Resources: Posters

Cell killing dynamics and heterogeneity in engineered T-cells measured in live CellCage enclosures

April 21, 2026

AACR | American Association for Cancer Research

Shawn Levy Ph.D., SVP Scientific Affairs

Keywords: T-cell cytotoxicity, Live-cell imaging, Immunotherapy, Functional heterogeneity

This poster details a longitudinal study of engineered T-cells within CellCage™ enclosures, linking real-time killing dynamics and functional heterogeneity to specific transcriptomic profiles. The analysis reveals distinct "super-killer" subsets and exhaustion patterns that remain invisible to traditional end-point analysis.

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Case Study: Functional Profiling of Microglia in Neuroinflammation

Link microglial behavior to gene expression at single-cell resolution, for insight into neuroinflammation, drug response, and immune dysfunction in CNS disease.

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Phagocytosis assay in CellCage enclosures - (click to expand image).

Researchers used the Cellanome R3200 to enclose individual microglia with fluorescent particles and track phagocytosis over 12 hours via fluorescent imaging. Each cell’s transcriptome was then sequenced, linking activity levels to gene expression.

What they found:

High-activity microglia upregulated genes in complement signaling, lipid metabolism, and lysosomal function–key pathways in neuroinflammation and repair.

Why it matters:

This approach overcomes key limitations in standard assays by capturing phagocytic function and gene expression in the same individual cells without dissociation, pooling, or inference. It enables a direct, scalable readout of immune heterogeneity, and reveals the transcriptional programs driving effective or impaired microglial responses.

‍What’s next:

Extend to co-cultures by layering enclosed microglia over intact neuronal networks. Study how cell-cell interactions shape phagocytic behavior and fate. Combine with cytokines, CRISPR libraries, or immunotherapies to generate time-resolved, multi-modal datasets that can be used for MoA analysis, early biomarker discovery, and AI-guided modeling in CNS disease.

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Case Study: Modeling Synapse Formation and Developmental Trajectories in 3D

Track development, function, and gene expression in intact neurospheres, a human-relevant 3D model increasingly vital as regulators move away from animal studies.

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Neurospheres in windowed cages that allow them to reach out to form a synapse - (click to expand image).

Stem-cell-derived neurospheres offer a robust 3D model of early brain development, but standard assays disrupt their structure and miss critical dynamics.

Approach:

Using the Cellanome R3200, the research team explored,

Hundreds of intact neurospheres (100–200 cells each) were cultured inside individual CellCage™ enclosures.
Axon extension, synapse formation and calcium activity were tracked over multiple days.
End-point RNA-Seq was linked back to each neurosphere’s functional behavior.
UMAP clustering revealed lineage-specific gene programs, validated by fluorescent markers.

‍What's next:

This lays the groundwork for CRISPR-based multimodal screens to probe mechanisms of development, degeneration, and repair within preserved 3D architecture.

‍Why it matters:

As the FDA and others move to reduce reliance on animal models, human-relevant in vitro systems like this are increasingly essential.

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FAQ's

How does the R3200 platform measure T-cell killing dynamics?

The R3200 platform utilizes CellCage™ enclosures to enable the continuous, longitudinal monitoring of T-cell interactions within a stable microenvironment. By integrating live-cell imaging with transcriptomics, the system tracks the specific timing and intensity of cell-mediated killing events and correlates these behaviors with the gene expression of individual cells.

What is the significance of capturing functional heterogeneity in engineered T-cells?

Capturing functional heterogeneity allows for the identification of distinct cytotoxic subsets, such as "super-killers" versus exhausted populations. This approach provides a high-resolution view of population efficacy that traditional end-point assays often fail to detect.

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