A new 3D spatial transcriptomics platform at CNAG in Barcelona lets researchers study gene activity in tumours while keeping tissue structure intact. The first project focuses on colorectal cancer.
Spain has installed its first three-dimensional spatial transcriptomics platform at the Centro Nacional de Análisis Genómico (CNAG) in Barcelona. Only two other labs in Europe have this technology. It lets scientists map gene activity inside intact tissue samples, keeping their original 3D structure. The first project will study colorectal cancer, which remains one of the most common and aggressive tumours worldwide. The platform, called Pyxa and made by Stellaromics, is now up and running at CNAG, according to EFE.
Earlier genomic tools could show which genes were active and in which cells, but not where those cells sat within the tissue. The new system reveals the exact position of each cell, so researchers can see how cells interact and how their neighbourhoods affect tumour growth. This brings analysis closer to real biological conditions, which is key for understanding how tumours develop and interact with healthy tissue. EFE and CNAG confirm this is the first time such a 3D spatial transcriptomics platform has been used in Spain, with support from the Ministry of Science and the Generalitat de Catalunya.
The Pyxa platform allows analysis of tissue samples up to 20 times thicker than previous spatial genomics methods, preserving the three-dimensional architecture crucial for tumour research.
The CNAG platform can process tissue slices up to 20 times thicker than before. This means researchers can study a wider range of samples, including primary tumours, metastatic lesions, and healthy tissue, all while keeping their 3D context. Anna Pascual Reguant, who leads the Spatial Genomics Team at CNAG, says the technology gives researchers a close-up view of tumour development, capturing gene activation, RNA production, and protein translation in much greater detail. She notes this is essential for finding new biomarkers and developing more personalised therapies.
The platform also includes spatial translatomics, which maps ribosomes and tracks how RNA messages turn into proteins. By combining these layers of information, scientists can build a fuller picture of the biological processes behind disease. While the first project focuses on colorectal cancer, the technology could also be used to study immune disorders and chronic inflammatory diseases. EFE reports that the first research project using this platform is already underway and is focused on colorectal cancer, one of the most frequent and aggressive tumour types.
The installation cost nearly €500,000, funded by the European Union’s Next Generation programme as part of Spain’s Recovery, Transformation and Resilience Plan. The CNAG, with support from the Ministry of Science, Innovation and Universities and the Generalitat de Catalunya, will make the platform available to hospitals and research centres across Spain. The ability to create 3D molecular maps of tissues could speed up the discovery of new biomarkers and, over time, help develop more effective and personalised treatments.
The CNAG’s adoption of the Pyxa system from Stellaromics makes Spain only the third country in Europe to implement this advanced 3D spatial genomics technology, following significant institutional backing and a project budget of approximately €500,000.
Spain’s move to 3D spatial transcriptomics marks a shift in research priorities. By moving beyond flat tissue analysis, Spanish scientists are now able to study the real complexity of cellular architecture. This investment aims to close the gap between lab models and the unpredictable reality of human disease. The new platform at CNAG puts Spain in a stronger position to compete for discoveries that could change how tumours are understood and treated, with practical benefits for patients and the national health system.
