Christina Homberger   email
Helmholtz Institute for RNA-based Infection Research

Supervisor:
Prof. Dr. Jörg Vogel (Würzburg)

Promotion Committee:
Prof. Dr. Jörg Vogel (Würzburg)
Prof. Dr. Thomas Rudel (Würzburg)
Dr. Antoine-Emmanuel Saliba (Würzburg)

Investigating the effect of peptide nucleic acids on the gene expression profile of bacterial pathogenic communities using single-cell RNA-seq

 

RNA-seq technologies have provided much insight into the transcriptional and regulatory networks in many bacterial and host populations. However, these approaches typically report only average expression profiles in populations and fail to provide information on the single-cell level. Heterogeneity at the single-cell level has been explored mostly in eukaryotic cells, bacterial populations that are genetically identical have also been shown to be phenotypically heterogeneous. Thus, having the transcriptomes from single bacterial cells will promises a better understanding of cell-to-cell heterogeneity, persister cell formation, and antibiotic resistance mechanisms.

The focus of my project is to establish single-cell RNA-seq (scRNA-seq) on model bacteria of infection biology and microbiome studies. These include Salmonella enterica, Pseudomonas aeruginosa and Escherichia coli as well as various Gram-positive bacterial species. In order to develop bacterial scRNA-seq, several hurdles have to be overcome, ranging from the bacterial cell wall that prevents effective lysis, the extremely low amount of RNA and the detection efficiency. Further, any protocol to be developed must be made compatible with automation and high-throughput analysis.

I am also interested in bacterial scRNA-seq as a means to study bacterial subpopulations that are relevant during infections. Further, this method can be also applied to various bacterial pathogenic communities and help us to understand changes under antimicrobial treatment which is a project currently studied in my host lab. These antimicrobials, called peptide nucleic acids (PNAs) are used as antisense nucleotides to target essential genes and thereby silencing their mRNAs. This will enable a precise manipulation of the human microbiome community by applying those "programmable antibiotics". Thereby host responses as well as antibiotic resistance mechanisms are of particular interest, which can be investigated using single-cell resolution RNA-seq in combination with already well established high-throughput sequencing approaches like bulk RNA-seq or dual-RNA-seq.