Leveraging Single-Cell ‘Omics’ to Unravel New Insights into Human Immune System

Achieving detailed understanding of the composition and function of the immune system at the fundamental unit of life — the cell — is essential to determining the prerequisites of health and disease. Historically, leukocyte populations have been defined by a combination of morphology, localization, functions, developmental origins, and the expression of a restricted set of markers. These strategies are inherently biased and recognized today as inadequate. Single-cell RNA sequencing (scRNAseq) analysis provides an unbiased, data-driven way of systematically detecting cellular states that can reveal diverse simultaneous facets of cellular identity, from discrete cell types to continuous dynamic transitions, which cannot be defined by a handful of pre-defined markers or for which markers are not yet known.

We combine scRNAseq strategies together with in-depth followup profiling, phenotypic and functional characterization of prospectively isolated immune subsets defined by scRNAseq data to overcome such limitations. Our analyses of the human blood mononuclear phagocyte system resulted in the identification of six dendritic cell (DC), four monocyte, and one DC progenitor populations, thus revising the taxonomy of these cells (Villani et al., Science 2017). Noteworthy, five of these subsets had never been reported, illustrating the power of our integrative strategies to reopen the definition of these cell types.

Our study highlighted the value of embarking on a comprehensive Human Cell Atlas initiative and offered a useful framework for conducting this kind of analysis on other cell types and tissues. We are currently contributing to the immune cell atlas effort by charting at high-resolution the human blood cellular landscape, and are studying paired human tissues with blood to better establish how circulating immune cells mirror those in tissue microenvironment in the context of health and disease.

We also continuously support development of in-depth expertise in single-cell ‘omics’ approaches, including single-cells strategies to map X-chromosome inactivation (Tukiainen, Villani, Nature 2017), new enrichment method targeting individual cell transcriptome in pooled library (Ranu, Villani, Nucleic Acid Res 2019), method’s development to study single-T cells (Villani, Methods Mol Biol 2016) and application to study T cells infiltrates in tumor lesions (Izar Science 2016; Sade-Feldman, Cell 2019; Di Pilato, Nature 2019) and myeloid cell infiltrates (Olah M, Nat Commun 2018; Balan S, Cell Rep 2018; Chapuy L, Mucosal Immunol 2019).