Fabian Imdahl     email
Helmholtz Institute for RNA-based Infection Research

Dr. Antoine-Emmanuel Saliba (Würzburg)
Promotion Committee:
Dr. Antoine-Emmanuel Saliba (Würzburg)
Prof. Dr. Roy Gross (Würzburg)
Jun. Prof. Dr. Alexander J. Westermann (Würzburg)

Development of novel experimental approaches to decipher host-pathogen interactions at the single-cell level

In case of infection, the transcriptome provides information about the current state of the cell and indicates how the infection is developing. On the basis of this information it is possible to identify potential adaptations of the host cell to the pathogen and vice versa. 

RNA molecules are very powerful proxies to report cellular identities and physiologies. The development of RNA-seq and dual-RNA-seq has opened a new window to decipher host-pathogen interactions. However, most of these methods have been averaging the signal of thousands of cells disregarding the heterogeneity of every individual infected cell. Recently the breakthrough of single-cell RNA-seq paved the way to understand cell-to-cell variability notably the opportunity to discover cellular subpopulations that convey chronic infections. Also, single cell analysis promises to reveal the variety of strategies used by both the pathogen and the host to promote or control disease spread. Although, single-cell RNA-seq is a well-established technique for eukaryotic cells, it failed so far to capture the transcriptome of single bacteria. Bacterial RNAs are extremely rare compared to their eukaryotic counterparts and their transient nature in the order of few minutes of half-life has prevented easy adaptation of existing protocols. My PhD studies focus on the development of novel protocols for bacterial RNA-seq down to a single cell using the model organism Salmonella Typhimurium. Furthermore I will study host-pathogen interactions at the single cell level.