Inside the First Practical Playbook for Spatial Transcriptomics

Technological development is key to improving the way hematologic cancer is diagnosed and treated. With this vision, the Josep Carreras Leukemia Research Institute is committed to the creation and implementation of new systems that push the limits of omics technologies. Spatial Transcriptomics, the intersection of genomics, transcriptomics, and advanced microscopy, is one of them.

Spatial transcriptomics allows researchers to understand what each cell in a histological section is doing compared to the others. Indeed, one can literally see which molecular markers are present in each cell of a biopsy, in their actual position, and gain a much more detailed understanding of the tumor's structure. This deeper understanding will allow clinical researchers to develop new, ultra-personalized therapeutic strategies, unthinkable until now.

However, this methodology is so recent that a global standard is still lacking, seriously hindering the reproducibility of experiments, a pillar of the scientific system. To address this issue, the Spatial Biology team at the Josep Carreras Institute, led by Dr. Eduard Porta and Dr. Daniela Grases, has condensed their experience after more than 1,000 analyzed samples into the first practical guide to Spatial Transcriptomics, recently published in the journal Trends in Biotechnology.

According to Grases, “The rapid growth of Spatial Transcriptomics means that many groups are facing practical obstacles: platform choice, sample quality, sequencing depth, etc.” Therefore, the team offers advice on how to correct common errors and “integrate the methodology in a robust and reproducible manner.”

The publication covers all the key elements of a Spatial Transcriptomics experiment, such as defining the biological question, the optimal number of samples, selecting the appropriate technological platform, and how staff should process and interpret the data.

In Grases's opinion, the future of Spatial Transcriptomics is "its integration into clinical workflows, as another element in hospital protocols for routine pathology, to facilitate patient diagnosis." This is an ambitious future, given that this technology is still under development and its implementation is currently economically unviable due to the costs of materials and the need for highly specialized personnel.

Thanks to the development of new analytical tools, much more powerful than those currently used, we are on the verge of a revolution in the diagnosis of hematological cancers. Diagnosis will be faster, more accurate, and more personalized, key points that the Josep Carreras Leukemia Research Institute embraces to achieve its founding mission: to end blood cancer for all patients.

Reference: Grases D, Porta-Pardo E. A practical guide to spatial transcriptomics: lessons from over 1000 samples. Trends Biotechnol. 2025:S0167779925003579. doi: 10.1016/j.tibtech.2025.08.020

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