Distinctive cellular and metabolic reprogramming in porcine lung myeloid cells infected with type I PRRSV strains

The Porcine Reproductive and Respiratory Syndrome (PRRS) has an extensive impact on pig production. The causative virus (PRRSV) is divided in 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 phagocytes (MNP) subtypes including conventional dendritic cells type 1 (cDC1) and type 2 (cDC2), monocyte-derived DCs (moDC) and parenchymal macrophages (PIM) have not been thoroughly investigated. Here, we analysed 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 while in vitro infection with Lena confirmed the higher ability of this strain to modulate host response. Machine learning (ML) and GSEA analyses unraveled additional relevant genes and pathways modulated by FL13 infection that were not identified by conventional analyses. GSEA increased the cellular pathways enriched in FL13 dataset, but ML allowed a more complete comprehension of functional profiles during FL13 in vitro infection. Data indicated that cellular reprogramming differed upon Lena and FL13 infection, and that the latter keeps antiviral and inflammatory macrophages/DC functions silent, suggesting a different mechanism of pathogenesis during early infection. Overall design: transcriptome profiles of in vivo FL13-infected parenchymal MNP subpopulations and in vitro FL13- and Lena-infected parenchymal MNP obtained using RNAseq

猪繁殖与呼吸综合征（Porcine Reproductive and Respiratory Syndrome, PRRS）对生猪养殖产业造成了广泛影响。其致病病毒（PRRSV）可分为两个物种：欧洲起源的PRRSV-1与北美起源的PRRSV-2。在PRRSV-1中，以Lena株为代表的PRRSV-1.3亚型毒株，其致病力显著强于以Flanders 13（FL13）为代表的PRRSV-1.1亚型毒株。截至目前，PRRSV与肺原代单核吞噬细胞（primary lung mononuclear phagocytes, MNP）各亚型——包括1型常规树突状细胞（conventional dendritic cells type 1, cDC1）、2型常规树突状细胞（conventional dendritic cells type 2, cDC2）、单核细胞衍生树突状细胞（monocyte-derived DCs, moDC）以及实质巨噬细胞（parenchymal macrophages, PIM）——之间的分子互作尚未得到系统深入的研究。本研究对体内（in vivo）感染FL13的实质MNP亚群，以及体外（in vitro）感染FL13与Lena株的实质MNP的转录组谱进行了分析。体内分选细胞的细胞特异性表达谱，除实质巨噬细胞（PIM）外，与对应小鼠细胞群（肺泡巨噬细胞（alveolar macrophages, AM）、cDC1、cDC2、moDC）的表达谱具有相关性。无论体内还是体外，FL13感染仅改变了少量宿主基因的表达；而体外Lena株感染实验则证实，该毒株具有更强的宿主应答调控能力。机器学习（Machine Learning, ML）与基因集富集分析（Gene Set Enrichment Analysis, GSEA）进一步揭示了常规分析未发现的、受FL13感染调控的关键基因与通路。GSEA扩增了FL13数据集所富集的细胞通路，而ML则让我们对FL13体外感染过程中的功能特征有了更全面的认知。研究数据表明，Lena株与FL13株感染所诱导的细胞重编程存在差异，FL13株可抑制抗病毒与炎性巨噬细胞/树突状细胞的功能，提示其在感染早期存在不同的致病机制。本研究的整体实验设计为：采用RNA测序（RNAseq）技术，获取体内感染FL13的实质MNP亚群，以及体外感染FL13与Lena株的实质MNP的转录组谱。