Single-cell Analysis

Pathogenic bacteria can reside in a mammalian host for a life-long period and chronic carriers form a reservoir leading to recurrent infections. Despite the importance of chronic infections for public health, how a subset of pathogens escape the host’s immune surveillance and how the host contains the spread of bacteria are still poorly understood. Scientists within the Single-Cell Analysis group develop and use single-cell transcriptomics and computational approaches to decipher the microenvironments of individual pathogens and ultimately their functional consequences on infection outcome.


Our Research

Persistent bacterial infections are caused by a minor subpopulation of intracellular pathogens, called ‘persisters’, that reside in different cell types and tissue locations for years asymptomatically. These subpopulations establish specific cellular organization to enable them to evade immune surveillance and chemotherapy treatments. Histological studies have described complex tissue remodeling during the infection and emerging in vivo studies at the single-cell level have begun to reveal the heterogeneity of infection foci.

t-SNE projection in 3D the transcriptome signatures of immune cells. © HIRI

However, the cellular architecture of the infection foci and which are the favorite niches among this complex anatomical tissue landscape that impact disease outcome remain open questions. For example, Salmonella spp. are believed to reside in a large variety of cells including macrophages, neutrophils, dendritic cells and epithelial cells. These large cell types exist as a myriad of different sub-classes, which were, until recently, not appreciated. Similarly, within an infected tissue such as the spleen, many infected cells escape inflammatory lesions and disseminate into tissues. Therefore, single-cell studies in an in vivo context are necessary to understand the heterogeneity inherent in infected cells, their microenvironment and their function. The Single-Cell Analysis group develop and combine in vitro and in vivo single-cell transcriptomics to decipher the cellular organization of infection foci and their functional consequences on infection outcome.

Single-cells from mouse, human or in vitro culture can be isolated and analysed using flow cytometry based or microfluidic-based scRNA-seq. (adapted from Saliba et al. 2017 Biospektrum) © HIRI

The recent emergence of single-cell genome-wide transcriptomics is proving to be a powerful approach to decipher both cellular identities and function making possible to study heterogeneity. It is being facilitated by the development of automated platforms that enable the processing of hundreds and thousands of single-cells in parallel. In the context of infection, we have pioneered the use of single-cell RNA-seq to investigate heterogeneity in the response of mouse bone-marrow-derived macrophages to Salmonella, focusing on bacteria with different growth status including non-growing ‘persisters’ that have been linked to recurrent infections. We have described how Salmonella impact the wide spectrum of host polarization and revealed the existence of a subset of macrophages that escape inflammatory and immune activation programs. While providing new insights into the host response, the study was limited to analyzing infected cells from in vitro mono-cultures. The next step is now to decipher the response of single cells of infected tissues, which remains an unmet challenge.
Moreover, the Single-cell Analysis group is fully committed to developing the full potential of single-cell RNA-seq for addressing fundamental scientific questions of infection biology in general, at the HIRI as well as other locations of the HZI.

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