A comparative analysis of label-free liquid chromatography-mass spectrometry liver proteomic profiles highlights metabolic differences between pig breeds

Liver is a complex organ governing several physiological processes that define biological mechanisms affecting growth, feed efficiency and performance traits in all livestock species, including the pig. Proteomics may contribute to better understand the relationship between liver functions and complex production traits in pigs and to characterize this specie as biomedical model. This study applied, for the first time, a label?free liquid chromatography-mass spectrometry (LC?MS) proteomic approach to compare the liver proteome profiles of two important heavy pig breeds, Italian Duroc (IDU) and Italian Large White (ILW). Liver specimens were collected (after slaughtering) from performance tested pigs of these two breeds, raised in standard conditions. The label?free LC?MS method captured a total of 501 proteins of which 200 were subsequently considered in the between breeds comparison. A statistical pipeline based on the sparse Partial Least Squares Discriminant Analysis (sPLS-DA), coupled with stability and significance tests, was applied for the identification of up or down regulated proteins between breeds. Analyses revealed a total of 25 proteins clearly separating IDU and ILW pigs. Among the top proteins differentiating the two breeds ACAA2 and CES3 were up-regulated in ILW and HIST2H2BF and KHK were up-regulated in IDU. FASN, involved in fatty acid metabolism and encoded by a gene located in a QTL region for fatty acid composition, was up-regulated in ILW. Protein interaction analysis showed that 16 of these proteins were connected in one big module. Functional analyses indicated that differentially expressed proteins were involved in several biological processes related to the metabolism of lipids, amino-acids, carbohydrates, cofactors and antibiotics/drugs, supporting that these functions might distinguish IDU and ILW pigs. This comparative proteomic analysis of the porcine liver highlighted several biological factors that could determine the peculiar production potentials of these two heavy pig breeds, derived by their different genetic backgrounds.