An in-depth comparison of the porcine, murine and human inflammasomes; lessons from the porcine genome and transcriptome.
Emerging evidence suggests that swine are a scientifically acceptable intermediate species between rodents and humans to model immune function relevant to humans. The swine genome has recently been sequenced and several preliminary structural and functional analysis of the porcine immunome have been published. Herein we provide an expanded in silico analysis using an improved assembly of the porcine transcriptome that provides an in depth analysis of genes that are related to inflammasomes, responses to Toll-like receptor ligands, and M1 macrophage polarization and Escherichia coli as a model organism. Comparisons of the expansion or contraction of orthologous gene families indicated more similar rates and classes of genes in humans and pigs than in mice; however several novel porcine or artiodactyl-specific paralogs or pseudogenes were identified. Conservation of homology and structural motifs of orthologs revealed that the overall similarity to human proteins was significantly higher for pigs compared to mouse. Despite these similarities, two out of four canonical inflammasome pathways, Absent in melanoma 2 (AIM2) and NLR family and CARD domain containing 4 (NLRC4), were found to be missing in pigs. Pig M1 Mφ polarization in response to interferon-γ (IFN-γ) and lipopolysaccharide (LPS) was assessed, via the transcriptome, using next generation sequencing. Our analysis revealed predominantly human-like responses however some, mouse-like responses were observed, as well as induction of numerous pig or artiodactyl-specific genes. This work supports using swine to model both human immunological and inflammatory responses to infection. However, caution must be exercised as pigs differ from humans in several fundamental pathways.
Rm 224, Bld 307C, Beltsville Human Nutrition Research Center, Beltsville, MD 20705, USA; U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD 20705, USA. Electronic address: Harry.Dawson@ars.usda.gov.
Harry D
HD
Dawson
U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD 20705, USA.
Allen D
AD
Smith
U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD 20705, USA.
Celine
C
Chen
U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD 20705, USA.
Joseph F
JF
Urban
D000818:Animals; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000276:immunology*; D016678:Genome / Q000276:immunology*; D006801:Humans; D058847:Inflammasomes / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D008954:Models, Biological; D010802:Phylogeny; D013045:Species Specificity; D013552:Swine; D059467:Transcriptome / Q000276:immunology*
D058847:Inflammasomes
Escherichia coli; Genome; Human; Inflammasome; Macrophage; Mouse; Pig