The Department of Spatial Biology & Cellular Dynamics investigates how cells are organized within tissues and how their behaviours evolve over time to shape biological function in health and disease. By integrating spatial biology with high-content live-cell imaging, the team examine tissue architecture, cellular heterogeneity, and the dynamic interactions between cells and their microenvironment. They combine advanced imaging, molecular profiling, and quantitative analysis to uncover the mechanisms governing cellular function, disease progression, and therapeutic responses. These insights advance our understanding of biology and support the development of innovative diagnostic and therapeutic strategies.
Spatial Biology and Cellular Dynamics
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Dr. Özlem Akilli
Director Spatial Biology and Cellular Dynamics
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Dr. Eliana Stanganello
Associate Director Spatial Biology and Cellular
Our vision
To advance tissue biology by revealing how the spatial organization and dynamic behavior of cells drive health, disease, and therapeutic responses, and to translate these discoveries into clinically actionable targets
Spatial Biology
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Dr. Özlem Akilli
Head of Functional Unit Spatial Biology
The Spatial Biology unit focuses on the study of cells and tissues in both health and disease within its native spatial context. By analyzing gene and protein expression in situ, the unit focuses on how spatial organization dictates function. The primary objective is to investigate the molecular composition of individual cells, their interactions with other cells in the microenvironment, the impact of the microenvironment on disease progression and therapeutic responses, as well as discovery of spatial niches and ecosystems with distinct functions in tumor evasion and therapy response with ultimate aim to translate those discoveries into clinical applications. A particular research focus is understanding how the nervous system regulates TME with a specific focus on repurposing neurological drugs as novel cancer therapies. To achieve these goals, the unit employs a variety of cutting-edge instruments and techniques to generate high-resolution qualitative and quantitative data.
Our activities and competences
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Spatial Transcriptomics
Profiling genome-wide gene expression while preserving spatial context using using short-read and long-read sequencing technologies to map tissue architecture, cellular interactions, and molecular networks in fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) (short-read only) tissue sections.
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Spatial Proteomics
High-dimensional protein profiling via multiplexed cyclic imaging to characterize tissue composition, cellular phenotypes, functional states, and cell-cell interactions at single-cell resolution.
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Low-Plex (multiplex) Immunohistochemistry (IHC)
Characterization of tissue microenvironments, cellular composition, metabolic/epigenetic states, and mRNA vaccine expression at injection sites and peripheral tissues using Tyramide Signal Amplification (TSA)-based assays.
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RNAscope, Basescope, & Multiomic Assays
Next-generation in situ hybridization (ISH) technologies for spatial gene expression, detection of splice variants, isoforms, and gene fusions, simultaneous RNA-protein profiling, and mRNA vaccine biodistribution studies.
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Histopathology & Chromogenic IHC
Evaluation of tissue architecture, tumor microenvironment (TME), and protein expression in FF and FFPE tissues under physiological and perturbed conditions.
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Quantitative Image Analysis
Development of automated image analysis workflows combining community-created tools with Visiopharm and QuPath for automated tissue segmentation, cell phenotyping, spatial network mapping, and quantitative biomarker assessment
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Spatial Transcriptomics Data Analysis Pipeline
Establishment of quality control pipelines and analysis workflows for Visium HD and Xenium datasets in close collaboration with the Computational Genomics Unit, enabling integrative spatial transcriptomic analyses.
Our methods and platforms
10X Visium CytAssist
Automated probe transfer system for the Visium Spatial Transcriptomics workflow, enabling high-throughput sample processing with a capacity of two slides
PhenoCycler-Fusion (PCF)
Fully automated high-plex spatial proteomics platform integrating cyclic immunofluorescence imaging and whole-slide scanning, with a capacity of two slides.
PhenoImager HT (PHT)
High-throughput multispectral whole-slide scanner for fluorescence and brightfield imaging with a capacity of 80 slides.
Parhelia Spatial Station (PSS)
Automated research staining platform supporting multiplex IHC, immunofluorescence (IF), PhenoCycler slide preparation, and Visium HD sample preparation with a capacity of 12 & 30 slides.
Leica BOND Rx
Fully automated research stainer for high-throughput IHC, IF, RNAscope, ISH, FISH, and TSA-based multiplex IHC with a capacity of 30 slides.
Publications
Hepatocellular Carcinoma (HCC) is the most common form of primary liver cancer, with cirrhosis being its strongest risk factor. Interestingly, an increasing number of HCC cases is also observed without cirrhosis. We developed an HCC model via intrasplenic injection of highly tumorigenic HCC cells, which, due to cellular tropism, invade the liver and allow for a controllable disease progression. Specifically, C57BL/6JRj mice were intrasplenically inoculated with Dt81Hepa1-6 HCC cells, with a subgroup pre-treated with CCl4 to induce cirrhosis (C-HCC). At four weeks post-inoculation, mice were sacrificed, and diseased livers were analyzed via histology, flow cytometry, and RT-qPCR to profile the extracellular matrix (ECM), angiogenesis, and immune cells. In addition, tumor-bearing mice were treated with the first-line therapy, AtezoBev, to assess therapeutic responsiveness of the model. Dt81Hepa1-6 cells displayed similar gene expression as human HCC. After intrasplenic injection, all mice developed multifocal disease. C-HCC mice had a significantly higher tumor load than non-cirrhotic HCC mice. Both HCC and C-HCC models displayed extensive ECM formation, increased levels of vascularization, and immune cell infiltration compared to healthy and non-cancerous cirrhotic livers. AtezoBev treatment produced robust antitumor efficacy, validating the model's suitability for therapy testing. In conclusion, we established a rapidly developing and high-yield HCC model through a simple intrasplenic injection, with or without cirrhotic damage. The model overexpressed key human HCC genes and showed high responsiveness to first-line treatment. Our model uniquely combines all the above-mentioned features, promoting its use towards HCC therapy testing.
Head and neck squamous cell carcinomas (HNSCCs) are heterogeneous in terms of origin and aetiology. In addition, there is uncertainty about the genetic evolution from initial diagnosis to recurrence after primary treatments and further disease progression following systemic treatment. Changes in the genetic profile have implications on the selection of appropriate treatments for patients, especially in the era of targeted therapies and immunotherapies.
Major histocompatibility complex (MHC) class I antigen presentation deficiency is a common cancer immune escape mechanism, but the mechanistic implications and potential strategies to address this challenge remain poorly understood. Studying b2-microglobulin (B2M) deficient mouse tumor models, we find that MHC class I loss leads to a substantial immune desertification of the tumor microenvironment (TME) and broad resistance to immune-, chemo-, and radiotherapy. We show that treatment with long-lasting mRNA encoded interleukin-2 (IL-2) restores an immune cell infiltrated, IFNg-promoted, highly proinflammatory TME signature, and when combined with a tumor-targeting monoclonal antibody (mAB), can overcome therapeutic resistance. Unexpectedly, the effectiveness of this treatment is driven by IFNg-releasing CD8+ T cells that recognize neoantigens cross-presented by TME-resident activated macrophages. These macrophages acquire augmented antigen presentation proficiency and other M1-phenotype-associated features under IL-2 treatment. Our findings highlight the importance of restoring neoantigen-specific immune responses in the treatment of cancers with MHC class I deficiencies.
High Content Imaging & Cellular Dynamics
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Dr. Eliana Stanganello
Head of Functional Unit High Content Imaging & Cellular Dynamics
The High Content Live Imaging and Cellular Dynamics (HCI-CD) Unit investigates the molecular mechanisms and cellular dynamics that drive biological processes, with the goal of identifying novel therapeutic strategies and improving drug delivery. Using state-of-the-art high-resolution live-cell imaging and quantitative image analysis, the unit visualizes and measures cellular processes in real time, with a particular focus on immunology.
Our activities and competences
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High-content live-cell imaging and quantitative analysis
Real-time visualization and measurement of cellular processes using advanced imaging technologies, with a particular focus on immunology and disease mechanisms.
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Protein localization, trafficking, and signaling dynamics
Analysis of molecule internalization, protein localization, intracellular trafficking, degradation, ubiquitination, and signaling pathways using live-cell imaging, immunofluorescence, and quantitative image analysis.
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Cellular dynamics and interactions
Quantitative assessment of cell behavior, cytotoxicity, migration, cell-cell interactions, and phenotypic changes through time-lapse imaging and cell tracking.
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Intercellular communication
Investigation of molecular exchange and cellular communication to understand their impact on biological function, disease progression, and therapeutic responses.
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Advanced experimental models
Quantitative imaging in 2D and 3D cell culture systems and zebrafish models to study cellular dynamics in physiologically relevant environments.
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Therapeutic discovery and drug evaluation
Development of imaging-based assays to investigate disease mechanisms, therapeutic responses, and drug delivery strategies.
Our methods and platforms
High-content live-cell imaging
Automated high-resolution imaging for real-time monitoring and quantitative analysis of dynamic cellular processes.
Time-lapse and immunofluorescence microscopy
Imaging approaches for studying cellular behavior, protein localization, molecular interactions, and intracellular organization.
Nanolive Holotomographic Imaging
Label-free 3D quantitative imaging of living cells based on refractive index measurements, enabling high-resolution structural analysis.
CQ1 Spinning Disk High-Content Analysis System
High-speed, low-phototoxicity confocal imaging platform for long-term live-cell imaging, co-localization studies, and quantitative analysis.
ZEISS LSM 910 Confocal Microscope
Advanced laser-scanning confocal microscope with Airyscan and Lightfield technologies, enabling high-resolution, super-resolution, spectral imaging, 3D reconstruction, and quantitative fluorescence analysis.
Image analysis platforms
Integrated computational workflows using Imaris, CellPathfinder, Eve, and ImageJ/Fiji for segmentation, tracking, and quantitative phenotyping. Customized pipelines integrate multiparametric imaging data to characterize cellular behavior, protein expression and localization, intracellular trafficking, and cell-cell interactions.
Zebrafish imaging platform
In vivo imaging approach to study cellular dynamics, immune responses, and cell-cell interactions within a physiological context.
Publications
Checkpoint inhibitors (CPI) haverevolutionized the treatment paradigm for advanced solid tumors; however, thereremains an opportunity to improve response rates and outcomes. In preclinicalmodels, 4-1BB costimulation synergizes with CPIs targeting the programmed celldeath protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) axis byactivating cytotoxic T-cell-mediated antitumor immunity. DuoBody-PD-L1×4-1BB(GEN1046) is an investigational, first-in-class bispecific immunotherapy agentdesigned to act on both pathways by combining simultaneous and complementaryPD-L1 blockade and conditional 4-1BB stimulation in one molecule. GEN1046induced T-cell proliferation, cytokine production, and antigen-specificT-cell-mediated cytotoxicity superior to clinically approved PD-(L)1 antibodiesin human T-cell cultures and exerted potent antitumor activity intransplantable mouse tumor models. In dose escalation of the ongoingfirst-in-human study in heavily pretreated patients with advanced refractorysolid tumors (NCT03917381), GEN1046 demonstrated pharmacodynamic immune effects in peripheralblood consistent with its mechanism of action, manageable safety, and earlyclinical activity [disease control rate: 65.6% (40/61)], including patientsresistant to prior PD-(L)1 immunotherapy.
We preclinically characterize BNT162b3, a nucleoside-modified mRNA-based coronavirus disease 2019 (COVID-19) vaccine encoding a trimerized, cell surface-tethered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor-binding domain (RBD-foldon), formulated in lipid nanoparticles. Intramuscular immunization with BNT162b3 induced high antigen-specific antibody titers with early seroconversion kinetics in mice and rhesus macaques. One dose of BNT162b3 induced high neutralizing antibody titers against pseudoviruses harboring the spike of the SARS-CoV-2 Wuhan-Hu-1 strain and early variants of concern up to Delta, but lower titers against Omicron, the phylogenetically more distant variant. In mice, a second immunization boosted Omicron neutralizing antibody titers to levels comparable to those of other tested variants. The cellular immune response was T helper 1 cell driven. The cell surface-tethered RBD-foldon was more immunogenic than its soluble counterpart. This study demonstrated the suitability of BNT162b3 as COVID-19 vaccine and supported its evaluation in a phase I/II clinical trial (BNT162-04, NCT04537949).
