Collaborating for precision: bringing spatial transcriptomics to the clinic

Collaborating across disciplines is often highlighted as a key ingredient for scientific progress. At SciLifeLab, this type of collaboration is a daily occurrence. A perfect example is the collaboration between SciLifeLab researchers Joakim Lundeberg at KTH and Camilla Engblom at Karolinska Institutet (KI). In a recent commentary article in Nature Biotechnology they talk about how spatial transcriptomics-based technologies can be brought to the clinic and the benefits of doing so.

These tools allow the mapping of cellular and molecular components of tumors with high precision. Revealing how different cell types interact within their natural tissue context.

One example is Spatial VDJ, a method developed at SciLifeLab in a collaboration between Engblom’s post-doc lab (Frisen lab, KI) and the Lundeberg Lab (KTH). Spatial VDJ tracks B and T cell receptors within tissues (see SciLifeLab article from 2023 and Engblom/Thrane/Lin et al Science 2023). It essentially acts as a molecular “GPS,” allowing researchers to map immune cell lineages and track how these cells move between tissues like tumors and lymph nodes. This kind of detailed mapping may reveal which immune cells are actively targeting tumors and how these interactions change over time, providing insights into treatment responses and resistance.

Clinical adoption of spatial transcriptomics requires both resources and experience

While these technologies are becoming more robust and commercially available, they still require significant resources. Such as, advanced laboratory equipment and substantial data analysis. But the potential is there. Spatial transcriptomics-based technologies could offer tangible impact for cancer patients. Including discovering new therapeutic targets, biomarkers or predictive information for patient outcome.

Putting these tools into routine clinical practice will require a lot of effort. Lundeberg and Engblom say we could learn from previous experiences, from when whole genome sequencing was brought to the clinic in Sweden. It’s not only possible to achieve, but highly beneficial to put complex technologies into the clinic.

DOI: 10.1038/s41587-025-02596-x

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