Unraveling the intricacies of host-pathogen interaction through single-cell genomics

Emanuele Gioacchino; Koen Vandelannoote; Anthony A Ruberto; Jean Popovici; Tineke Cantaert

doi:10.1016/j.micinf.2024.105313

Unraveling the intricacies of host-pathogen interaction through single-cell genomics

Microbes Infect. 2024 Feb 16:105313. doi: 10.1016/j.micinf.2024.105313. Online ahead of print.

Authors

Emanuele Gioacchino¹, Koen Vandelannoote², Anthony A Ruberto³, Jean Popovici⁴, Tineke Cantaert⁵

Affiliations

¹ Immunology Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia.
² Bacterial Phylogenomics Group, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia.
³ Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
⁴ Malaria Research Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia; Infectious Disease Epidemiology and Analytics, Institut Pasteur, Paris, France.
⁵ Immunology Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia. Electronic address: tcantaert@pasteur-kh.org.

PMID: 38369008
DOI: 10.1016/j.micinf.2024.105313

Abstract

Single-cell genomics provide researchers with tools to assess host-pathogen interactions at a resolution previously inaccessible. Transcriptome analysis, epigenome analysis, and immune profiling techniques allow for a better comprehension of the heterogeneity underlying both the host response and infectious agents. Here, we highlight technological advancements and data analysis workflows that increase our understanding of host-pathogen interactions at the single-cell level. We review various studies that have used these tools to better understand host-pathogen dynamics in a variety of infectious disease contexts, including viral, bacterial, and parasitic diseases. We conclude by discussing how single-cell genomics can advance our understanding of host-pathogen interactions.

Keywords: Host-pathogen interaction; Infectious disease biology; Single-cell RNA sequencing; Single-cell genomics.