Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells

Noa Bossel Ben-Moshe, Shelly Hen-Avivi, Natalia Levitin, Dror Yehezkel, Marije Oosting, Leo A. B. Joosten, Mihai G. Netea and Roi Avraham ()
Additional contact information
Noa Bossel Ben-Moshe: Weizmann Institute of Science
Shelly Hen-Avivi: Weizmann Institute of Science
Natalia Levitin: Weizmann Institute of Science
Dror Yehezkel: Weizmann Institute of Science
Marije Oosting: Radboud University Medical Center
Leo A. B. Joosten: Radboud University Medical Center
Mihai G. Netea: Radboud University Medical Center
Roi Avraham: Weizmann Institute of Science

Nature Communications, 2019, vol. 10, issue 1, 1-16

Abstract: Abstract Complex interactions between different host immune cell types can determine the outcome of pathogen infections. Advances in single cell RNA-sequencing (scRNA-seq) allow probing of these immune interactions, such as cell-type compositions, which are then interpreted by deconvolution algorithms using bulk RNA-seq measurements. However, not all aspects of immune surveillance are represented by current algorithms. Here, using scRNA-seq of human peripheral blood cells infected with Salmonella, we develop a deconvolution algorithm for inferring cell-type specific infection responses from bulk measurements. We apply our dynamic deconvolution algorithm to a cohort of healthy individuals challenged ex vivo with Salmonella, and to three cohorts of tuberculosis patients during different stages of disease. We reveal cell-type specific immune responses associated not only with ex vivo infection phenotype but also with clinical disease stage. We propose that our approach provides a predictive power to identify risk for disease, and human infection outcomes.

Date: 2019
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/s41467-019-11257-y Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11257-y

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-019-11257-y

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().