Spatial distribution of RNA molecules

T cells play a central role in human immune system by combating viruses and tumors. When they encounter a cell that needs to be cleared, T cells become activated and produce specific set of proteins, called cytokines, which are vital for target cell clearance. Production of cytokines must be tightly controlled as producing too much may lead to autoimmune diseases, whereas insufficient production causes inability to effectively clear viruses and tumors.

In this project, we will explore the spatial distribution of cytokine RNAs in human T cells. We will analyze 3D microscopy images of T cells in which positions of individual cytokine RNA molecules were captured by smFISH (single molecule fluorescence in situ hybridization). More specifically, we will investigate distances between RNAs, whether they’re forming clusters (structures in which translation can be blocked/enhanced or the RNA can be stored to preserve stability), polarization of RNA spots within the cells, as well as distribution of nuclear RNAs with respect to transcription sites. We will also be able to analyze this for different cytokines, experimental timepoints, and for different cellular compartments.

For this project, we are looking for a student interested in programming.

Cover figure: smFISH image of human T lymphocytes with cytokine RNAs for TNF and IFNγ in two different colors. Data from Wolkers group.