single cell gene expression

In this project we aimed to study the gene expression of engineered T cells exposed to different environmental conditions and displaying different behaviors in a 3D in vitro assay.

Type of data: Single cell sequencing on engineered T cells harvested from a co-culture with patient derived tumoroids. T cells were harvested at different conditions in order to discriminate cell environment and behavior.

Background: In our assay we found the T cells displayed heterogenous behavior with only a subpopulation of cells actively engaging and killing the tumor cells. To get insight into the genetic mechanism behind this behavior we explored the single cell expression data derived from these cells.

Goal: Characterize the gene expression of engineered T cells displaying distinct behaviors.

Approach: Using single cell gene expression analysis toolbox (seurat) we performed differential expression analysis followed by gene ontology analysis to get insight in the pathways that were different between behaviors displayed. Using dotplot I could visualize the differential expression of some key genes involved in T cell activation and killing processes.

Main result: I could identify a subset of genes that were involved in serial killer behavior by T cells.