Resources: Posters

Dissecting Treatment Response in Heterogeneous Cell Populations by Linking Live-Cell Dynamics to Transcriptomics

April 27, 2026

Stanford Drug Discovery Symposium

Yunmin Li

This research demonstrates how the Cellanome platform links longitudinal live-cell dynamics to single-cell transcriptomics to identify drug-resistant and drug-responsive clones in lung cancer cells. Using CellCage enclosures to track morphology, proliferation, and cell death over time alongside matched sequencing, the study uncovers novel resistant phenotypes and pathway drivers missed by either imaging or transcriptomics alone. The platform's flexibility, shown through EGFR inhibitor and antibody-drug conjugate studies plus a multiplexed "cell village" screening format, positions it as a scalable tool for oncology drug discovery.

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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 longitudinal datasets linking live-cell behavior with molecular readouts 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 approach supports CRISPR-based screens to probe mechanisms of development, degeneration, and repair by linking perturbations to longitudinal functional and molecular readouts 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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