Resources: Posters

Unveiling genes in dendritic cells that enhance T cell priming through functional multiplexed single cell-cell interaction analysis

April 12, 2026

2nd Annual ARC Symposium 2026/ SITC 2025

Camilla Valente, Ph.D., UCSF

Keywords: Dendritic cells, T cell priming, CRISPR screening, CellCage technology, single-cell analysis, immunosuppression, immunotherapy, Cellanome R3200.

‍

View Poster

In this poster, Camilla Valente (UCSF), details a novel pooled CRISPR screening workflow to identify genetic regulators of dendritic cell (DC) function. Using the Cellanome R3200 Platform, researchers enclosed single edited DCs with T cells in CellCage™ enclosures (CCEs) to monitor priming dynamics via time-lapse imaging. The study successfully links specific genomic perturbations to the rescue of T cell activation (CD69+ expression) in DCs conditioned with immunosuppressive factors like IL-10 and TGF-beta

‍

Key Takeaways

Functional CRISPR Mapping: Directly links specific gene knockouts in dendritic cells to functional T cell outcomes (proliferation and activation) at a single-cell-pair level.
Overcoming Suppression: Identifies genetic targets that allow DCs to resist cancer-driven immunosuppression and successfully prime OT-I T cells.
High-Throughput Imaging: Utilizes longitudinal imaging to capture the "cellular choreography" of immune synapse formation and activation markers over 3 days.

Back to Posters

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.

View Case Study Details

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.

View Poster

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.

View Case Study Details

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.

View Poster

View Poster Presentation

FAQ's

What conditions were used to simulate the immunosuppressive tumor microenvironment in this study?

Researchers conditioned bone-marrow-derived dendritic cells (BMDCs) with IL-10 and TGF-beta to model the suppressive signaling typical of a tumor environment. This conditioning was shown to significantly impair the DCs' ability to prime T cells—reducing CD69 expression and proliferation—which established the baseline for testing CRISPR-based genetic rescues on the Cellanome R3200 platform.

What markers were used to define successful T cell priming?

Priming success was quantified by tracking T cell proliferation and the upregulation of the early activation marker CD69 through longitudinal fluorescent imaging within the CellCage™ enclosures.

What is the advantage of using CellCage™ (CCE) technology for this screen?

CCEs allow for the isolation of single DC-T cell interactions in a biocompatible, semi-permeable environment. This prevents the "averaging" effect of bulk co-cultures and enables researchers to link a specific CRISPR edit in one DC to the exact functional response of the T cells it interacted with.

Explore Applications

See a Demo