Team: Guus Smit, Maarten Bijlsma 

It has become increasingly clear that bulk omics analyses lack the resolution to identify for instance key cell-cell crosstalk events, for clinically relevant cell populations. Also, without focus on cells that are engaged in a disease relevant crosstalk, further scientific breakthroughs are unlikely to happen. In SCONE, we will prepare for the ability to perform proteomics at truly single cell resolution by delineating the cellular interactions that drive key disease processes. We will compile data from multiple types of omics technologies. First, this will provide the necessary data supporting an integrative view on cell biological disease states. Second, it will allow the project to be successful, whilst setting up the single cell proteomics technology within Adore (SCAPE). The sub-projects are as follows:

Scone A (Neurology) aims to understand why some brain cells are more vulnerable than others in frontotemporal dementia (FTD) and how disease signals propagate between neurons and glia. Using three complementary -omics approaches—single nucleus RNA sequencing, spatial transcriptomics and (single‑cell) proteomics—the project integrates data from both post‑mortem FTD brain tissue and patient‑derived iPSC neurons. In brain tissue, the disease gradient along the anterior–posterior axis of the cortex is exploited to compare relatively healthy and severely affected regions. High‑resolution sectioning followed by multi‑omics analysis will reveal early dysregulated cellular processes and identify vulnerable versus resilient cell types. In parallel, patient‑derived neurons and mixed neuron–glia cultures are used to model disease in vitro, studying how gene and protein expression depend on cell type, cell–cell contacts and spatial context. Perturbations of disease‑relevant genes are introduced to see how pathological states arise and spread to neighboring cells. Finally, 3D culture models with grafted patient cells in a healthy environment, including microglia, will be used to study disease spreading in a more tissue‑like context.

SCONE B (Oncology) focuses on gastrointestinal cancers, where aggressive behavior and therapy resistance are linked to tumor cells with stem cell–like, clonogenic properties. These properties are highly plastic and shaped by interactions between tumor cells themselves and with stromal cells. The project first uses single‑nucleus RNA sequencing of patient tumors to define the cellular composition, identify markers and infer key crosstalk pathways that support clonogenic growth. These interactions are then reconstructed and manipulated in 2D cocultures and 3D organoid systems containing fibroblasts and immune cells, with effects monitored by imaging, FACS and repeated snRNA‑seq (and sc‑proteomics when possible). Protein‑level insights come from proteomics on sorted cell populations, including xenograft models, to validate signaling networks across contexts. Finally, probe‑based spatial profiling in patient tissues links the presence and activity of critical cell types and signals to clinical outcomes, providing translational evidence and potential therapeutic targets.

SCONE C serves as the bridge between the neuro- and oncological projects, bringing together insights from projects A and B to investigate how neuronal and tumour-related processes influence one another.