A novel set of hepatic mRNAs preferentially expressed during an acute inflammation in rat represents mostly intracellular proteins

Selecting potential biomarkers of plasma proteins in mares with endometritis

BACKGROUND

Endometritis is a common condition in mares that causes significant economic loss. Lacking obvious clinical signs, the clinical diagnosis of endometritis in mares relies on case-by-case clinical examinations, which can be particularly inefficient in large-scale farms. Therefore, the identification of potential biomarkers can serve as a non-invasive and efficient screening technique for endometritis in mares.

OBJECTIVES

To compare the blood proteome between fertile mares and mares with endometritis to identify biomarkers potentially associated with the development of endometritis and validate their predictive potential.

STUDY DESIGN

Observational and experimental study.

METHODS

Differentially expressed proteins were identified via Data Independent Acquisition (DIA) proteomic profiling in a screening cohort composed of eight healthy mares and eight mares with endometritis. Subsequently, enzyme-linked immunosorbent assay was employed that included a validation cohort of 40 healthy mares and 40 mares with endometritis to verify the accuracy and sensitivity of the identified proteins, thereby establishing a diagnostic threshold.

RESULTS

In the screening cohort, 12 proteins were significantly differentially expressed between endometritis mares and healthy controls (p < 0.05, outside the 1/1.2 to 1.2-fold). In the validation experiment, all six screened proteins were assessed with area under the curve (AUC) >0.8.

MAIN LIMITATIONS

The samples displayed certain levels of individual heterogeneity, and the number of samples analysed was limited. Additionally, the identified biomarkers were primarily associated with generalised inflammation, which potentially limited their specificity for endometritis.

CONCLUSION

Levels of plasma proteins are sensitive indicators of equine endometritis and potential tools for endometritis screening. In plasma, fetuin B, von Willebrand factor, vitamin K-dependent protein C, insulin-like growth factor binding protein 3, interleukin 1 receptor accessory protein, and type II cell cytoskeleton showed great predictive ability, with fetuin B being the best predictor (AUC = 0.93, 95% CI: 0.89-0.98), which performs better when combined with all six detected proteins (AUC = 1, 95% CI: 0.99-1.00).

Hepatokine Fetuin B expression is regulated by leptin-STAT3 signalling and associated with leptin in obesity

Obesity is an expanding global public health problem and a leading cause of metabolic disorders. The hepatokine Fetuin B participates in regulating insulin resistance, glucose metabolism and liver steatosis. However, the mechanism underlying Fetuin B activation remains unclear. Our previous population-based study demonstrated a significant association between serum Fetuin B and body fat mass in an obese population, which indicates its potential in mediating obesity-related metabolic disorders. In the present study, we further revealed a significant correlation between Fetuin B and leptin, the classic adipokine released by expanding adipose tissue, in this obese population. Consistently, elevated Fetuin B and leptin levels were confirmed in diet-induced obese mice. Furthermore, an in vitro study demonstrated that the leptin signalling pathway directly activated the transcription and expression of Fetuin B in primary hepatocytes and AML12 cells in a STAT3-dependent manner. STAT3 binds to the response elements on FetuB promoter to directly activate FetuB transcription. Finally, the mediating effect of Fetuin B in insulin resistance induced by leptin was confirmed according to mediation analysis in this obese population. Therefore, our study identifies leptin-STAT3 as an upstream signalling pathway that activates Fetuin B and provides new insights into the pathogenic mechanisms of obesity-related metabolic disorders.

Complementary liver and serum protein profile in wild boars infected by the giant liver fluke Fascioloides magna using tandem mass tags quantitative approach

Liver fluke, Fascioloides magna, is an important non-native parasite introduced to Europe, posing a threat to survival of local wildlife populations. The aim of this study was to assess the serum and liver protein profile of control and F. magna infected wild boars, by means of shotgun tandem mass tag - based quantitative high resolution proteomics approach. In serum, 4 differentially abundant proteins were found out of total 1073 identified, while in liver from 3520 identified proteins, 116 were differentially abundant between healthy and F. magna infected wild boars. Pathway analysis revealed that most of the proteins differing in abundance are involved in metabolism, biological oxidations, cellular responses to stimuli, fatty acid metabolism, and others. Validation of proteomic results was performed for paraoxonase-1, ceruloplasmin, glutathione S-transferase and liver enzymes by ELISA and automated assays. Complementary analysis of liver and serum in F. magna infection enabled insight into changes of proteome profile of the host at local and sistemic level. Our findings showed that chronic infection with F. magna is associated with immune response in host, oxidative stress and metabolomic changes in liver. SIGNIFICANCE: Liver fluke infections are recognised as worldwide neglected diseases with considerable veterinary and public health importance. Pathological changes, clinical signs and outcome of F. magna infection are strongly related to the type of final hosts and their different tolerance to infection. In order to gain insight into host-parasite interactions in wild boars, dead-end host for F. magna, we assessed proteomics profile of serum and liver of control animals and those infected with F. magna. Proteomics analysis of serum and liver in parallel showed as advantageous and beneficial, demonstrating protein alterations mainly at local level. Bioinformatics analysis enabled elucidation of molecular pathways associated with F. magna infection. Identification and validation of proteins associated with infection may have added value to current tools for efficient liver fluke control.

Identification and expression analysis of fetuin B (FETUB) in turbot (Scophthalmus maximus L.) mucosal barriers following bacterial challenge

Fetuin B (FETUB), a recently described cysteine proteinase inhibitor, has numerous conserved N-glycosylation sites, species-specific O-glycosylation sites, and two cystatin (CY) domains. FETUB is likely to play regulatory roles in acute inflammation, female infertility, fish organogenesis and tumor suppression. In the present study, transcript of turbot FETUB gene was captured, its protein structure and expression patterns in different tissues with emphasis on mucosal barriers following different bacterial infection were characterized. Turbot FETUB gene showed the closest relationship with Takifugu rubripes in phylogenetic analysis. In addition, FETUB was ubiquitously expressed in all examined tissues with the highest expression level in skin. Finally, FETUB gene showed different expression patterns following both bacterial challenge. The rapidly and significantly differential expression patterns of FETUB in mucosal surfaces against bacterial infections might indicate its key roles to prevent pathogen attachment and entry in turbot mucosal immunity. Functional studies should be carried out to further characterize the FETUB and avail utilization of its function to increase the disease resistance of turbot in maintaining the integrity of the mucosal barriers against infections and to facilitate selection of the fine family/varieties of disease resistance in turbot.

Identification of differential pattern of protein expression in canine osteoarthritis serum after anterior cruciate ligament transection: a proteomic analysis

Osteoarthritis (OA) management remains a great challenge and there is considerable effort to understand its pathophysiology and to identify new therapeutic targets and biomarkers. Canine OA surgically induced by the transection of the anterior cruciate ligament (ACLT) is a widely used and relevant model. This study reports a proteome mapping of dog serum and an analysis of the differentially expressed proteins between before and after ACLT. In the first part of the study, 261 picked protein spots were identified from preparative 2D gels and 71 different proteins were identified among the 261 spots present on the reference map. Canine serum proteome mapping reveals the presence of proteins of interest, such as fetuin B, complement C3 and C1s and pregnancy zone protein. The comparison between serum from dogs before and after ACLT reveals the differential expression of several proteins that could play a key role in the pathogenesis of OA. A number of proteins, such as fetuin B and complement C3, were increased in dog OA serum whereas others, such as hyaluronan binding protein 2, inter-alpha-trypsin inhibitor H4 (ITIH4), complement C1s and C4 and haptoglobin were decreased. Some of these proteins could be candidate biomarkers for diagnosis, prognosis and treatment evaluation. The results of the study also reinforced the similarities between dog experimental OA and human cases of OA.

Proteomic techniques identify urine proteins that differentiate patients with interstitial cystitis from asymptomatic control subjects

OBJECTIVE

The purpose of this study was to identify differences in urine proteins between patients with interstitial cystitis (IC) and asymptomatic control (AC) subjects with the use of proteomic techniques.

STUDY DESIGN

Nine patients with IC and their age-, race-, and sex-matched AC subjects volunteered a urine specimen. Urine proteins were separated with the use of 2-dimensional polyacrylamide gels. Differing proteins underwent digestion and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Computer-assisted data analysis was used to identify the corresponding protein. Differences in urine protein responses between patients with IC and AC subjects were evaluated by the Mann-Whitney U test to account for the nonnormal frequency distribution of the parameter estimate or chi-square when data were bimodal.

RESULTS

Four proteins differed significantly between patients with IC and AC subjects. The AC subjects had a greater concentration of a uromodulin (P = .019) and two kininogens (P = .023, .046). The patients with IC had a greater concentration of inter-alpha-trypsin inhibitor heavy chain H4 (P = .019).

CONCLUSION

These urine protein isoforms may be biomarkers for IC.

Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri

The acute nature of disease outbreaks in aquaculture settings has served to emphasize the importance of the innate immune response of fish for survival and led to the recent identification and characterization of many of its components. Catfish, the predominant aquaculture species in the United States, is an important model for the study of the teleost immune system. However, transcriptomic-level studies of disease-related gene expression in catfish have only recently been initiated, and understanding of immune responses to pathogen infections is limited. Here, we have developed and utilized a 28K in situ oligonucleotide microarray composed of blue catfish (Ictalurus furcatus) and channel catfish (Ictalurus punctatus) transcripts. While channel catfish accounts for the majority of commercial production, the closely related blue catfish possesses several economically important phenotypic traits. Microarray analysis of gene expression changes in blue catfish liver after infection with Gram-negative bacterium Edwardsiella ictaluri indicated the strong upregulation of several pathways involved in the inflammatory immune response and potentially in innate disease resistance. A multifaceted response to infection could be observed, encompassing the complement cascade, iron regulation, inflammatory cell signaling, and antigen processing and presentation. The induction of several components of the MHC class I-related pathway following infection with an intracellular bacterium is reported here for the first time in fish. A comparison with previously published expression profiles in the channel catfish liver was also made and the microarray results extended by use of quantitative RT-PCR. Our results add to the understanding of the teleost immune responses and provide a solid foundation for future functional characterization, genetic mapping, and QTL analysis of immunity-related genes from catfish.

Expression of the phospholipid scramblase (PLSCR) gene family during the acute phase response

Phospholipid scramblase 1 (PLSCR1) is a member of PLSCR gene family that has been implicated in multiple cellular processes including movement of phospholipids, gene regulation, immuno-activation, and cell proliferation/apoptosis. In the present study, we identified PLSCR1 as a positive intracellular acute phase protein that is upregulated by LPS in liver, heart, and adipose tissue, but not skeletal muscle. LPS administration resulted in a marked increase in PLSCR1 mRNA and protein levels in the liver. This stimulation occurred rapidly (within 2 h), and was very sensitive to LPS (half-maximal response at 0.1 microg/mouse). Moreover, two other APR-inducers, zymosan and turpentine, also produced significant increases in PLSCR1 mRNA and protein levels, indicating that PLSCR1 was stimulated in a number of models of the APR. To determine signaling pathways by which LPS stimulated PLSCR1, we examined the effect of proinflammatory cytokines in vitro and in vivo. TNFalpha, IL-1beta, and IL-6 all stimulated PLSCR1 in cultured Hep B3 hepatocytes, whereas only TNFalpha stimulated PLSCR1 in cultured 3T3-L1 adipocytes, suggesting cell type-specific effects of cytokines. Furthermore, the LPS-stimulated increase in liver PLSCR1 mRNA was greatly attenuated by 80% in TNFalpha and IL-1beta receptor null mice as compared to wild-type controls. In contrast, PLSCR1 levels in adipose tissue were induced to a similar extent in TNFalpha and IL-1beta receptor null mice and controls. These results indicate that maximal stimulation of PLSCR1 by LPS in liver required TNFalpha and/or IL-1beta, whereas the stimulation of PLSCR1 in adipose tissue is not dependent on TNFalpha and/or IL-1beta. These data provide evidence that PLSCR1 is a positive intracellular acute phase protein with a tissue-specific mechanism for up-regulation.

Genome-wide response of the human Hep3B hepatoma cell to proinflammatory cytokines, from transcription to translation

Given the unknown timing of the onset of an acute systemic inflammation in humans, the fine tuning of cascades and pathways involved in the associated hepatocyte response cannot be appraised in vivo. Therefore, the authors used a genome-wide and kinetic analysis in the human Hep3B hepatoma cell line challenged with a conditioned medium from bacterial lipopolysaccharide-stimulated macrophages. A complete coverage of the liver transcriptome disclosed 648 mRNAs whose change in abundance allowed for their clustering in mRNA subsets with an early, intermediate, or late regulation. The contribution of transcription, stability, or translation was appraised with genome-wide studies of the changes in nuclear primary transcripts, mRNA decay, or polysome-associated mRNAs. A predominance of mRNAs with decreased stability and the fact that translation alone controls a significant number of acute phase-associated proteins are prominent findings. Transcription and stability act independently or, more rarely, cooperate or even counteract in a gene-by-gene manner, which results in a unidirectional change in mRNA abundance. Waves of mRNAs for groups of functionally related proteins are up- or downregulated in an ordered fashion. This includes an early regulation of transcription-associated proteins, an intermediate repression of detoxication and metabolism proteins, and finally an enhanced translation and transport of a number of membranous or secreted proteins along with an enhanced protein degradation. In conclusion, this study provides a comprehensive and simultaneous overview of events in the human hepatocyte during the inflammatory acute phase.

Adjuvants and Antibody Production: Dispelling the Myths Associated with Freund's Complete and Other Adjuvants

Adjuvants have been used for more than 70 yr to enhance the immune response of the host animal to an antigen. Among the mechanisms that adjuvants use to enhance the immune response are the "depot" effect, antigen presentation, antigen targeting, immune activation/modulation, and cytotoxic lymphocyte induction. The immunostimulatory properties of adjuvants result in inflammation, tissue destruction, and the potential for resulting pain and distress in the host animal. The inflammatory lesions produced by adjuvants such as Freund's complete adjuvant (FCA) have led some to conclude that pain and distress are present, even in cases where the scientific evidence fails to support this conclusion. Recommendations and regulations in the literature, based on available scientific evidence, provide guidance on total adjuvant volumes, volumes per site, routes of injection, booster injections, and adjuvants used for antibody production. Among the numerous adjuvants that are used for experimental antibody production reviewed in this article, many claim to be less inflammatory, tissue destructive, and painful than FCA while producing equal or superior antibody responses. Although no adjuvant surpasses FCA for experimental antibody production against a wide range of antigenic molecules, many produce excellent antibody responses with less inflammation and tissue destruction. Balancing the requisite degree of immuno-stimulation and the extent of inflammation, necrosis, and potential pain and distress requires consideration of the nature of the antigen, the host immune responsiveness, the adjuvant's mechanisms of action, and the desired end-product. In cases where the antigen is a weak immunogen or has a very limited availability, the type and role of adjuvant becomes a critical component in producing an acceptable immune response and humoral antibody response.

Identification of changes in the transcriptome profile of human hepatoma HepG2 cells stimulated with interleukin-1 beta

Interleukin-1 (IL-1) is the principal pro-inflammatory cytokine participating in the initiation of acute phase response. Human hepatoma HepG2 cells were exposed to 15 ng/ml of IL-1beta for times ranging from 1 to 24 h and the total RNA was isolated. Then cDNA was obtained and used for differential display with 10 arbitrary primers and 9 oligo(dT) primers designed by Clontech. Validation of observed changes of differentially expressed known genes was carried out by RT-PCR or Northern blot analysis. Out of 90 cDNA strands modulated by IL-1, 46 have been successfully reamplified and their sequencing indicates that they represent 36 different cDNA templates. By GenBank search, 26 cDNA clones were identified as already known genes while 10 showed no homology to any known gene. The identified transcripts modulated by IL-1 in HepG2 cells code for intracellular proteins of various function: trafficking/motor proteins (3 genes), proteins participating in the translation machinery or posttranscriptional/posttranslational modifications (7 genes), proteases (1 gene), proteins involved in metabolism (6 genes), activity modulators (3 genes), proteins of the cell cycle machinery (2 genes) and those functionally unclassified (4 genes). Majority of genes responded to IL-1 within 1 to 6 h (early genes), while two were late response genes (12-24 h) and four showed prolonged response over the whole 24-h period. Most of the observed changes of expression were in the range of two- to threefold increase in comparison to control untreated cells. Among identified genes, no typical secretory acute phase protein was found. The obtained results suggest that IL-1 affects the expression of several genes in HepG2 cells, especially those engaged in the synthesis and modifications of proteins.

Altered gene expression in acute systemic inflammation detected by complete coverage of the human liver transcriptome

The goal of the current study was to provide complete coverage of the liver transcriptome with human probes corresponding to every gene expressed in embryonic, adult, and/or cancerous liver. We developed dedicated tools, namely, the Liverpool nylon array of complementary DNA (cDNA) probes for approximately 10,000 nonredundant genes and the LiverTools database. Inflammation-induced transcriptome changes were studied in liver tissue samples from patients with an acute systemic inflammation and from control subjects. One hundred and fifty-four messenger RNAs (mRNA) correlated statistically with the extent of inflammation. Of these, 134 mRNA samples were not associated previously with an acute-phase (AP) response. The hepatocyte origin and proinflammatory cytokine responsiveness of these mRNAs were confirmed by quantitative reverse-transcription polymerase chain reaction (Q-RT-PCR) in cytokine-challenged hepatoma cells. The corresponding gene promoters were enriched in potential binding sites for inflammation-driven transcription factors in the liver. Some of the corresponding proteins may provide novel blood markers of clinical relevance. The mRNAs whose level is most correlated with the AP extent (P <.05) were enriched in intracellular signaling molecules, transcription factors, glycosylation enzymes, and up-regulated plasma proteins. In conclusion, the hepatocyte responded to the AP extent by fine tuning some mRNA levels, controlling most, if not all, intracellular events from early signaling to the final secretion of proteins involved in innate immunity. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html).

Alterations in the expression and modification of histonesin the liver after injury

Chromatin remodeling plays a key role in the transcriptional activation of regulatory factors in the liver in response to a variety of stress signals. The effects of burn injury on histone expression and its modification were investigated in this study. Liver tissues collected after a flame burn injury were subjected to RT-PCR and Western blot analyses of histone regulation. There was a marked induction of histone H3-D variant mRNA at 3 and 6 h. In contrast, histone H2A.2 variant mRNA had a downregulation at 3 days. No apparent changes were noted in other histone variants examined. Western blot analysis revealed a downregulation of all 5 histone subtypes (H1, H2A, H2B, H3, and H4) at 1 day and there was a subsequent induction of H1 and H2A subtypes at 3 days after injury. There was an induction of modified forms (phospho-, acetyl-, and dimethyl-) of histone H3 subtype at day 3. Furthermore, a transient elevation in PCNA (proliferating cell nuclear antigen) levels was apparent in the liver at day 3, which parallels the induction of phospho-histone H3, which is a mitosis marker. These findings suggest that histones participate in a cascade of events associated with phenotypic alterations in the liver after injury.

Tissue distribution and activity testing suggest a similar but not identical function of fetuin-B and fetuin-A

Fetuins are serum proteins with diverse functions including the regulation of osteogenesis and inhibition of unwanted mineralization. Besides the alpha2-Heremans and Schmid glycoprotein/fetuin-A, the recently identified fetuin-B is a second member of the fetuin family [Olivier, Soury, Risler, Smih, Schneider, Lochner, Jouzeau, Fey and Salier (1999) Genomics 57, 352-364; Olivier, Soury, Ruminy, Husson, Parmentier, Daveau and Salier (2000) Biochem. J. 350, 589-597], which belongs to the cystatin superfamily. We compared the expressions of fetuin-B and fetuin-A at the RNA level and established that both genes are most highly expressed in liver tissue. Like fetuin-A, fetuin-B mRNA is also highly expressed in tongue and placenta tissues. We demonstrated for the first time that fetuin-B is also expressed at the protein level in sera and several organs of mouse, rat and human. We isolated contiguous genomic clones containing both fetuin-B and fetuin-A genes, indicating that these genes are closely linked at the genome level. The close proximity of both these genes may explain our observation that fetuin-B expression was decreased in fetuin-A-deficient mice. Unlike fetuin-A, the amount of fetuin-B protein in human serum varied with gender and was higher in females than in males. Functional analysis revealed that fetuin-B, similarly to fetuin-A, is an inhibitor of basic calcium phosphate precipitation, albeit less active when compared with fetuin-A. Therefore fetuin-B may have a function that is partly overlapping, if not identical, with the function of fetuin-A.

Gene expression analysis of the acute phase response using a canine microarray

The safety of pharmaceuticals is typically assessed in the dog and rat prior to investigation in humans. As a result, a greater understanding of adverse effects in these preclinical testing species would improve safety assessment. Despite this need, there is a lack of tools to examine mechanisms and identify biomarkers in the dog. To address this issue, we developed an Affymetrix-based oligonucleotide microarray capable of monitoring the expression of thousands of canine genes in parallel. The custom canine array contains 22,774 probe sets, consisting of 13,729 canine and 9045 human-derived probe sets. To improve cross-species hybridization with human-derived probes, the detection region was moved from the variable 3' UTR to the more homologous coding region. Testing of this strategy was accomplished by comparing hybridization of naive dog liver RNA to the canine array (coding region design) and human U133A array (standard 3' design). Although raw signal intensity was greater with canine-specific probe sets, human-derived probes detected the expression of additional liver transcripts. To assess the ability of this tool to detect differential gene expression, the acute phase response was examined in beagle dogs given lipopolysaccharide (LPS). Hepatic gene expression 4 and 24 h post-LPS administration was compared to gene expression profiles of vehicle-treated dogs (n=3/group). Array data was consistent with an acute inflammatory response, with transcripts for multiple cytokines and acute phase proteins markedly induced 4 h after LPS challenge. Robust changes in the expression of transcripts involved with glucose homeostasis, biotransformation, and extracellular matrix remodeling were observed 24 h post-dose. In addition, the canine array identified several potential biomarkers of hepatic inflammation. Strong correlations were found between gene expression data and alterations in clinical chemistry parameters such as serum amyloid A (SAA), albumin, and alkaline phosphatase (ALP). In summary, this new genomic tool successfully detected basal canine gene expression and identified novel aspects of the acute phase response in dog that shed new light on mechanisms underlying inflammatory processes.

A new tool for rheumatology: large-scale analysis of gene expression

Large-scale analysis of gene expression with cDNA arrays is spreading over many biological fields, including rheumatology. In this report, we wish to explain the principle and main advantages of this tool in the context of our discipline. Until 1995, analysis of gene expression was conducted for a few genes at a time but DNA chips now allow one to monitor the expression of thousands of genes in a single experiment and analyze the transcriptome, i.e. the whole of the transcripts in a given cell or tissue. Whatever the platform used (macro- or microarrays, oligo-chips), this technology rests upon the hybridization of i) a set of cDNA clones tethered to a solid support (nylon or glass) as probes, and ii) labelled cDNAs that are reverse-transcribed from bulk mRNAs extracted from a cell or tissue sample as a target. The end result is information on the relative abundance of every mRNA between two or more samples. The transcriptome analysis has two main objectives in rheumatology: i) identifying a gene expression profile that is a hallmark of a pathology and using it for a diagnostic or prognostic purpose, and ii) gathering genes with similar changes of expression, which allows one to specify the identity of novel proteins involved in a well-known intracellular cascade of regulation or even to identify new cascades.