IMIB - Institute for Molecular Infection Biology

Establishment of spatial transcriptomics methods to resolve host-pathogen interactions

The transcriptome is the sum of all RNA transcripts in an individual or population of cells. Transcriptomic profiling can provide information about the physiological state of cells and the development of infection. Recent progress in RNA sequencing allows to capture the transcriptome of a single eukaryotic or bacterial cell. Investigating single cells is changing our understanding of host-pathogen interactions because it reveals so far hidden cellular phenotypes. However, single-cell RNA-seq does not preserve spatial information. My aim is to spatially resolve the transcriptome of the host and pathogen at the same time and to investigate their physical state and interactions. To validate the findings from single-cell RNA-seq with high sensitivity and capture the spatial context, I apply multiplexed single-molecule FISH in combination with super-resolution fluorescence microscopy techniques.