Traditionally, biologists have been constrained by analytical techniques that sacrifice spatial information, reducing tissues to a mixture of cells where location is lost. This limitation has hindered our comprehension of how cellular neighborhoods influence physiological and pathological states. The emergence of spatial transcriptomics and proteomics now permits high-resolution mapping of RNA and protein molecules inside intact tissues, lending an unprecedented spatial dimension to molecular profiling. Spatial transcriptomics reveals the location-specific gene expression patterns, whereas spatial proteomics identifies the distribution and interplay of functional proteins, thereby elucidating the molecular choreography underlying cellular behavior.

IRB Barcelona’s new platform uniquely integrates multiple core technologies encompassing spatial genomics, proteomics, histopathology, advanced microscopy, and bioinformatics into a seamless workflow designed to generate comprehensive spatially resolved molecular maps. This integrated approach not only enables rigorous sample processing and data acquisition but also incorporates sophisticated computational tools to interpret multilayered datasets. By combining these modalities, researchers can create detailed molecular atlases that reveal how distinct cell types and molecular states coalesce to maintain tissue homeostasis or drive disease progression.

The launch of this platform reflects IRB Barcelona’s longstanding commitment to pioneering technologies that push the boundaries of molecular biology. Over the last two decades, the institute has been a trailblazer in genomic microarrays and single-cell gene expression profiling from minimal samples, establishing itself as a reference center of excellence. Their prior innovations in proteomics, including advanced top-down analysis techniques, and the adoption of light-sheet microscopy for three-dimensional tissue imaging, have laid the foundation for this next leap forward into spatial biology.

This powerful platform facilitates detailed investigation of a wide array of diseases characterized by complex tissue architecture, including cancer, neurodegenerative disorders, cardiovascular ailments, and immune dysfunction. For instance, in oncology, spatial omics can elucidate the cellular heterogeneity within tumors, map the spatial distribution of resistant cell subpopulations, and unravel cellular interactions that influence tumor microenvironment and therapy response. Such spatially-informed molecular data are critical for understanding why certain therapies fail and for identifying novel, spatially targeted therapeutic interventions.

The uniqueness of IRB Barcelona’s initiative lies not only in its technological sophistication but also in its multidisciplinary and collaborative framework. By coordinating expertise from multiple core facilities, the platform delivers an end-to-end pipeline that spans from sample preparation to deep computational analysis. This holistic integration ensures scientific robustness, reproducibility, and the generation of high-resolution spatial datasets that can be cross-compared across studies and over time, accelerating discovery and translational applications.

Moreover, this platform serves as a national hub and a collaborative nexus, opening its infrastructure to the wider scientific community, including academic institutions, hospitals, and industry collaborators. Such open access fosters synergy, drives innovation, and broadens the impact of spatial omics technologies across Spain and internationally. It is envisaged that this initiative will significantly propel precision medicine, enabling patient-specific molecular diagnostics and the development of personalized therapeutic strategies grounded in spatial cellular biology.

A critical aspect of this platform is its integration of advanced computational methods. Spatial omics generates complex, multilayered data that requires novel bioinformatics algorithms to align and co-analyze transcriptomic, proteomic, and phenotypic information within spatial coordinates. IRB Barcelona’s bioinformatics teams are developing and implementing these sophisticated pipelines to construct multidimensional molecular landscapes of tissues. Such atlases not only enhance our understanding of tissue organization and function but also provide invaluable resources for hypothesis generation and mechanistic studies.

The platform is also a testament to successful collaborative funding efforts, having been supported by Spanish and Catalan governmental bodies, Next Generation funds, and prominent foundations such as the Spanish Association Against Cancer, La Caixa Foundation, and the BBVA Foundation. This financial backing underscores the importance and potential impact of spatial omics on public health and biomedical research.

Looking ahead, the integration of spatial omics with other emerging technologies such as single-cell multi-omics and advanced imaging modalities promises to unlock even deeper insights into cellular ecosystems. The ability to spatially resolve multiple biomolecular layers simultaneously will provide a holistic view of biological systems, bridging the gap between molecular detail and tissue physiology. This comprehensive understanding is essential to confront the complexities of human diseases and to develop innovative treatment paradigms.

By enabling researchers to ‘see biology in place’, IRB Barcelona’s Spatial Omics Platform is not merely an incremental technological upgrade but represents a paradigm shift in life sciences. It turns the metaphor of the body as a city into a tangible reality, where cells, genes, and proteins are mapped with neighborhood precision. This spatial perspective is critical for decoding cellular behavior within the rich tapestry of tissue architecture and microenvironmental influences, ultimately advancing both basic biology and precision medicine.

In sum, this pioneering facility positions IRB Barcelona at the forefront of spatial biology, empowering scientists to unlock the spatial dimension of molecular biology that has remained elusive until now. The resulting knowledge is expected to transform our approach to diagnosing, treating, and preventing diseases with unprecedented accuracy and specificity, heralding a new era in biomedical research.

Subject of Research: Spatial Omics, Spatial Transcriptomics, Spatial Proteomics, Integrated Molecular Profiling

Article Title: IRB Barcelona Launches Spain’s First Integrated Spatial Omics Platform Revolutionizing Molecular Mapping in Tissues

News Publication Date: 9 February 2026

Image Credits: IRB Barcelona

Keywords: Genomics, Proteomics, Microscopy, Cancer, Bioinformatics, Health and Medicine

A pioneering team at IRB Barcelona has developed DiffInvex, an innovative computational framework designed to dissect this dynamic evolutionary landscape. By tracking shifting evolutionary pressures on genes as healthy cells morph into malignant tumours and subsequently adapt under chemotherapy assault, DiffInvex offers a powerful lens through which to understand, and ultimately challenge, the genetic strategies tumours exploit to resist drugs.

Harnessing data from over 11,000 human genomes—including both healthy and cancerous tissue samples from around 30 distinct tissue types—DiffInvex maps the mutational paths tumours embark upon as they develop and respond to treatment. This groundbreaking research, recently published in Nature Communications, illuminates the “escape routes” cancers take to overcome chemotherapy, pinpointing key genes whose mutations are selected for during these critical phases.

Chemotherapy, a mainstay of cancer treatment for decades, remains dogged by the problem of tumour relapse. Tumours initially shrink under treatment but frequently bounce back, often in more aggressive forms. Decoding how cancer cells acquire mutations that enable them to endure chemotherapy has been a formidable challenge. This complexity arises because chemotherapy itself introduces additional DNA damage, effectively obscuring the genetic signals researchers strive to detect. Moreover, patients rarely receive single-agent types of chemotherapy; instead, they are treated with complex drug cocktails, further complicating analysis.

Dr. Fran Supek, senior author and group leader at IRB Barcelona as well as a professor at the University of Copenhagen’s Biotech Research & Innovation Centre (BRIC), emphasizes the novelty of the approach: "We needed a method that could cut through the noise and observe evolution in real-time during tumour development and treatment." DiffInvex meets this need by ingeniously estimating a baseline “neutral” mutation rate in essential coding regions of the genome, using neighboring non-coding regions as comparative controls. This empirical baseline effectively isolates the influences that bias mutation rates and spectra in tumour evolution and therapeutic response.

One of DiffInvex’s transformative insights comes from uncovering that cancer resistance to therapy is often not driven by mutations in specialized, drug-resistance genes. Instead, the accumulation of additional driver mutations in well-known cancer genes amplifies the tumour’s core survival circuitry, rendering it broadly resilient to different chemotherapeutic agents. Among these genes are prominent oncogenes such as PIK3CA, tumor suppressors like SMAD4, and metabolic regulators such as STK11. The selection of mutations in these genes upon exposure to chemotherapy exemplifies the evolutionary flexibility tumours leverage to escape eradication.

Delving deeper, the team compared 1,722 genomes from healthy tissues alongside their matched tumour counterparts, highlighting an intriguing evolutionary nuance. The gene ARID1A, historically classified as a tumour suppressor driver, along with other purported cancer genes, was found to be frequently mutated and positively selected during normal aging. This observation challenges prevailing dogma, suggesting that some mutations long considered as cancer initiators might instead be evolutionary relics: genetic changes that accumulate in tissue over time but don’t necessarily spark malignancy on their own.

This revelation carries profound implications. If certain so-called driver mutations are evolutionary baggage rather than active disease catalysts, this nuance must be integrated into cancer diagnostics and therapeutics. It redefines the distinction between mutations that signal imminent cancer risks and those that are innocuous hallmarks of cellular aging, potentially refining early detection panels and reducing false alarms that cause undue patient anxiety.

Dr. Supek summarizes their findings with a striking metaphor: "Cancer doesn’t craft bespoke shields tailored to each drug. Instead, it fortifies its fundamental machinery so that nearly any assault inflicts less damage." This conceptual shift underscores the importance of targeting the tumour’s core survival pathways—a strategy with far-reaching potentials in the development of more effective combination therapies.

Recognizing this, the researchers advocate for therapeutic regimens that pair standard chemotherapy with drugs that inhibit these central genes’ signaling pathways. For example, coupling chemotherapy with inhibitors targeting PIK3CA or STK11 pathways could forestall or even prevent the emergence of resistant tumours. Such rational drug combinations represent a promising frontier in precision oncology, where treatments are strategically designed based on tumor evolutionary trajectories.

Crucially, the development of DiffInvex also opens possibilities for dynamically predicting the evolutionary courses tumours may take in individual patients. Dr. Ahmed Khalil, first author and former postdoctoral fellow at IRB Barcelona, now senior data scientist at IMIDomics, enthuses: “By filtering out the mutational ‘noise’, DiffInvex could someday empower clinicians with the foresight to anticipate tumour resistance mechanisms—and intervene proactively to shut them down.”

This foresight aligns perfectly with the broader vision of personalized medicine—tailoring interventions not just based on a static snapshot of the tumour’s genetics, but by understanding its evolving genetic landscape under therapeutic pressure. Effectively, treatments could outpace the cancer’s evolutionary arms race.

The significance of this research is amplified by its scale and rigor, drawing insights from thousands of whole-genome sequences and integrating complex mutational spectra with evolutionary models. Beyond its immediate clinical implications, DiffInvex sets a new methodological standard for studying mutational processes in cancer biology.

The research was generously supported by the European Union’s Horizon 2020 research and innovation programme through the DECIDER project, the European Research Council via its Starting Grant programme, the Spanish Ministry of Science and Innovation, and the Catalan Institution for Research and Advanced Studies (ICREA).

As cancer continues to evolve, so too must our scientific strategies. The advent of DiffInvex marks a decisive step towards unraveling cancer’s sophisticated adaptations—transforming how we understand, detect, and ultimately outsmart this complex disease.

Subject of Research: People
Article Title: DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy
News Publication Date: 13-May-2025
Web References: 10.1038/s41467-025-59397-8
Keywords: Cancer, Chemotherapy, Cancer treatments, Cancer genetics, Mutation rates