Dual-scRNA-seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection

Konstantinos Karagiannis; Sreenivas Gannavaram; Chaitenya Verma; Thalia Pacheco-Fernandez; Parna Bhattacharya; Hira L Nakhasi; Abhay R Satoskar

doi:10.1016/j.celrep.2023.113097

Dual-scRNA-seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection

Cell Rep. 2023 Sep 26;42(9):113097. doi: 10.1016/j.celrep.2023.113097. Epub 2023 Sep 8.

Authors

Konstantinos Karagiannis¹, Sreenivas Gannavaram², Chaitenya Verma³, Thalia Pacheco-Fernandez², Parna Bhattacharya², Hira L Nakhasi², Abhay R Satoskar⁴

Affiliations

¹ FDA-High-Performance Integrated Virtual Environment, CBER, FDA, Silver Spring, MD, USA.
² Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA.
³ Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA.
⁴ Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA. Electronic address: abhay.satoskar@osumc.edu.

PMID: 37682713
DOI: 10.1016/j.celrep.2023.113097

Abstract

Although phagocytic cells are documented targets of Leishmania parasites, it is unclear whether other cell types can be infected. Here, we use unbiased single-cell RNA sequencing (scRNA-seq) to simultaneously analyze host cell and Leishmania donovani transcriptomes to identify and annotate parasitized cells in spleen and bone marrow in chronically infected mice. Our dual-scRNA-seq methodology allows the detection of heterogeneous parasitized populations. In the spleen, monocytes and macrophages are the dominant parasitized cells, while megakaryocytes, basophils, and natural killer (NK) cells are found to be unexpectedly infected. In the bone marrow, the hematopoietic stem cells (HSCs) expressing phagocytic receptors FcγR and CD93 are the main parasitized cells. Additionally, we also detect parasitized cycling basal cells, eosinophils, and macrophages in chronically infected mice. Flow cytometric analysis confirms the presence of parasitized HSCs. Our unbiased dual-scRNA-seq method identifies rare, parasitized cells, potentially implicated in pathogenesis, persistence, and protective immunity, using a non-targeted approach.

Keywords: CP: Immunology; CP: Microbiology; HSC; Leishmania donovani; bone marrow; chronic infection; eosinophils; latent infection; persistence; phagocytosis; scRNA-seq; trained immunity.