IMIB - Institute for Molecular Infection Biology

Integrating single-cell multi-omics to decipher host-pathogen interactions

The study of single cells gives us the ability to assess the heterogeneity of a population and its response to a stimulus. After everything started with a single blastomere, blood was one of the first tissues to be dissected by transcriptional profiling. However, most tissues are solid and have a more strict architecture that is lost during single-cell isolation. In order to understand the factors that govern the susceptibility of cells to superinfection, disease tolerance or clinical outcome, we also have to understand the spatial patterns and temporal dynamics.

We have started by analyzing the transcriptome of hundreds to tens of thousands of cells. More recently we used oligo-conjugated antibodies to also assess protein expression as well as pooling multiple conditions to increase the complexity of experiments.

In the future, I want to complement the sequencing-based profiling methods by using multiplexed single-molecule FISH to detect the subpopulations identified by scRNA-seq in their native environment and during the development of disease.

In the framework of the GRK2157 (3D Infect) I am collaborating with infection biologists and tissue engineers to characterize advanced tissue models and their response to infection. In addition, I am working with clinicians to study the the cellular response to cancer immunotherapy and immune response to COVID-19.