Proteomic analysis of swine serum following highly virulent classical swine fever virus infection

Proteomic methods for the study of porcine acute phase proteins - anything new to detect?

Acute phase proteins (APPs) reflect the health status of individuals and are important tools in diagnostics, as their altered levels are a sign of disturbed homeostasis. While, in most cases, quantitation of known serum APPs is routinely performed by immunoassays, proteomics is helpful in discovery of new biomarker candidates, especially in samples other than body fluids. Besides putting APP regulation into an overall context of differentially abundant proteins, this approach can detect further details or outright new features in protein structure or specific modifications, and help understand better their function. Thus, it can show up ways to make present diagnostic assays more sensitive and/or specific, or correlate regulations of disease-specific proteins. The APP repertoire is dependent on the species. The pig is both, an important farm animal and a model animal for human diseases, due to similarities in physiology. Besides reviewing existing literature, yet unpublished examples for two-dimensional electrophoresis in connection with pig APPs highlight some of the benefits of proteomics. Of further help would be the emerging targeted proteomics, offering the possibility to determine particular isoforms or proteoforms, without the need of specific antibodies, but this method is presently scarcely used in veterinary medicine.

African swine fever virus infection activates inflammatory responses through downregulation of the anti-inflammatory molecule C1QTNF3

African swine fever (ASF) is the most dangerous pig disease, and causes enormous economic losses in the global pig industry. However, the mechanisms of ASF virus (ASFV) infection remains largely unclear. Hence, this study investigated the host response mechanisms to ASFV infection. We analyzed the differentially expressed proteins (DEPs) between serum samples from ASFV-infected and uninfected pigs using quantitative proteomics. Setting the p-value < 0.05 and |log2 (fold change)| > 1.5, we identified 173 DEPs, comprising 57 upregulated and 116 downregulated proteins, which belonged to various biological processes and pathways based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. The enriched pathways include immune responses, metabolism, and inflammation signaling pathways. Western blot analysis validated the DEPs identified using quantitative proteomics. Furthermore, our proteomics data showed that C1QTNF3 regulated the inflammatory signaling pathway. C1QTNF3 knockdown led to the upregulation of pro-inflammatory factors IL-1β, IL-8, and IL-6, thus inhibiting ASFV replication. These results indicated that C1QTNF3 was critical for ASFV infection. In conclusion, this study revealed the molecular mechanisms underlying the host-ASFV interaction, which may contribute to the development of novel antiviral strategies against ASFV infection in the future.

Liquid chromatography-tandem mass spectrometry glycoproteomic study of porcine IgG and detection of subtypes

RATIONALE

While high-throughput proteomic methods have been widely applied to monoclonal antibodies and human immunoglobulin gamma (IgG) samples, less information is available on porcine IgG. As pigs are considered one of the most suitable species for xenotransplantation, it is important to characterize IgG amino acid sequences and glycosylation profiles, which is the focus of this study.

METHODS

Three different purified porcine IgG samples, including wild-type and knockout species, were digested with trypsin and enriched for glycopeptides. Digestion mixtures were spiked with a mixture of six standard peptides. Analysis was performed using electrospray ionization liquid chromatography-tandem mass spectrometry (MS/MS) in standard MS/MS data-dependent acquisition mode on a hybrid triple quadrupole time-of-flight mass spectrometer.

RESULTS

To facilitate the classification of subtypes detected experimentally, UniprotKB database entries were organized using comparative alignment scores. Sequences were grouped based on 11 different subtypes as translated from GenBank entries. Proteomic searches were accomplished automatically using specialized software, whereas glycoprotein searches were performed manually by monitoring the extracted chromatograms of diagnostic MS/MS glycan fragments and studying their corresponding mass spectra; 40-50 non-glycosylated peptides and 4-5 glycosylated peptides were detected in each sample, with several glycoforms per sequence.

CONCLUSIONS

Proteomic analysis of porcine IgG is complicated by factors such as the presence of several subtypes, redundant heavy chain (HC) sequences in protein databases, and the lack of consistent cross-referencing between databases. Aligning and comparing HC sequences were necessary to eliminate redundancy. This study highlights the complexity of pig IgG and shows the importance of MS in proteomics and glycoproteomics.

Proteomics profiling of swine serum following lipopolysaccharide stimulation

RATIONALE

There are no approved animal drugs for management of inflammation in swine due to lack of validated animal models. To assess efficacy, it was essential to develop proteomics approaches to identify suitable biomarkers of inflammation as presented in this study.

METHODS

Serum samples were collected from a group of four pigs prior to (baseline) and 24 and 48 h following lipopolysaccharide (LPS) stimulation to reveal proteomic changes during inflammation. Two other pigs served as untreated controls. Proteins were separated by either one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or two-dimensional (2D) gel electrophoresis (2DE) prior to analysis by nano-flow liquid chromatography (nLC) coupled to tandem mass spectrometry (MS/MS).

RESULTS

We identified 165 proteins using SDS-PAGE, of which 47 proteins were also detected by 2DE prior to nLC/MS/MS. More than half (72%) of all characterized proteins were modulated as a result of LPS stimulation, many of which are known to be involved with innate and adaptive immunity. Pig serum samples obtained 24 h after LPS initiation of inflammation showed protein modulations of serum albumin, serotransferrin, light and heavy immunoglobulin chains (IGs), and major acute phase proteins including haptoglobin (HPT), serum amyloid A2 (SAA2), C-reactive protein (CRP), β-2-glycoprotein 1 (B-2GP1), alpha-2-HS-glycoprotein (A2HS), α-1-antitrypsin (A1AT), and α-1-acid glycoprotein (A1AG). SAA2 was distinguished from the other SAA isoforms by the unique peptide sequence of SAA2.

CONCLUSIONS

The results provided proteomics analysis of swine serum due to LPS stimulation and indicated the importance of SAA2, which appears to be unique and may be regarded as a potential clinical diagnostic biomarker of inflammation.

Comparative Proteomic Analysis of Serum from Pigs Experimentally Infected with Trichinella spiralis, Trichinella britovi, and Trichinella pseudospiralis

Although the available proteomic studies have made it possible to identify and characterize Trichinella stage-specific proteins reacting with infected host-specific antibodies, the vast majority of these studies do not provide any information about changes in the global proteomic serum profile of Trichinella-infested individuals. In view of the above, the present study aimed to examine the protein expression profile of serum obtained at 13 and 60 days postinfection (d.p.i.) from three groups of pigs experimentally infected with Trichinella spiralis, Trichinella britovi, and Trichinella pseudospiralis and from uninfected, control pigs by two-dimensional gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The comparative proteomic analysis of the T. spiralis group vs. the control group revealed 5 differently expressed spots at both 13 and 60 d.p.i. Experimental infection with T. britovi induced significant expression changes in 3 protein spots at 13 d.p.i. and in 6 protein spots at 60 d.p.i. in comparison with the control group. Paired analyses between the group infected with T. pseudospiralis and the uninfected control group revealed 6 differently changed spots at 13 d.p.i. and 2 differently changed spots at 60 d.p.i. Among these 27 spots, 15 were successfully identified. Depending on the Trichinella species triggering the infection and the time point of serum collection, they were IgM heavy-chain constant region, antithrombin III-precursor, immunoglobulin gamma-chain, clusterin, homeobox protein Mohawk, apolipoprotein E precursor, serum amyloid P-component precursor, Ig lambda chains, complement C3 isoform X1, and apolipoprotein A-I. Our results demonstrate that various Trichinella species and different phases of the invasion produce a distinct, characteristic proteomic pattern in the serum of experimentally infected pigs.

Differential quantitative proteomics study of experimental Mannheimia haemolytica mastitis in sheep

Objective was the differential quantitative proteomics study of ovine mastitis induced by Mannheimia haemolytica; clinical, microbiological, cytological and histopathological methods were employed for confirmation and monitoring. Proteins were separated by two-dimensional gel electrophoresis (2-DE) for all samples and differentially abundant proteins were identified by mass spectrometry; comparisons were performed with pre- (blood, milk) and post- (milk of contralateral gland) inoculation findings. Animals developed mastitis, confirmed by isolation of challenge strain and increase of neutrophils in milk and by histopathological evidence. In blood plasma, 33 differentially abundant proteins (compared to findings before challenge) were identified: 6 with decrease, 13 with new appearance and 14 with varying abundance. In a post-challenge milk whey protein reference map, 65 proteins were identified; actin cytoplasmic-1, beta-lactoglobulin-1/B, cathelicidin-1 predominated. Further, 89 differentially abundant proteins (compared to findings before challenge) were identified: 18 with decrease, 53 with new appearance, 3 with increase and 15 with varying abundance; 15 proteins showed status changes in blood plasma and milk whey. Differential abundance from inoculated and contralateral glands revealed 74 proteins only from the inoculated gland. Most differentially abundant proteins in milk whey were involved in cell organisation and biogenesis (n = 17) or in inflammatory and defence response (n = 13). SIGNIFICANCE: The proteomes of blood and milk from ewes with experimental mastitis caused by Mannheimia haemolytica and the differential proteomics in sequential samples after challenge are presented for the first time. This is the first detailed proteomics study in M. haemolytica-associated mastitis in ewes. An experimental model fully simulating natural mastitis has been used. Use of experimentally induced mastitis minimised potential variations and allowed consistency of results. The study included evaluation of changes in blood plasma and milk whey. Protein patterns have been studied, indicating with great accuracy changes that had occurred as part of the disease process and development, during the acute phase of infection. Relevant protein-protein interactions were studied. The entirety of proteomics findings has suggested that affected ewes had mounted a defence response that had been regulated by many proteins (e.g., cathelicidins, haptoglobin, serum amyloid A) and through various pathways (e.g., acute phase response, binding and transporting significant ions and molecules); these were interdependent at various points. Potential biomarkers have been indicated for use in diagnostic assays of mastitis.

Cellular Hsp27 interacts with classical swine fever virus NS5A protein and negatively regulates viral replication by the NF-κB signaling pathway

Classical swine fever virus (CSFV) nonstructural protein NS5A is a multifunctional protein functioning in regulation of viral genome replication, protein translation and assembly by interaction with viral or host proteins. Here, heat shock protein 27 (Hsp27) has been identified as a novel binding partner of NS5A by using His tag "pull down" coupled with shotgun LC-MS/MS, with interaction of both proteins further confirmed by co-immunoprecipitation and laser confocal assays. In PK-15 cells, silencing of Hsp27 expression by siRNA enhanced CSFV replication, and upregulation of Hsp27 inhibited viral proliferation. Additionally, we have shown that overexpression of Hsp27 increased NF-κB signaling induced by TNFα. Blocking NF-κB signaling in PK-15 cells overexpressing Hsp27 by ammonium pyrrolidinedithiocarbamate (PDTC) eliminated the inhibition of CSFV replication by Hsp27. These findings clearly demonstrate that the inhibition of CSFV replication by Hsp27 is mediated via the NF-κB signaling pathway.

Classical swine fever in pigs: recent developments and future perspectives

Classical swine fever (CSF) is one of the most devastating epizootic diseases of pigs, causing high morbidity and mortality worldwide. The diversity of clinical signs and similarity in disease manifestations to other diseases make CSF difficult to diagnose with certainty. The disease is further complicated by the presence of a number of different strains belonging to three phylogenetic groups. Advanced diagnostic techniques allow detection of antigens or antibodies in clinical samples, leading to implementation of proper and effective control programs. Polymerase chain reaction (PCR)-based methods, including portable real-time PCR, provide diagnosis in a few hours with precision and accuracy, even at the point of care. The disease is controlled by following a stamping out policy in countries where vaccination is not practiced, whereas immunization with live attenuated vaccines containing the 'C' strain is effectively used to control the disease in endemic countries. To overcome the problem of differentiation of infected from vaccinated animals, different types of marker vaccines, with variable degrees of efficacy, along with companion diagnostic assays have been developed and may be useful in controlling and even eradicating the disease in the foreseeable future. The present review aims to provide an overview and status of CSF as a whole with special reference to swine husbandry in India.

Discovery and characterization of potential prognostic biomarkers for dengue hemorrhagic fever

Half a million patients are hospitalized with severe dengue every year, many of whom would die without timely, appropriate clinical intervention. The majority of dengue cases are uncomplicated; however, 2-5% progress to severe dengue. Severe dengue cases have been reported with increasing frequency over the last 30 years. To discover biomarkers for severe dengue, we used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry to analyze dengue virus positive serum samples from the acute phase of infection. Using this method, 16 proteins were identified as candidate biomarkers for severe dengue. From these 16 biomarkers, three candidates were selected for confirmation by enzyme-linked immunosorbent assay and Western blot: vitronectin (Vtn, 55.1 kDa), hemopexin (Hx, 52.4 kDa), and serotransferrin (Tf, 79.2 kDa). Vitronectin, Hx, and Tf best differentiated between dengue and severe dengue.

Farm animal serum proteomics and impact on human health

Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum proteomics in order to identify novel biomarkers for animal welfare, early diagnosis, prognosis and monitoring of infectious disease treatment, and develop new vaccines, aiming at determining the reciprocal benefits for humans and animals.

Analysis of the bovine plasma proteome by matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry

In this study, the bovine plasma proteome was analysed using a three step protocol: (1) plasma was treated with a combinatorial peptide ligand library (CPLL) to assimilate the differences in concentrations of different proteins in raw plasma; (2) CPLL-treated material was fractionated by three standard electrophoretic separation techniques, and (3) samples were analysed by nano-liquid chromatography (nLC) matrix-assisted laser desorption/ionisation (MALDI) time-of-flight tandem (TOF/TOF) mass spectrometry. The efficiencies of three fractionation protocols for plasma proteome analysis were compared. After size fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), resolution of proteins was better and yields of identified proteins were higher than after charge-based fractionation by preparative gel-free isoelectric focussing. For proteins with isoelectric points >6 and molecular weights ⩾ 63 kDa, the best results were obtained with a 'shotgun' approach, in which the CPLL-treated plasma was digested and the peptides, rather than the proteins, were fractionated by gel-free isoelectric focussing. However, the three fractionation techniques were largely complementary, since only about one-third of the proteome was identified by each approach.

Proteomics in Veterinary Medicine

Advancement in electrophoresis and mass spectrometry techniques along with the recent progresses in genomics, culminating in bovine and pig genome sequencing, widened the potential application of proteomics in the field of veterinary medicine. The aim of the present review is to provide an in-depth perspective about the application of proteomics to animal disease pathogenesis, as well as its utilization in veterinary diagnostics. After an overview on the various proteomic techniques that are currently applied to veterinary sciences, the article focuses on proteomic approaches to animal disease pathogenesis. Included as well are recent achievements in immunoproteomics (ie, the identifications through proteomic techniques of antigen involved in immune response) and histoproteomics (ie, the application of proteomics in tissue processed for immunohistochemistry). Finally, the article focuses on clinical proteomics (ie, the application of proteomics to the identification of new biomarkers of animal diseases).

Current approaches on viral infection: proteomics and functional validations

Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way.

Serum proteome changes in dengue virus-infected patients from a dengue-endemic area of India: towards new molecular targets?

The global burden of dengue continues to worsen, specifically in tropical and subtropical countries, and has evolved as a major public health problem. We investigated the changes in serum proteome in dengue fever (DF) patients from a dengue-endemic area of India to obtain mechanistic insights about the disease pathogenesis, the host immune response, and identification of potential serum protein biomarkers of this infectious disease. In this study, serum samples from DF patients, healthy subjects, and patients with falciparum malaria (an infectious disease control) were investigated by 2D-DIGE in combination with MALDI-TOF/TOF MS. The findings were validated with Western blotting. Functional clustering of the identified proteins was performed using PANTHER and DAVID tools. Compared to the healthy controls, we found significant changes in the expression levels of 48 protein spots corresponding to 18 unique proteins (7 downregulated and 11 upregulated) in DF patients (p<0.05). Among these differentially-expressed proteins, 11 candidates exhibited different trends in dengue fever compared to falciparum malaria. Importantly, our results suggest that dengue virus infection leads to alterations in expression levels of multiple serum proteins involved in diverse and vital physiological pathways, including acute phase response signaling, complement cascades, hemostasis, and blood coagulation. For the first time we report here that the serum levels of hemopexin, haptoglobin, serum amyloid P, and kininogen precursor, are altered in DF. This study informs the pathogenesis and host immune response to dengue virus infection, as well as the current search for new diagnostic and molecular drug targets.