Advancing Tissue Mapping: Spapros Refines Spatial Transcriptomics for Biological Insights
A team led by Prof. Fabian Theis, Director of the Computational Health Center and the Institute of Computational Biology at Helmholtz Munich, has developed Spapros, a computational pipeline set to transform the design of spatial transcriptomics experiments. By improving gene selection and probe design, Spapros enhances the understanding of cellular diversity within complex tissue structures, marking a significant advancement in the field of spatial biology.
Unlocking Tissue Architecture Through Gene Expression Mapping
Spatial transcriptomics is a technology that allows scientists to study gene expression within the context of tissue architecture. This enables the mapping of cellular interactions and the discovery of how tissues are organized on a molecular level. The success of spatial transcriptomics experiments depends on carefully selecting genes tailored to the tissue of interest. Spapros overcomes this challenge by optimizing gene set selection under precise probe design constraints, allowing researchers to focus on the most relevant genes while accounting for spatial gene expression variations and ensuring the accurate identification of individual cell types at single-cell resolution.
“Spapros significantly enhances the capabilities of spatial transcriptomics,” says Louis Kümmerle, the study’s first author. “It elevates our ability to explore cellular heterogeneity and tissue-specific gene expression patterns.” Co-first author Dr. Malte Lücken elaborates: “By optimizing gene selection while considering probe design limitations, Spapros enables high-resolution mapping of cellular interactions, which will be crucial for understanding the complexities of tissue environments.”
Transforming Precision Medicine with High-Resolution Insights
One of Spapros’ most remarkable features is its ability to simultaneously achieve two critical objectives: identifying different cell types within a tissue sample and detecting spatial variations in gene expression. This dual optimization has the potential to transform the understanding of tissue organization, cellular communication, and intercellular interactions—key areas for exploring development, disease progression, and therapeutic targeting.
Spapros holds the promise of accelerating the advancement of precision medicine. By providing unprecedented insights into the molecular drivers of disease, the tool could enable the development of more effective, targeted therapies that take into account the intricate spatial and cellular context of disease environment.
Original publication
Kuemmerle et al. (2024): Probe set selection for targeted spatial transcriptomics, Nature Methods, DOI: 10.1038/s41592-024-02496-z
