Cell-Cell-Seq resolves contact-associated NK cell activation in defined tumor cell dyads
Liang, J.; Shao, D.; Di Carlo, D.; de Rutte, J. M.
Show abstract
Cell-cell interactions shape immune recognition, but most single-cell transcriptomic methods measure cells after their interaction history has been lost or inferred. Here we apply Cell-Cell-Seq, a Nanovial-based workflow for sequencing defined cell pairs, to resolve contact-associated activation of natural killer cells paired with leukemia targets. Nanovials enabled controlled dyad formation, incubation, flow enrichment and droplet-based sequencing while reducing uncontrolled partner exchange and aggregation seen in suspension co-culture. Cell-Cell-Seq recovered a reproducible activation program marked by chemokine, cytokine, cytotoxic and immediate-early response genes. Compared with randomly mixed suspension co-culture, defined dyads emphasized contact-proximal activation, whereas suspension co-culture showed stronger features of early overstimulation. Dyad-resolved measurements also benchmarked computational models of cell-cell communication, identifying inferred signalling axes that were recovered and contact-induced programs missed by current approaches. These results establish Cell-Cell-Seq as a scalable strategy for mapping how defined immune-tumour encounters reshape cell state.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling 97%
- Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors 96%
- APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence 96%
Similar papers in this journal
- Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions 97%
- Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq 96%
- NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells 96%
Similar papers in this journal
Similar papers in this journal
- Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE 96%
- Conserved epigenetic regulatory logic infers genes governing cell identity 95%
- Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.