allowing researchers to see individual transcript molecules and precisely map their location relative to the cell nucleus and membrane.
This subcellular detail is significant because it allows for the analysis of intracellular organization, such as how mRNA molecules are trafficked and localized within a neuron or other large cell. Furthermore, Xenium offers a high-plex capability, simultaneously profiling up to 5,000 genes. This combination of high gene throughput and subcellular resolution distinguishes Xenium from older technologies, like single-cell RNA sequencing, which loses the spatial context entirely by dissociating the tissue.