Spatial transcriptomics is a collection of technologies that enables the analysis of biological molecules within intact tissues or single cells at high resolution. By preserving the spatial organization of biomolecules inside tissues and cells, spatial transcriptomics allows researchers to gain a more complete understanding of complex biological systems. Some key techniques in spatial transcriptomics include spatial transcriptomics, spatial proteomics, and high-plex imaging mass spectrometry.

Spatial Transcriptomics

One of the most widely used spatial transcriptomics methods is spatial transcriptomics, which analyzes RNA expression profiles within tissues at subcellular resolution. In Spatial Omics, a tissue sample is placed on a solid support containing an array of molecular barcodes, with each barcode corresponding to a distinct spot on the array. Cells within the tissue lyse upon contact, releasing their RNA which then hybridizes to the barcodes. The barcode location reveals where in the tissue each RNA molecule originated from. By extracting and sequencing the barcoded RNAs, researchers gain insights into regional patterns of gene expression throughout the entire tissue sample. Spatial transcriptomics has been applied to study many different tissue types and disease states. For example, it has uncovered previously unknown molecular domains within the brain as well as new subtypes of breast cancer correlated with spatial gene expression patterns.

Imaging Mass Cytometry

Imaging mass cytometry, sometimes called high-parameter tissue imaging, utilizes mass cytometry to quantitatively analyze the abundance and spatial organization of dozens of proteins and post-translational modifications within intact tissues at subcellular resolution. In this technique, tissue samples are labeled with metal-conjugated antibodies against various biomarkers of interest and ablated using a laser. The ionized metal tags are then identified and quantified using a mass cytometer, generating a high-dimensional image of biomarker expression. When applied to clinical samples, imaging mass cytometry has revealed insights into tumor microenvironments, disease progression models, and predictive markers. It also enables discovery of new cell types and characterization of their protein fingerprints within native tissue contexts.

Spatial Proteomics

Similar to Spatial Omics, spatial proteomics investigates regional protein expression profiles within tissues. However, while spatial transcriptomics analyzes RNA which provides an indirect view of cellular states, spatial proteomics directly profiles the proteome—the actual set of proteins expressed. Technologies for spatial proteomics include methods like mass spectrometry imaging, which maps the distribution of proteins directly from tissue slices without needing to isolate cells or disaggregate tissues. Mass spectrometry imaging works by bombarding tissue sections with laser pulses that desorb and ionize proteins from the sample surface so their masses and spatial locations can be measured. When combined with immuno-based extraction techniques, spatial proteomics promises to advance our understanding of protein behaviors at subcellular scales.

Integrative Approaches and Applications

The greatest potential of spatial transcriptomics lies in combining different techniques to build multi-omic profiles of tissues with single-cell resolution. For instance, spatial transcriptomics can be paired with imaging mass cytometry to correlate regional gene expression patterns with corresponding protein signatures. Such integrative approaches provide a more comprehensive view of the intricate biological interplay between different molecular layers from RNA to proteins within their native spatial contexts.

Spatial Omics is also being applied across various fields to address important biological and medical questions. In neuroscience, it helps decipher neuronal connectivity and local circuit architectures in the brain. In immunology, it enhances understanding of immune cell behaviors and interactions within lymphoid tissues. For cancer research, spatial transcriptomics reveals invaluable insights into tumor heterogeneity, microenvironment influences, and biomarkers correlated with progression and therapy responses. With rapid technological advances, spatial transcriptomics promises to transform our ability to investigate the operational logic of living systems at their fundamental cellular scales.

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