DOI: 10.5061/dryad.280gb5mzw
title: IFN-γ primes bone marrow neutrophils to acquire regulatory functions in severe viral respiratory infections

description: Neutrophil subsets endowed with regulatory/suppressive properties are
 widely regarded as deleterious immune cells that can jeopardize
 antitumoral response and/or antimicrobial resistance. Here, we describe a
 sizeable fraction of neutrophils characterized by the expression of
 Programmed death-ligand 1 (PD-L1) in biological fluids of humans and mice
 with severe viral respiratory infections (VRI). Biological and
 transcriptomic approaches indicated that VRI-driven PD-L1+ neutrophils are
 endowed with potent regulatory functions and reduced classical
 antimicrobial properties, as compared to their PD-L1- counterparts.
 VRI-induced regulatory PD-L1+ neutrophils were generated remotely in the
 bone marrow in an IFN-γ-dependent manner and were quickly mobilized into
 the inflamed lungs where they fulfilled their maturation. Neutrophil
 depletion and PD-L1 blockade during experimental VRI resulted in higher
 mortality, increased local inflammation, and reduced expression of
 resolving factors. These findings suggest that PD-L1+ neutrophils are
 important players in disease tolerance by mitigating local inflammation
 during severe VRI and that they may constitute relevant targets for future
 immune interventions.
description: # IFN-γ primes bone marrow neutrophils to acquire regulatory functions in
 severe viral respiratory infections
 [https://doi.org/10.5061/dryad.280gb5mzw](https://doi.org/10.5061/dryad.280gb5mzw) ## Description of the data and file structure We have submitted our raw single-cell datasets. The zip file contains 2 folders, one dataset for PDL1-Pos mouse neutrophils and a second dataset for PDL1-neg mouse neutrophils from IAV-infected mice. There is a link to the R script to retrieve the list of genes for the Preneus signature and the file used ( from Evrard M, Kwok IWH, Chong SZ, Teng KWW, et al. Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions. *Immunity* 2018 Feb 20;48(2):364-379.e8.)  ### Files and variables #### File: PDL1.zip **Description:** Filtered matrix/output of cellranger PDL1 ├── PDL1_neg_filtered_feature_bc_matrix │   ├── barcodes.tsv.gz │   ├── features.tsv.gz │   └── matrix.mtx.gz └── PDL1_pos_filtered_feature_bc_matrix ``` ├── barcodes.tsv.gz ├── features.tsv.gz └── matrix.mtx.gz ``` 3 directories, 6 files #### File: final\_neutro.rds This is a Seurat 5 Object, containing aggregated single cell data of PDL1 pos and neg. neutrophil subsets. Please read it with R. ### Script All scripts were made using R 4.3.1. #### script\_Bulk\_RNA\_Preneus.R This is an R script to load and retrieve the differential gene expression between granulocyte-macrophage progenitor (GMP) and pre-neutrophils (PN) using DESeq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” *Genome Biology*, **15**, 550. [doi:10.1186/s13059-014-0550-8](https://doi.org/10.1186/s13059-014-0550-8).)  ##### IFN-γ primes bone marrow neutrophils for regulatory functions in severe viral pneumonia.ipynb This is a Jupyter Notebook using an R kernel to reproduce the figure of the paper. To run this script please use the rds provided named "final_neutro.rds" There is a homemade function: basic*pipe(seurat*object, dimensions_to_use, resolution_of_clustering) This function can be found in utils.R ([https://github.com/TEAM-4-CEPR/Utils/blob/main/Utils.R](https://github.com/TEAM-4-CEPR/Utils/blob/main/Utils.R)