Notably, caution should be taken when interpreting results of ROS and RNS measurements due to this dual role of free radicals in protecting and injuring the graft.Research in xenotransplantation implies a high experimental complexity comprising molecular, cellular, and in vivo studies to investigate the mechanisms of xenograft immune rejection and functional failure, as well as the strategies to counteract them. After major advances associated with the identification of the carbohydrate xenoantigens and their elimination through genomic edition of the source pigs, the study of the cellular immune response against the xenograft is gaining particular attention. Xenogeneic cell-based assays that put together pig cells and human leukocytes such as monocytes, NK cells, and T cells are relevant to address this hurdle. Thus, we describe here coculture, co-stimulatory, and cytotoxicity assays for investigating the cellular and molecular mechanisms of xenograft rejection. These techniques allow elucidating the key pathways that take place during the xenogeneic immune response in a simplified setting.  https://www.selleckchem.com/products/Acadesine.html  Treatment with either pro-inflammatory or anti-inflammatory cytokines can be used for studying the regulation of adhesion, co-stimulatory molecules, and receptors involved in triggering the immune response under various conditions. Furthermore, these assays can be used for the follow-up of the immune response of in vivo studies as well as for the development of tolerogenic approaches that promote xenograft survival.Endothelial cells (EC) play a crucial role in the pathophysiology of cardiovascular diseases, ischemia/reperfusion injury, and graft rejection in (xeno-)transplantation. In such nonphysiological conditions, EC are known to lose their quiescent phenotype and switch into an actively pro-inflammatory, procoagulant, and anti-fibrinolytic state. This case happens essentially because the endothelial glycocalyx-a layer of proteoglycans and glycoproteins covering the luminal surface of the endothelium-is shed. Heparan sulfate, one of the main components of the endothelial glycocalyx, contributes to its negative charge. In addition, many plasma proteins such as antithrombin III, superoxide dismutase, C1 inhibitor, and growth factors and cytokines bind to heparan sulfate and by this scenario contribute to the establishment of an anticoagulant and anti-inflammatory endothelial surface. Shedding of the glycocalyx results in a loss of plasma proteins from the endothelial surface, and this phenomenon causes the switch in p situation in small vessels.In pig-to-primate xenotransplantation, flow cytometry assays allow the examination of antibody reactivity to intact antigens in their natural conformation and location on cell membranes. Here we describe in detail the procedures of two flow cytometry assays to measure the antibody-mediated complement-dependent cytotoxicity (CDC) response or serum levels of IgG and IgM xenoantibodies. This information is key for understanding the rejection process of vascularized xenografts and finding strategies to overcome it.One of the major obstacles in xenotransplantation is tissue expression of the non-human mammalian carbohydrate N-glycolylneuraminic acid (Neu5Gc). This 9-carbon backbone acidic sugar is the hydroxylated form of N-acetylneuraminic acid (Neu5Ac), and both constitute the two most common sialic acid types in mammals. Loss of CMP-Neu5Ac hydroxylase encoding gene in humans dictates the immunogenic nature of Neu5Gc-containing xenografts. Here we describe an immunohistochemistry method for the detection of Neu5Gc in mammalian-derived tissues using affinity-purified chicken anti-Neu5Gc IgY. Specificity is further demonstrated by competitive inhibition with free Neu5Gc or Neu5Gc-glycoproteins, but not with Neu5Ac or Neu5Ac-glycoproteins. This method can be used to evaluate potential Neu5Gc-immunogenicity of xenografts.Protocols are described for preparation of various types of samples for differential protein expression proteomics using nano liquid chromatography-tandem mass spectrometry (nLCMS/MS). Fresh frozen tissue, formalin-fixed paraffin-embedded (FFPE) tissue, cells, pull-downs, immunoprecipitations, and plasma or serum can be processed. For transplantation studies, it should be noted that samples must be comparable; thus, similar cells or organ systems from the same species can be compared when only a minority of the proteins change expression levels. For xenotransplantation studies, caution should be taken, as different species possess proteins with differences in primary structure. The sample preparation technique is based on spin filter devices using sodium deoxycholate (SDC) as detergent for extraction of proteins. The detergent is removed using phase extraction with ethyl acetate, and samples can be used for label-free quantification (LFQ) analysis or peptides can be labeled with tandem mass tags (TMT).Understanding the molecular bases of xenograft rejection is one of the highest priorities in the xenotransplantation field. This information is needed for the successful development of genetic modifications of the animal source of xenogeneic cells and organs that prevent rejection. Furthermore, the identification of physiological incompatibilities in the xenogeneic setting is also necessary for developing the appropriate strategies that allow long-term xenograft function. As the pig is the species of choice for the development of the majority of xenogeneic applications, the cloning of pig genes or cDNA is a key step to elucidate the interactions of pig and human molecules. In addition, there are currently multiple bioinformatic tools which facilitate the study in silico of protein structures, molecular interactions, and docking sites. Thus, we describe a basic cloning method that comprises total RNA extraction, reverse transcription (RT), and polymerase chain reaction (PCR) for cDNA amplification and include some links for databases and bioinformatics tools available on the Internet for the subsequent analyses and predictions. Finally, some procedures of protein expression and analysis of protein interactions by surface plasmon resonance (SPR) are described for elucidating the molecular mechanisms of xenograft function and rejection.