The study of life at the molecular level involves transcriptomics, which quantifies the messenger RNA (mRNA) molecules produced during gene expression. This process is fundamental to all biological function and disease. Traditional methods often require grinding up tissue, destroying the physical organization of cells. Spatial transcriptomics is a breakthrough that measures gene activity while preserving and recording the precise location of those measurements within an intact tissue sample. Nanostring provides platforms that enable researchers to map molecular profiles back onto the physical architecture of a cell or tissue.
Understanding Spatial Transcriptomics
Traditional methods like bulk RNA sequencing involve homogenizing an entire tissue sample to extract all the RNA. This yields an average measurement of gene activity across thousands of cells, but it loses the context of where those activities occurred. Tissues are highly organized structures where location dictates function, not random collections of cells.
Spatial transcriptomics captures the complete molecular profile—the list of active genes—and assigns exact positional coordinates to it. This creates a high-resolution map of the tissue, allowing researchers to see gene expression patterns that define distinct tissue microenvironments.
How Nanostring Measures Gene Expression
Nanostring employs two distinct, highly multiplexed technologies for spatial measurement, each optimized for different levels of resolution: the GeoMx Digital Spatial Profiler (DSP) and the CosMx Spatial Molecular Imager (SMI).
GeoMx Digital Spatial Profiler (DSP)
The GeoMx DSP utilizes a region-of-interest approach. It begins with a tissue section stained with fluorescent markers to highlight cellular structures and specific cell types. Researchers select areas of interest, which can be defined by morphology or the presence of certain marker proteins.
The gene expression probes used in GeoMx are bound to photocleavable unique molecular identifiers (UMIs), which are short segments of DNA that act as digital barcodes. When the selected region is illuminated with ultraviolet light, the light cleaves the barcodes only within that precise area. These released barcodes are then collected through a microcapillary tube and counted using a high-throughput method like next-generation sequencing or the nCounter system. This process assigns a highly multiplexed gene expression profile, potentially measuring over 18,000 RNA targets, back to the exact spatial coordinate of the sampled region.
CosMx Spatial Molecular Imager (SMI)
The CosMx SMI platform uses a cyclic imaging method to achieve true single-cell and even subcellular resolution. Tissue sections are hybridized with probes that target up to 1,000 RNA transcripts simultaneously.
The system uses a series of imaging and stripping cycles. A small subset of the probes is fluorescently labeled and imaged, and the signal is then erased before the next cycle begins. By recording the signal from each molecule across multiple cycles, the system builds a unique digital code for every RNA molecule. This allows its identity and precise location to be mapped back to the individual cell, providing a molecular census of gene activity with exceptional spatial granularity.
The Value of Spatial Data in Biology
Biological function is dependent on physical organization. Cells in a tissue constantly communicate with their immediate neighbors, forming complex cellular neighborhoods. Analyzing homogenized tissue obscures these cell-to-cell interactions and the signaling gradients that drive tissue behavior.
Mapping gene expression in space reveals the true heterogeneity that bulk sequencing averages out. For instance, a tumor might appear uniform under traditional analysis, but spatial profiling can differentiate between the malignant core, surrounding connective tissue, and infiltrating immune cells at the boundary. Understanding these localized communication pathways provides a more accurate picture of tissue function and disease progression.
Key Scientific Applications
Spatial transcriptomics provides a new lens for understanding complex biological states across diverse fields of life science.
In oncology, the technology is used to dissect the tumor microenvironment (TME), which includes cancer cells, immune cells, and blood vessels surrounding a tumor. Researchers map the precise location of immune cell subtypes, such as T-cells and macrophages, relative to cancerous cells. This helps identify markers for therapeutic resistance in specific regions of the tumor, which is necessary for designing targeted therapies.
Neuroscience utilizes spatial mapping to unravel the complexity of the brain, where distinct cell types are organized into intricate circuits. By tracking gene expression gradients, scientists create high-resolution atlases of cell types and their active genes across brain regions, such as the hippocampus or cortex. This is relevant for understanding neurodegenerative conditions, as it can reveal localized molecular changes and the specific cell populations affected early in the disease.
In developmental biology, spatial technology tracks the dynamic process of embryogenesis and organ formation. Researchers map the sequential activation of genes during the formation of complex structures like the heart or the limb bud. This has led to the identification of previously unknown embryonic cell types by correlating their unique gene expression signature with their exact location and timing.