Comparative transcriptomics of phylogenetically selected pathogenic treponemes cultivated in vitro under different conditions: First insight to the expression changes linked with genomic variants

Projektbeschreibung

Komparative Transkriptomik pathogener in vitro kultivierter Treponema-Arten

Treponema pallidum ist ein Bakterium, das Syphilis verursacht, eine wieder auftretende Erkrankung mit über 5,6 Millionen Fällen weltweit. Es ist jedoch erstaunlich wenig über die biologischen Grundlagen und die Pathogenese von Treponema pallidum bekannt. Grund dafür ist die komplizierte In-vitro-Vermehrung der Bakterien. Ein kürzlich beschriebenes In-vitro-Kulturmodell auf Basis von Epithelzellen von Kaninchen eröffnet neue Möglichkeiten zur Untersuchung der biologischen Grundlagen dieses Pathogens. Ziel des EU-finanzierten Projekts ComTransTrep ist die Anwendung des In-vitro-Modells in Kombination mit genomischen Ansätzen mit hohem Durchsatz, um Daten zu den Genexpressionsprofilen des Pathogens Treponema pallidum zu erhalten.

Ziel

Syphilis, caused by the bacterium Treponema pallidum subsp. pallidum (TPA) is considered a re-emerging disease with over 5.6 million cases worldwide. Despite causing severe life-threatening infections, very little is known about the basic biology and pathogenesis of TPA, largely as the result of the inability to routinely propagate it in vitro.
The recently described in vitro culture model (containing rabbit epithelial cells) has opened new avenues for the study of the basic biology of this pathogen. The ultimate goal of my research proposal is to take advantage of the in vitro model and link its use to high throughput genomic approaches to provide unique insights into the gene expression profiles of this pathogen. This has been transformative for other bacteria, enhancing our knowledge of genetic regulation: essential genes vs differentially expressed genes and intra- and inter-strain differences in response to different growth conditions. This has not been possible until now for TPA. Here, I will perform dual RNA-seq of multiple strains grown in vitro under different conditions. This research proposal has three aims. First, to describe global gene expression patterns of phylogenetically selected TPA strains. Second, to describe genome-wide interaction-linked transcriptional alterations of the infected host cells. And lastly, to correlate the whole transcriptome data with genomic and allelic diversity we see in circulating clinical TPA populations.
This project will generate novel fundamental data which can lead to identification of functional pathways and prediction of the function for hypothetical genes, give light to the patterns of selection we see in genomic data and a better understanding of the key growth dependencies that could inform future axenic cultivation of TPA and combined a better understanding of basic biology introduce a more mechanistic understanding to surveillance and genomic epidemiology.