Spatial multi-omics analysis has rapidly gained prominence in bioscience research. This technique allows for the comprehensive analysis of multiple molecular data types, such as transcriptome, epigenome, proteome, and metabolome within their native spatial context in tissues (1). In addition, it enables researchers to study the spatial organization and interactions of cells within tissues, providing a more detailed understanding of cellular heterogeneity and tissue microenvironments (2). Thus, it helps connect complex genetic, transcriptomics and proteomic changes with the cell type, interactions and pathophysiology of the tissue.
Some of the key advantages of this approach include
- Concurrent analysis of multiple molecular data types in the same tissue section (or adjacent tissue sections).
- Provides spatial information, enabling the study of cellular interactions and tissue architecture.
- The high resolution can resolve individual molecules at subcellular levels.
- It facilitates the discovery of novel biomarkers and effect of therapies in disease tissue
Key technologies that played a role in this revolution include.
- High throughput sequencing.
- Spatial proteomics using antibody-based probes.
- Image data analysis using deep learning approaches.
Given the advances in this area, a number of companies have developed tools and brought assays to the market. The most prominent include 10X genomics, Nanostring and Canopy biosciences.
| Platform Name/ Company/ Technology | Features | Applications |
| Visium HD/10X Genomics / Spatial transcriptomics | – whole transcriptome analysis – compatible with fresh frozen and FFPE tissue samples — ideal for discovery analysis | Cancer research, neuroscience, developmental biology |
| Xenium / 10X genomcis/ Spatial multi-omics | Offers preselect and custom panels of genes for spatial transcriptomics Ideal for detailed analysis at higher resolution Can be combined with H&E and immuno fluorescence imaging of tissues Multiplexing of tissues and tissue arrays can be performed on a single slide | Tumor biopsies, tumor microenvironment and normal tissue profiling |
| GeoMX / NanoString Technologies (Bruker) / Spatial transcriptomics & proteomics | – High-plex protein and RNA analysis, – compatible with FFPE and fresh frozen tissue samples | Oncology, immunology, neuroscience |
| ChipCytometry/ Canopy Biosciences (Bruker) / Spatial proteomics | – Quantitative measurement of multiple proteins at single-cell resolution – Uses a multiplex panel of fluorescently labeled antibodies – Compatible with FFPE and fresh frozen tissue samples |
In the following posts I will delve into the applications of spatial multi-omics and bioinformatics approaches to analyze and interpret such datasets.
References
- Park J et al, Genome Biology volume 23, Article number: 256 (2022)
- Keissling P et al, Genome Medicine volume 16, Article number: 14 (2024)
- Spatial genomics to study tumor evolution and sub clone Spatial genomics maps the structure, nature and evolution of cancer clones | Nature
- 10X Genomics: Visium Spatial Gene Expression https://www.10xgenomics.com/platforms/visium
- NanoString Technologies: GeoMx Digital Spatial Profiler https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/
- Canopy Biosciences: ChipCytometry https://canopybiosciences.com/geomx/