Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains

Abstract

Porcine reproductive and respiratory syndrome (PRRS) has an extensive impact on pig production. The causative virus (PRRSV) is divided into two species, PRRSV-1 (European origin) and PRRSV-2 (North American origin). Within PRRSV-1, PRRSV-1.3 strains, such as Lena, are more pathogenic than PRRSV-1.1 strains, such as Flanders 13 (FL13). To date, the molecular interactions of PRRSV with primary lung mononuclear phagocyte (MNP) subtypes, including conventional dendritic cells types 1 (cDC1) and 2 (cDC2), monocyte-derived DCs (moDC), and pulmonary intravascular macrophages (PIM), have not been thoroughly investigated. Here, we analyze the transcriptome profiles of in vivo FL13-infected parenchymal MNP subpopulations and of in vitro FL13- and Lena-infected parenchymal MNP. The cell-specific expression profiles of in vivo sorted cells correlated with their murine counterparts (AM, cDC1, cDC2, moDC) with the exception of PIM. Both in vivo and in vitro, FL13 infection altered the expression of a low number of host genes, and in vitro infection with Lena confirmed the higher ability of this strain to modulate host response. Machine learning (ML) and gene set enrichment analysis (GSEA) unraveled additional relevant genes and pathways modulated by FL13 infection that were not identified by conventional analyses. GSEA increased the cellular pathways enriched in the FL13 data set, but ML allowed a more complete comprehension of functional profiles during FL13 in vitro infection. Data indicates that cellular reprogramming differs upon Lena and FL13 infection and that the latter might keep antiviral and inflammatory macrophage/DC functions silent. Although the slow replication kinetics of FL13 likely contribute to differences in cellular gene expression, the data suggest distinct mechanisms of interaction of the two viruses with the innate immune system during early infection.

Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression

“…First, we compared the WT libraries against mock ( Figure 11A , Figure 11—source data 1 ) and the KO2 libraries against mock ( Figure 11B , Figure 11—source data 2 ). Similarly to other studies ( Pröll et al, 2017 ; Badaoui et al, 2013 ; Crisci et al, 2020 ), we found transcription of genes related to regulation of the cell cycle (amongst other GO terms) to be perturbed by WT PRRSV infection ( Figure 11—source data 1 , sheet: ‘GO_TS_up’; GO term GO:0051726 ~26-fold enriched in transcriptionally upregulated genes). However, a comparison of transcriptional fold changes with those of TE reveals that the majority of transcriptionally upregulated genes in WT or KO2 compared to mock are downregulated in terms of TE ( Figure 11A and B , top-left quadrants of right-column panels).…”

Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression

“…First, we compared the WT libraries against mock (Figure 11A, Supplementary Table 9) and the KO2 libraries against mock (Figure 11B, Supplementary Table 10). Similarly to other studies 79,86,87 , we found transcription of genes related to regulation of the cell cycle (amongst other GO terms) to be perturbed by WT PRRSV infection (Supplementary Table 9, sheet: 'GO_TS_up'; GO term GO:0051726 ~26-fold enriched in transcriptionally up-regulated genes). However, a comparison of transcriptional fold changes with those of TE reveals that the majority of transcriptionally up-regulated genes in WT or KO2 compared to mock are down-regulated in terms of TE (Figure 11A and B, top-left quadrants of right-column panels).…”

The pig as a medical model for acquired respiratory diseases and dysfunctions: An immunological perspective

“…Swine DC have been identified in tonsils (Soldevila et al, 2018), tracheal epithelium and pulmonary parenchyma (Maisonnasse et al, 2016). They can be divided in cDC1, cDC2 and moDC whose RNAseq signatures cluster with their mouse spleen and/or lung counterparts (Crisci et al, 2020). Plasmacytoid DC have also been identified in swine tonsil, they are E2.2 and IRF7 positive as observed in mouse and man.…”

“…PIM are resident lung intravascular macrophages intimately tight with endothelial cells, what differentiates them from marginated blood monocytes (for review see (Kuebler and Goetz, 2002)). We recently isolated porcine PIM and demonstrated that they were very similar to AM (Bordet et al, 2018;Crisci et al, 2020), indeed PIM and AM overexpressed genes such as PU.1 and HDAC10, leading us to suggest than PIM were, like AM, self-renewable embryonically derived macrophages, and/or that PIM may directly originate from AM (Bordet et al, 2018). PIM have been involved in acute lung inflammation in Laurasiatheria species (Cantu et al, 2007;Singh et al, 2004).…”