Proteomic analysis of liver tissues subjected to early ischemia/reperfusion injury during human orthotopic liver transplantation

Distinctive protein expression in elderly livers in a Sprague-Dawley rat model of normothermic ex vivo liver machine perfusion

BACKGROUND

Liver grafts are frequently declined due to high donor age or age mismatch with the recipient. To improve the outcome of marginal grafts, we aimed to characterize the performance of elderly vs. young liver grafts in a standardized rat model of normothermic ex vivo liver machine perfusion (NMP).

METHODS

Livers from Sprague-Dawley rats aged 3 or 12 months were procured and perfused for 6 h using a rat NMP system or collected as a reference group (n = 6/group). Tissue, bile, and perfusate samples were used for biochemical, and proteomic analyses.

RESULTS

All livers cleared lactate during perfusion and continued to produce bile after 6 h of perfusion (614 mg/h). Peak urea levels in 12-month-old animals were higher than in younger animals. Arterial and portal venous pressure, bile production and pH did not differ between groups. Proteomic analysis identified a total of 1477 proteins with oxidoreductase and catalytic activity dominating the gene ontology analysis. Proteins such as aldehyde dehydrogenase 1A1 and 2-Hydroxyacid oxidase 2 were significantly more present in livers of older age.

CONCLUSIONS

Young and elderly liver grafts exhibited similar viability during NMP, though proteomic analyses indicated that older grafts are less resilient to oxidative stress. Our study is limited by the elderly animal age, which corresponds to mature but not elderly human age typically seen in marginal human livers. Nevertheless, reducing oxidative stress could be a promising therapeutic target in the future.

Genome-wide DNA methylation and transcriptomic analysis of liver tissues subjected to early ischemia/reperfusion injury upon human liver transplantation

INTRODUCTION AND OBJECTIVES

Epigenetic changes represent a mechanism connecting external stresses with long-term modifications of gene expression programs. In solid organ transplantation, ischemia-reperfusion injury (IRI) appears to induce epigenomic changes in the graft, although the currently available data are extremely limited. The present study aimed to characterize variations in DNA methylation and their effects on the transcriptome in liver transplantation from brain-dead donors.

PATIENTS AND METHODS

12 liver grafts were evaluated through serial biopsies at different timings in the procurement-transplantation process: T0 (warm procurement, in donor), T1 (bench surgery), and T2 (after reperfusion, in recipient). DNA methylation (DNAm) and transcriptome profiles of biopsies were analyzed using microarrays and RNAseq.

RESULTS

Significant variations in DNAm were identified, particularly between T2 and T0. Functional enrichment of the best 1000 ranked differentially methylated promoters demonstrated that 387 hypermethylated and 613 hypomethylated promoters were involved in spliceosomal assembly and response to biotic stimuli, and inflammatory immune responses, respectively. At the transcriptome level, T2 vs. T0 showed an upregulation of 337 and downregulation of 61 genes, collectively involved in TNF-α, NFKB, and interleukin signaling. Cell enrichment analysis individuates macrophages, monocytes, and neutrophils as the most significant tissue-cell type in the response.

CONCLUSIONS

In the process of liver graft procurement-transplantation, IRI induces significant epigenetic changes that primarily act on the signaling pathways of inflammatory responses dependent on TNF-α, NFKB, and interleukins. Our DNAm datasets are the early IRI methylome literature and will serve as a launch point for studying the impact of epigenetic modification in IRI.

Downregulation of praja2 restrains endocytosis and boosts tyrosine kinase receptors in kidney cancer

Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer in the adult population. Late diagnosis, resistance to therapeutics and recurrence of metastatic lesions account for the highest mortality rate among kidney cancer patients. Identifying novel biomarkers for early cancer detection and elucidating the mechanisms underlying ccRCC will provide clues to treat this aggressive malignant tumor. Here, we report that the ubiquitin ligase praja2 forms a complex with-and ubiquitylates the AP2 adapter complex, contributing to receptor endocytosis and clearance. In human RCC tissues and cells, downregulation of praja2 by oncogenic miRNAs (oncomiRs) and the proteasome markedly impairs endocytosis and clearance of the epidermal growth factor receptor (EGFR), and amplifies downstream mitogenic and proliferative signaling. Restoring praja2 levels in RCC cells downregulates EGFR, rewires cancer cell metabolism and ultimately inhibits tumor cell growth and metastasis. Accordingly, genetic ablation of praja2 in mice upregulates RTKs (i.e. EGFR and VEGFR) and induces epithelial and vascular alterations in the kidney tissue.In summary, our findings identify a regulatory loop between oncomiRs and the ubiquitin proteasome system that finely controls RTKs endocytosis and clearance, positively impacting mitogenic signaling and kidney cancer growth.

Contribution of Proteomics in Transplantation: Identification of Injury and Rejection Markers

Solid organ transplantation saves thousands of lives suffering from end-stage diseases. Although early transplants experienced acute organ injury, medical breakthroughs, such as tissue typing, and use of immunosuppressive agents have considerably improved graft survival. However, the overall incidence of allograft injury and chronic rejection remains high. Often the clinical manifestations of organ injury or rejection are nonspecific and late. Current requirement for successful organ transplantation is the identification of reliable, accurate, disease-specific, noninvasive methods for the early diagnosis of graft injury or rejection. Development of noninvasive techniques is important to allow routine follow-ups without the discomfort and risks associated with a graft biopsy. Multiple biofluids have been successfully tested for the presence of potential proteomic biomarkers; these include serum, plasma, urine, and whole blood. Kidney transplant research has provided significant evidence to the potential of proteomics-based biomarkers for acute and chronic kidney rejection, delayed graft function, early detection of declining allograft health. Multiple proteins have been implicated as biomarkers; however, recent observations implicate the use of similar canonical pathways and biofunctions associated with graft injury/rejection with altered proteins as potential biomarkers. Unfortunately, the current biomarker studies lack high sensitivity and specificity, adding to the complexity of their utility in the clinical space. In this review, we first describe the high-throughput proteomics technologies and then discuss the outcomes of proteomics profiling studies in the transplantation of several organs. Existing literature provides hope that novel biomarkers will emerge from ongoing efforts and guide physicians in delivering specific therapies to prolong graft survival.

Liver Graft Proteomics Reveals Potential Incipient Mechanisms behind Early Renal Dysfunction after Liver Transplantation

Acute kidney injury (AKI) is frequent after liver transplantation (LT) and correlates with later development of chronic kidney disease. Its etiology is multifactorial and combines pre-, intra-, and postoperative factors. Additionally, the liver graft itself seems an important element in the development of AKI, yet the detailed mechanisms remain unclear. We hypothesized that grafts of LT recipients developing significant early AKI may show distinct proteomic alterations, and we set out to identify proteome differences between LT recipients developing moderate or severe AKI (n = 7) and LT recipients without early renal injury (n = 7). Liver biopsies obtained one hour after reperfusion were assessed histologically and using quantitative proteomics. Several cytokines and serum amyloid A2 (SAA2) were analyzed in serum samples obtained preoperatively, 2−4 h, and 20−24 h after graft reperfusion, respectively. LT induced mild histological alterations without significant differences between groups but uniformly altered liver function tests peaking on postoperative day 1, with a trend towards more severe alterations in patients developing AKI. Global quantitative proteomic analysis revealed 136 proteins differing significantly in their expression levels (p < 0.05, FC 20%): 80 proteins had higher and 56 had lower levels in the AKI group. Most of these proteins were related to immune and inflammatory responses, host defense, and neutrophil degranulation. No differences between the studied pro- and anti-inflammatory cytokines or SAA2 between groups were found at any moment. Our results suggest that grafts of LT patients who develop early AKI reveal a distinct proteome dominated by an early yet prominent activation of the innate immunity. These findings support the hypothesis that AKI after LT may be favored by certain graft characteristics.

Proteomics in Liver Transplantation: A Systematic Review

Background

Although proteomics has been employed in the study of several models of liver injury, proteomic methods have only recently been applied not only to biomarker discovery and validation but also to improve understanding of the molecular mechanisms involved in transplantation.

Methods

The study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology and the guidelines for performing systematic literature reviews in bioinformatics (BiSLR). The PubMed, ScienceDirect, and Scopus databases were searched for publications through April 2020. Proteomics studies designed to understand liver transplant outcomes, including ischemia-reperfusion injury (IRI), rejection, or operational tolerance in human or rat samples that applied methodologies for differential expression analysis were considered.

Results

The analysis included 22 studies after application of the inclusion and exclusion criteria. Among the 497 proteins annotated, 68 were shared between species and 10 were shared between sample sources. Among the types of studies analyzed, IRI and rejection shared a higher number of proteins. The most enriched pathway for liver biopsy samples, IRI, and rejection was metabolism, compared to cytokine-cytokine receptor interactions for tolerance.

Conclusions

Proteomics is a promising technique to detect large numbers of proteins. However, our study shows that several technical issues such as the identification of proteoforms or the dynamic range of protein concentration in clinical samples hinder the successful identification of biomarkers in liver transplantation. In addition, there is a need to minimize the experimental variability between studies, increase the sample size and remove high-abundance plasma proteins.

Global proteome profiling of human livers upon ischemia/reperfusion treatment

Hepatic ischemia/reperfusion (I/R) injury represents a major risk factor for liver transplantation and is related to graft dysfunction and acute/chronic rejection. However, a significant part of these processes remain poorly characterized. To reveal differences in the proteome during liver I/R injury, we collected human liver biopsy samples during hepatectomy before and after the Pringle maneuver and conducted a TMT-based proteomic analysis through quantitative high-throughput mass spectrometry. We used a fold-change threshold of 1.3 and a t-test p-value < 0.05 as the criteria to identify 5,257 total quantifiable proteins. The levels of 142 proteins were increased, while the levels of 103 proteins were decreased in response to hepatic I/R treatment. Bioinformatic analysis further revealed that these differentially expressed proteins are mainly involved in multiple biological functions and enzyme-regulated metabolic pathways. Most proteins whose expression was changed are related to the defense, immune and inflammatory responses as well as lipid and steroid metabolic processes. Based on this finding, we developed a panel for targeted proteomic analysis and used the parallel reaction monitoring (PRM) method, qPCR and western blotting experiments to validate alterations in the expression of some of the identified proteins. The upregulated proteins were found to be involved in immunity and inflammatory responses, and downregulated proteins were enriched in metabolic pathways. This study therefore may provide a research direction for the design of new therapeutic strategies for hepatic ischemia/reperfusion injury.

Comprehensive and combined omics analysis reveals factors of ischemia-reperfusion injury in liver transplantation

AIM

To explore molecular mechanisms underlying liver ischemia-reperfusion injury (IRI).

MATERIALS & METHODS

Four Gene Expression Omnibus datasets comprising liver transplantation data were collected for a comprehensive analysis. A proteomic analysis was performed and used for correlations analysis with transcriptomic.

RESULTS & CONCLUSION

Ten differentially expressed genes were co-upregulated in four Gene Expression Omnibus datasets, including ATF3, CCL4, DNAJB1, DUSP5, JUND, KLF6, NFKBIA, PLAUR, PPP1R15A and TNFAIP3. The combined analysis demonstrated ten coregulated genes/proteins, including HBB, HBG2, CA1, SLC4A1, PLIN2, JUNB, HBA1, MMP9, SLC2A1 and PADI4. The coregulated differentially expressed genes and coregulated genes/proteins formed a tight interaction network and could serve as the core factors underlying IRI. Comprehensive and combined omics analyses revealed key factors underlying liver IRI, and thus having potential clinical significance.

Poplar woody taproot under bending stress: the asymmetric response of the convex and concave sides

Background and Aims Progress has been made in understanding the physiological and molecular basis of root response to mechanical stress, especially in the model plant Arabidopsis thaliana, in which bending causes the initiation of lateral root primordia toward the convex side of the bent root. In the case of woody roots, it has been reported that mechanical stress induces an asymmetric distribution of lateral roots and reaction wood formation, but the mechanisms underlying these responses are largely unknown. In the present work, the hypothesis was tested that bending could determine an asymmetric response in the two sides of the main root axis as cells are stretched on the convex side and compressed on the concave side. Methods Woody taproots of 20 seedlings were bent to an angle of 90° using a steel net. Changes in the anatomy, lignin and phytohormone content and proteome expression in the two sides of the bent root were analysed; anatomical changes, including dissimilarities and similarities to those found in poplar bent woody stem, were also considered. Key Results Compression forces at the concave side of poplar root induced the formation of reaction wood which presented a high lignin content and was associated with the induction of cambium cell activity. Auxin seemed to be the main hormone triggering lignin deposition and cell wall strengthening in the concave sides. Abscisic acid appeared to function in the water stress response induced by xylem structures and/or osmotic alterations in the compression sides, whereas gibberellins may control cell elongation and gravitropisms. Conclusions Poplar root reaction wood showed characteristics different from those produced in bent stem. Besides providing biomechanical functions, a bent root ensures water uptake and transport in the deforming condition induced by tension and compression forces by two different strategies: an increase in xylem thickness in the compressed side, and lateral root formation in the tension side.

Global MicroRNA Expression Profiling of Mouse Livers following Ischemia-Reperfusion Injury at Different Stages

Hepatic ischemia-reperfusion injury is a dynamic process consisting of two stages: ischemia and reperfusion, and triggers a cascade of physiological and biochemical events. Given the important role of microRNAs in regulating gene expression, we analyzed gene expression changes in mouse livers at sham control, ischemia stage, and reperfusion stage. We generated global expression profiles of microRNA and mRNA genes in mouse livers subjected to ischemia-reperfusion injury at the three stages, respectively. Comparison analysis showed that reperfusion injury had a distinct expression profile whereas the ischemia sample and the sham control were clustered together. Consistently, there are 69 differentially expressed microRNAs between the reperfusion sample and the sham control whereas 28 differentially expressed microRNAs between the ischemia sample and the sham control. We further identified two modes of microRNA expression changes in ischemia-reperfusion injury. Functional analysis of both the differentially expressed microRNAs in the two modes and their target mRNAs revealed that ischemia injury impaired mitochondrial function, nutrient consumption, and metabolism process. In contrast, reperfusion injury led to severe tissue inflammation that is predominantly an innate-immune response in the ischemia-reperfusion process. Our staged analysis of gene expression profiles provides new insights into regulatory mechanisms of microRNAs in mouse hepatic IR injury.

A proteomic analysis of transplanted liver in a rat model of chronic rejection

BACKGROUND

Chronic rejection (CR) is an important cause of liver allograft failure. In the latter condition, re-transplantation of the liver (ReLT) is the only option for survival. Unfortunately, with the current state of knowledge, it is difficult to diagnose and treat early CR.

OBJECTIVE

To explore the biomarkers of the chronic rejection in orthotopic liver transplantation (OLT).

METHODS

A rat model of chronic liver allograft rejection was established, and the differential protein expression in chronic allograft rejection (CR) was analyzed by iTRAQ-MALDI-TOF/TOF.

RESULTS

Expression of sixty-two proteins was found to be significantly changed in CR rats. In the present study, CLU, Lcn2 and Krt19 were identified and quantified as early and reliable biomarkers for chronic rejection.

CONCLUSION

Analysis of differential protein expression by iTRAQ-MALDI-TOF/TOF is a potentially effective method to help understand the mechanism of CR in orthotopic liver transplantation. The proteins CLU, Lcn2 and Krt19 might be potential prognostic markers for predicting chronic rejection after liver transplantation.

Impairment of enzymatic antioxidant defenses is associated with bilirubin-induced neuronal cell death in the cerebellum of Ugt1 KO mice

Severe hyperbilirubinemia is toxic during central nervous system development. Prolonged and uncontrolled high levels of unconjugated bilirubin lead to bilirubin-induced encephalopathy and eventually death by kernicterus. Despite extensive studies, the molecular and cellular mechanisms of bilirubin toxicity are still poorly defined. To fill this gap, we investigated the molecular processes underlying neuronal injury in a mouse model of severe neonatal jaundice, which develops hyperbilirubinemia as a consequence of a null mutation in the Ugt1 gene. These mutant mice show cerebellar abnormalities and hypoplasia, neuronal cell death and die shortly after birth because of bilirubin neurotoxicity. To identify protein changes associated with bilirubin-induced cell death, we performed proteomic analysis of cerebella from Ugt1 mutant and wild-type mice. Proteomic data pointed-out to oxidoreductase activities or antioxidant processes as important intracellular mechanisms altered during bilirubin-induced neurotoxicity. In particular, they revealed that down-representation of DJ-1, superoxide dismutase, peroxiredoxins 2 and 6 was associated with hyperbilirubinemia in the cerebellum of mutant mice. Interestingly, the reduction in protein levels seems to result from post-translational mechanisms because we did not detect significant quantitative differences in the corresponding mRNAs. We also observed an increase in neuro-specific enolase 2 both in the cerebellum and in the serum of mutant mice, supporting its potential use as a biomarker of bilirubin-induced neurological damage. In conclusion, our data show that different protective mechanisms fail to contrast oxidative burst in bilirubin-affected brain regions, ultimately leading to neurodegeneration.

Mouse hepatocytes and LSEC proteome reveal novel mechanisms of ischemia/reperfusion damage and protection by A2aR stimulation

BACKGROUND & AIMS

Ischemia-reperfusion (IR) of liver results in hepatocytes (HP) and sinusoidal endothelial cells (LSEC) irreversible damage. Ischemic preconditioning protects IR damage upon adenosine A2a receptor (A2aR) stimulation. Understanding the phenotypic changes that underlie hepatocellular damage and protection is critical to optimize strategies against IR.

METHODS

The proteome of HP and LSEC, isolated from sham or IR exposed mice, receiving or not the A2aR agonist CGS21680 (0.5mg/kg b.w.), was analyzed by 2-D DIGE/MALDI-TOF.

RESULTS

We identified 64 proteins involved in cytoprotection, regeneration, energy metabolism and response to oxidative stress; among them, 34 were associated with IR injury and A2aR protection. The main pathways, downregulated by IR and upregulated by CGS21680 in HP and LSEC, were related to carbohydrate, protein and lipid supply and metabolism. In LSEC, IR reduced stress response enzymes that were instead upregulated by CGS21680 treatment. Functional validation experiments confirmed the metabolic involvement and showed that inhibition of pyruvate kinase, 3-chetoacylCoA thiolase, and arginase reduced the protection by CGS21680 of in vitro hypoxia-reoxygenation injury, whereas their metabolic products induced liver cell protection. Moreover, LSEC, but not HP, were sensitive to H2O2-induced oxidative damage and CGS21680 protected against this effect.

CONCLUSIONS

IR and A2aR stimulation produces pathological and protected liver cell phenotypes, respectively characterized by down- and upregulation of proteins involved in the response to O2 and nutrients deprivation during ischemia, oxidative stress, and reactivation of aerobic energy synthesis at reperfusion. This provides novel insights into IR hepatocellular damage and protection, and suggests additional therapeutic options.

Proteomics in transplantation

Proteomics and biochemical profiling have emerged as exciting and powerful tools in clinical biomarker research. In the field of transplantation, proteomics aims not only at developing noninvasive means for immune monitoring but also to gain mechanistic insights into the pathophysiology of the alloimmune response and hence defining new therapeutic targets. This chapter provides an overview of proteomic biomarker-driven approaches and its underlying concepts and discusses the advantages, clinical implications, challenges, and limitations of this novel modality as it relates to solid organ transplantation.

Proteomic analysis of Populus × euramericana (clone I-214) roots to identify key factors involved in zinc stress response

Contamination of soil and water by heavy metals has become a widespread problem; environmental pollution by high zinc (Zn) concentration occurs frequently. Although poplar (Populus spp.) has been identified as suitable for phytoremediation approaches, its response to high Zn concentrations are still not clearly understood. For this reason, we investigated the effects of Zn in Populus×euramericana clone I-214 roots by proteomic analysis. Comparative experiments were conducted on rooted woody cuttings grown in nutrient solutions containing 1mM (treatment) or 1μM (control) Zn concentrations. A gel-based proteomic approach coupled with morphological and chemical analysis was used to identify differentially represented proteins in treated roots and to investigate the effect of Zn treatment on the poplar root system. Data shows that Zn was accumulated preferentially in roots, that the antioxidant system, the carbohydrate/energy and amino acid metabolisms were the main pathways modulated by Zn excess, and that mitochondria and vacuoles were the cellular organelles predominately affected by Zn stress. A coordination between cell death and proliferation/growth seems to occur under this condition to counteract the Zn-induced damage.

Temporal analysis of poplar woody root response to bending stress

Temperate perennial woody plants use different environmental signals to coordinate their growth and development in relation to seasonal changes. Preliminary evidences suggest that, even during dormancy, plants maintain effective metabolic activities and molecular mechanisms ensuring them an eventual recording of mechanical loads during winter times. Despite their great importance for productivity and survival, plant biology investigations have poorly characterized the root growth cycle and its response to environmental stresses. In this study, we describe the proteomic changes occurring over the time in poplar root either in the absence or in response to a bending stress; corresponding expression of cell cycle regulator and auxin transporter genes was also evaluated by reverse transcription polymerase chain reaction analysis. Our results confirm previous evidences on the effect of the bending stress on the anticipation of root growth resumption, providing additional insights on a temporal modulation of various plant metabolic processes involved in dormancy break, growth resumption and stress response in the bent root; these events seem related to the differential compression and tension force distribution occurring over the plant taproot.

Predicting early intrahepatic recurrence of hepatocellular carcinoma after microwave ablation using SELDI-TOF proteomic signature

BACKGROUND/AIMS

Despite great progress in the treatment of hepatocellular carcinoma (HCC) over the last-decade, intrahepatic recurrence is still the most frequent serious adverse event after all the treatments including microwave ablation. This study aimed to predict early recurrence of HCC after microwave ablation using serum proteomic signature.

METHODS

After curative microwave ablation of HCC, 86 patients were followed-up for 1 year. Serum samples were collected before microwave ablation. The mass spectra of proteins were generated using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Serum samples from 50 patients were randomly selected as a training set and for biomarkers discovery and model development. The remaining serum samples were categorized for validation of the algorithm.

RESULTS

According to preablation serum protein profiling obtained from the 50 HCC samples in the training set, nine significant differentially-expressed proteins were detected in the serum samples between recurrent and non-recurrent patients. Decision classification tree combined with three candidate proteins with m/z values of 7787, 6858 and 6646 was produced using Biomarker Patterns Software with sensitivity of 85.7% and specificity of 88.9% in the training set. When the SELDI marker pattern was tested with the blinded testing set, it yielded a sensitivity of 80.0%, a specificity of 88.5% and a positive predictive value of 86.1%.

CONCLUSIONS

Differentially-expressed protein peaks in preablation serum screened by SELDI are associated with prognosis of HCC. The decision classification tree is a potential tool in predicting early intrahepatic recurrence in HCC patients after microwave ablation.

Reactive metabolites and AGE-RAGE-mediated inflammation in patients following liver transplantation

Recent investigations have indicated that reactive metabolites and AGE-RAGE-mediated inflammation might play an important role in the pathogenesis of ischemia-reperfusion injury in liver transplantation. In this observational clinical study, 150 patients were enrolled following liver transplantation from deceased donors. The occurrence of short-term complications within 10 days of transplantation was documented. Blood samples were collected prior to transplantation, immediately after transplantation, and at consecutive time points, for a total of seven days after transplantation. Plasma levels of methylglyoxal were determined using HPLC, whereas plasma levels of L-arginine, asymmetric dimethylarginine, advanced glycation endproducts-carboxylmethyllysine, soluble receptor for advanced glycation endproducts, and total antioxidant capacity were measured by ELISA. Patients following liver transplantation were shown to suffer from increased RAGE-associated inflammation with an AGE load mainly dependent upon reactive carbonyl species-derived AGEs. In contrast, carboxylmethyllysine-derived AGEs were of a minor importance. As assessed by the ratio of L-arginine/asymmetric dimethylarginine, the bioavailability of nitric oxide was shown to be reduced in hepatic IRI, especially in those patients suffering from perfusion disorders following liver transplantation. For the early identification of patients at high risk of perfusion disorders, the implementation of asymmetric dimethylarginine measurements in routine diagnostics following liver transplantation from deceased donors should be taken into consideration.

Alterations in the redox state and liver damage: hints from the EASL Basic School of Hepatology

The importance of a correct balance between oxidative and reductive events has been shown to have a paramount effect on cell function for quite a long time. However, in spite of this body of rapidly growing evidence, the implication of the alteration of the redox state in human disease has been so far much less appreciated. Liver diseases make no exception. Although not fully comprehensive, this article reports what discussed during an EASL Basic School held in 2012 in Trieste, Italy, where the effect of the alteration of the redox state was addressed in different experimental and human models. This translational approach resulted in further stressing the concept that this topic should be expanded in the future not only to better understand how oxidative stress may be linked to a liver damage but also, perhaps more important, how this may be the target for better, more focused treatments. In parallel, understanding how alteration of the redox balance may be associated with liver damage may help define sensitive and ideally early biomarkers of the disorder.

Proteomic methods for biomarker discovery in a rat model of alcohol steatosis

Understanding changes in the expression of specific proteins and/or alterations in their posttranslational modifications is crucial to elucidating the molecular mechanisms underlying disease states such as alcoholic liver disease. Protein separation and analysis techniques such as two-dimensional electrophoresis and mass spectrometry can be used for identifying biomarker proteins that are altered during progression of alcoholic liver disease. In this chapter, we outline methods for resolving liver tissue proteins from a rodent model of alcoholic liver disease using two-dimensional electrophoresis and identifying differentially expressed proteins using mass spectrometry. In addition, since oxidative stress strongly correlates with alcoholic liver disease, we also describe methods for identifying oxidatively modified proteins from liver tissue. We specifically focus on identifying proteins that are carbonylated as protein carbonylation is a permanent modification and considered deleterious to cells. The combination of two-dimensional electrophoresis for protein resolution, mass spectrometry for protein identification, and affinity-based methods for enriching and identifying carbonylated proteins is a powerful methodology for protein biomarker identification.

Protein and peptide biomarkers in organ transplantation

Organ transplantation is the optimal treatment choice for end-stage organ failure in pediatric patients. The ideal maintenance of a transplanted organ requires efficient monitoring tools and an effective individualized post-transplant treatment plan. Currently available post-transplant monitoring options are not ideal because of their invasiveness or their lack of sensitivity and specificity when providing an accurate assessment of transplant injury. Current research on proteins and peptides, including mass spectrometry-based proteomics, can identify novel surrogate protein and peptide biomarkers that can assist in monitoring the graft in order to correctly assess the status of the transplanted organ. In this article, we have critically reviewed current relevant literature to highlight the importance of protein and peptide biomarkers in the field of pediatric organ transplantation, the status of research findings in the field of protein and peptide biomarkers in different organ transplantation and factors that impact and inhibit the progression of protein biomarker discovery in the field of solid-organ transplantation in pediatrics.

Proteomics reveals acute pro-inflammatory and protective responses in rat Kupffer cells and hepatocytes after chemical initiation of liver cancer and after LPS and IL-6

Inflammation is a key event in the development of liver cancer. We studied early inflammatory responses of Kupffer cells (KCs) and hepatocyte (HC) after cancer initiation. The chemical carcinogen N-nitrosomorpholine (NNM) was used in a rat model. We applied a comprehensive analytical strategy including metabolic labeling, 2-D PAGE, LC-MS/MS-based spot identification and shotgun proteomics and thus determined the rates of synthesis of individual proteins, compared whole tissue with isolated constituent cells and performed in vivo to in vitro comparisons of NNM effects. NNM increased synthesis of overall and 138 individual proteins identified in HC and/or KC, indicating reprogramming of metabolism favoring protection, repair and replacement of cell constituents in HC and KC. Secretome analysis by 2-D PAGE and shotgun proteomics of HC revealed the induction of acute phase proteins, in case of KC of proteases, cytokines and chemokines, indicating inflammatory effects. All responses were induced rapidly, independently of signals from other cells, and closely mimicked the pro-inflammatory and protective effects of inflammation modulators LPS in KC and IL-6 in HC. In conclusion, the carcinogen NNM exerts pro-inflammatory effects in the liver, partially by direct activation of KC. The acute inflammation and its protective component will enhance formation, survival and proliferation of initiated cells and may therefore act synergistically with the genotoxic action of the carcinogen.

Cell death biomarkers as early predictors for hepatic dysfunction in patients after orthotopic liver transplantation

BACKGROUND

Valid prognostic factors for early identification of a complicated course after orthotopic liver transplantation from deceased donors are rare. The aim of this study was to investigate the prognostic value of different cell death biomarkers and inflammatory markers in patients after orthotopic liver transplantation from deceased donors.

METHODS

In total, 100 patients were evaluated for short-term complications within 10 days after orthotopic liver transplantation from deceased donors. Blood samples were collected before surgery, immediately after the end of the surgical procedure, and 1 day and 3, 5, and 7 days later. Plasma levels of total keratin 18, keratin 18 fragments, interleukin 6, tumor necrosis factor α, and soluble intercellular adhesion molecule 1 were measured.

RESULTS

Total keratin 18 was demonstrated to be favorable in its prognostic value for early identification of a complicated course in comparison to routine markers of liver impairment (e.g., aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase). In contrast, inflammation markers (e.g., interleukin 6, tumor necrosis factor α and soluble intercellular adhesion molecule 1) were unsuitable for predicting early complications after liver transplantation from deceased donors.

CONCLUSIONS

For early identification of patients at high risk for complications, the implementation of total keratin 18 measurements in routine diagnostics after orthotopic liver transplantation from deceased donors should be taken into consideration.

The role of molecular chaperonins in warm ischemia and reperfusion injury in the steatotic liver: a proteomic study

BACKGROUND

The molecular basis of the increased susceptibility of steatotic livers to warm ischemia/reperfusion (I/R) injury during transplantation remains undefined. Animal model for warm I/R injury was induced in obese Zucker rats. Lean Zucker rats provided controls. Two dimensional differential gel electrophoresis was performed with liver protein extracts. Protein features with significant abundance ratios (p < 0.01) between the two cohorts were selected and analyzed with HPLC/MS. Proteins were identified by Uniprot database. Interactive protein networks were generated using Ingenuity Pathway Analysis and GRANITE software.

RESULTS

The relative abundance of 105 proteins was observed in warm I/R injury. Functional grouping revealed four categories of importance: molecular chaperones/endoplasmic reticulum (ER) stress, oxidative stress, metabolism, and cell structure. Hypoxia up-regulated 1, calcium binding protein 1, calreticulin, heat shock protein (HSP) 60, HSP-90, and protein disulfide isomerase 3 were chaperonins significantly (p < 0.01) down-regulated and only one chaperonin, HSP-1 was significantly upregulated in steatotic liver following I/R.

CONCLUSION

Down-regulation of the chaperones identified in this analysis may contribute to the increased ER stress and, consequently, apoptosis and necrosis. This study provides an initial platform for future investigation of the role of chaperones and therapeutic targets for increasing the viability of steatotic liver allografts.

The proteome of Populus nigra woody root: response to bending

BACKGROUND AND AIMS

Morphological and biomechanical alterations occurring in woody roots of many plant species in response to mechanical stresses are well documented; however, little is known about the molecular mechanisms regulating these important alterations. The first forest tree genome to be decoded is that of Populus, thereby providing a tool with which to investigate the mechanisms controlling adaptation of woody roots to changing environments. The aim of this study was to use a proteomic approach to investigate the response of Populus nigra woody taproot to mechanical stress.

METHODS

To simulate mechanical perturbations, the taproots of 30 one-year-old seedlings were bent to an angle of 90 ° using a steel net. A spatial and temporal two-dimensional proteome map of the taproot axis was obtained. We compared the events occurring in the above-bending, central bending and below-bending sectors of the taproot.

KEY RESULTS

The first poplar woody taproot proteome map is reported here; a total of 207 proteins were identified. Spatial and temporal proteomic analysis revealed that factors involved in plant defence, metabolism, reaction wood formation and lateral root development were differentially expressed in the various sectors of bent vs. control roots, seemingly in relation to the distribution of mechanical forces along the stressed woody taproots. A complex interplay among different signal transduction pathways involving reactive oxygen species appears to modulate these responses.

CONCLUSIONS

Poplar woody root uses different temporal and spatial mechanisms to respond to mechanical stress. Long-term bending treatment seem to reinforce the defence machinery, thereby enabling the taproot to better overcome winter and to be ready to resume growth earlier than controls.

Molecular interactions between the olive and the fruit fly Bactrocera oleae

BACKGROUND

The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively.

RESULTS

We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures.

CONCLUSIONS

This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.

Recent advances in biomarker discovery in solid organ transplant by proteomics

The identification and clinical use of more sensitive and specific biomarkers in the field of solid organ transplantation is an urgent need in medicine. Solid organ transplantation has seen improvements in the short-term survival of transplanted organs due to recent advancements in immunosuppressive therapy. However, the currently available methods of allograft monitoring are not optimal. Recent advancements in assaying methods for biomolecules such as genes, mRNA and proteins have helped to identify surrogate biomarkers that can be used to monitor the transplanted organ. These high-throughput 'omic' methods can help researchers to significantly speed up the identification and the validation steps, which are crucial factors for biomarker discovery efforts. Still, the progress towards identifying more sensitive and specific biomarkers remains a great deal slower than expected. In this article, we have evaluated the current status of biomarker discovery using proteomics tools in different solid organ transplants in recent years. This article summarizes recent reports and current status, along with the hurdles in efficient biomarker discovery of protein biomarkers using proteomics approaches. Finally, we will touch upon personalized medicine as a future direction for better management of transplanted organs, and provide what we think could be a recipe for success in this field.

Comparative proteomic analysis of human donor tissues during orthotopic liver transplantation: ischemia versus reperfusion

PURPOSE

To explore the specific alterations in protein profiles that occur during ischemia/reperfusion injury (I/RI) and find novel therapeutic strategies to reduce I/RI during orthotopic liver transplantation (OLT).

METHOD

We used the comparative proteomic approach of two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to compare the proteomic profiles of the same donor liver at three different time points: T1, immediately after cardiac arrest of donors (normal control); T2, before portal vein anastomosis (ischemia); and T3, 2 h after hepatic artery anastomosis (reperfusion).

RESULT

We identified 34 proteins that were significantly altered during I/RI. These differentially expressed proteins were functionally classified into seven categories: metabolic enzyme, molecular chaperone, antioxidant enzyme, cytoskeleton protein, signal transduction protein, cyclin, and binding protein. Among the 34 proteins, 9 changed during ischemia only (from T1 to T2), 11 changed during reperfusion only (from T2 to T3), and the others changed during both ischemia and reperfusion (from T1 to T3) periods.

CONCLUSION

Ischemia and reperfusion during LT may lead to different modifications of the liver proteins. Most metabolic enzymes and antioxidant enzymes were upregulated during ischemia, indicating that lipid metabolic disorder and oxidative stress are closely related to the development of ischemic injury. ER chaperones may play a vital role in mediating I/RI and preventing ER stress caused by I/RI. Modulation of ER chaperones could be used as a key therapeutic target to improve the outcomes of LT.

Cladosporol a stimulates G1-phase arrest of the cell cycle by up-regulation of p21(waf1/cip1) expression in human colon carcinoma HT-29 cells

Cladosporols, purified and characterized as secondary metabolites from Cladosporium tenuissimum, display an antifungal activity. In this study, we tested the antiproliferative properties of cladosporol A, the main isoform of this metabolite family, against human cancer cell lines. By assessing cell viability, we found that cladosporol A inhibits the growth of various human colon cancers derived cell lines (HT-29, SW480, and CaCo-2) in a time- and concentration-dependent manner, specifically of HT-29  cells. The reduced cell proliferation was due to a G1-phase arrest, as assessed by fluorescence activated cell sorting analysis on synchronized HT-29  cells, and was associated with an early and robust over-expression of p21(waf1/cip1) , the well-known cyclin-dependent kinases inhibitor. This suggests that the drug may play a role in the control of cancer cell proliferation. Consistently, cyclin D1, cyclin E, CDK2, and CDK4 proteins were reduced and histone H1-associated CDK2 kinase activity inhibited. In addition to p21(waf1/cip1) , exposure to 20 µM cladosporol A caused a simultaneous increase of pERK and pJNK, suggesting that this drug activates a circuit that integrates cell cycle regulation and the signaling pathways both involved in the inhibition of cell proliferation. Finally, we showed that the increase of p21(waf1/cip1) expression was generated by a Sp1-dependent p53-independent stimulation of its gene transcription as mutagenesis of the Sp1 binding sites located in the p21 proximal promoter abolished induction. To our knowledge, this is the first report showing that cladosporol A inhibits colon cancer cell proliferation by modulating p21(waf1/cip1) expression.

Soluble cytokeratin 18 biomarkers may provide information on the type of cell death during early ischemia and reperfusion periods of liver transplantation

Hepatocellular damage takes place as a result of ischemia and reperfusion during liver transplantation (LT). To discriminate the type of cell death and quantitate its severity may provide new insights into the mechanisms of hepatocellular damage. Therefore, we investigated the type of cell death by ELISA-based assays in patient sera. Apoptosis was specifically assessed by measuring a novel soluble biomarker, the caspase-cleaved cytokeratin 18, while total cell death (apoptosis and necrosis) by cytokeratin 18 released from dead (necrotic and apoptotic) cells. Twenty-seven live (LDLT) and 14 deceased (DDLT) donor liver transplantations were analyzed before the operation, at the anhepatic stage, first, sixth and 24th hour after the reperfusion. Both apoptosis and total cell death have successfully been demonstrated although they have not been confirmed by the liver biopsy that is impossible to perform in this setting. Apoptosis was not induced in LDLT. Total cell death (primarily necrosis) only transiently appeared the first hour after the reperfusion in LDLT, while it sharply increased the first hour after the reperfusion and maintained its level in DDLT. Soluble cytokeratin 18 biomarkers seem to be useful to discriminate and quantitate the type of cell death during early ischemia and reperfusion periods of LT.

Application of metabolomics to investigate the process of human orthotopic liver transplantation: a proof-of-principle study

To improve the outcome of orthotopic liver transplantation (OLT), knowledge of early molecular events occurring upon ischemia/reperfusion is essential. Powerful approaches for profiling metabolic changes in tissues and biofluids are now available. Our objective was to investigate the applicability of two technologies to a small but well-defined cohort of patients undergoing OLT: consecutive liver biopsies by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and microdialysates of extracellular fluid by coulometric electrochemical array detection (CEAD). FT-ICR MS detected reproducibly more than 4,000 peaks, revealing hundreds of significant metabolic differences between pre- and postreperfusion grafts. These included increased urea production, bile acid synthesis and clearance of preservation solution upon reperfusion, indicating a rapid resumption of biochemical function within the graft. FT-ICR MS also identified successfully the only graft obtained by donation-after-cardiac-death as a "metabolic outlier." CEAD time-profile analysis showed that there was considerable change in redox-active metabolites (up to 18 h postreperfusion), followed by their stabilization. Collectively these results verify the applicability of FT-ICR MS and CEAD for characterizing multiple metabolic pathways during OLT. The success of this proof-of-principle application of these technologies to a clinical setting, considering the potential metabolic heterogeneity across only eight donor livers, is encouraging.

Redox control of liver function in health and disease

Reactive oxygen species (ROS), a heterogeneous population of biologically active intermediates, are generated as by-products of the aerobic metabolism and exhibit a dual role in biology. When produced in controlled conditions and in limited quantities, ROS may function as signaling intermediates, contributing to critical cellular functions such as proliferation, differentiation, and cell survival. However, ROS overgeneration and, particularly, the formation of specific reactive species, inflicts cell death and tissue damage by targeting vital cellular components such as DNA, lipids, and proteins, thus arising as key players in disease pathogenesis. Given the predominant role of hepatocytes in biotransformation and metabolism of xenobiotics, ROS production constitutes an important burden in liver physiology and pathophysiology and hence in the progression of liver diseases. Despite the recognized role of ROS in disease pathogenesis, the efficacy of antioxidants as therapeutics has been limited. A better understanding of the mechanisms, nature, and location of ROS generation, as well as the optimization of cellular defense strategies, may pave the way for a brighter future for antioxidants and ROS scavengers in the therapy of liver diseases.

Association of MicroRNA-223 expression with hepatic ischemia/reperfusion injury in mice

MicroRNAs are a group of small non-coding RNAs with modulator activity of gene expression. Recent studies have uncovered a profound role of microRNAs in liver diseases. This study aimed to investigate a potential relationship between microRNA-223 (miR-223) expression and hepatic ischemia/reperfusion injury in mice. Quantitative RT-PCR analysis showed that miR-223 expression levels were greatly up-regulated in the livers after 75 min ischemia followed by 120 min reperfusion when compared to sham controls (2.59 +/- 0.23 vs. 0.83 +/- 0.15; P < 0.01). Correlation analysis also revealed that hepatic miR-223 expression level was significantly positively correlated with serum markers of ischemic injury. By prediction assay of miRNA targets mRNA, acyl-CoA synthetase long-chain family member 3, ephrin A1, and ras homolog gene family member B were predicted to be downstream targets of miR-223. Thus, we conclude that hepatic ischemia/reperfusion injury might be another form of liver disease that is associated with alteration in miR-223 expression.

Nitric oxide and redox regulation in the liver: part II. Redox biology in pathologic hepatocytes and implications for intervention

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are created in normal hepatocytes and are critical for normal physiologic processes, including oxidative respiration, growth, regeneration, apoptosis, and microsomal defense. When the levels of oxidation products exceed the capacity of normal antioxidant systems, oxidative stress occurs. This type of stress, in the form of ROS and RNS, can be damaging to all liver cells, including hepatocytes, Kupffer cells, stellate cells, and endothelial cells, through induction of inflammation, ischemia, fibrosis, necrosis, apoptosis, or through malignant transformation by damaging lipids, proteins, and/or DNA. In Part I of this review, we will discuss basic redox biology in the liver, including a review of ROS, RNS, and antioxidants, with a focus on nitric oxide as a common source of RNS. We will then review the evidence for oxidative stress as a mechanism of liver injury in hepatitis (alcoholic, viral, nonalcoholic). In Part II of this review, we will review oxidative stress in common pathophysiologic conditions, including ischemia/reperfusion injury, fibrosis, hepatocellular carcinoma, iron overload, Wilson's disease, sepsis, and acetaminophen overdose. Finally, biomarkers, proteomic, and antioxidant therapies will be discussed as areas for future therapeutic interventions.

Genome-wide analysis and proteomic studies reveal APE1/Ref-1 multifunctional role in mammalian cells

Apurinic apyrimidinic endonuclease/redox effector factor 1 (APE1/Ref-1) protects cells from oxidative stress by acting as a central enzyme in base excision repair pathways of DNA lesions and through its independent activity as a redox transcriptional co-activator. Dysregulation of this protein has been associated with cancer development. At present, contrasting data have been published regarding the biological relevance of the two functions as well as the molecular mechanisms involved. Here, we combined both mRNA expression profiling and proteomic analysis to determine the molecular changes associated with APE1 loss-of-expression induced by siRNA technology. This approach identified a role of APE1 in cell growth, apoptosis, intracellular redox state, mitochondrial function, and cytoskeletal structure. Overall, our data show that APE1 acts as a hub in coordinating different and vital functions in mammalian cells, highlighting the molecular determinants of the multifunctional nature of APE1 protein.

Proteomic analysis of hepatic ischemia/reperfusion injury and ischemic preconditioning in mice revealed the protective role of ATP5beta

Hepatic ischemia/reperfusion (I/R) injury is an inevitable consequence during liver surgery. Ischemic preconditioning (IPC) has been shown to protect the livers from I/R injury, partially mediated by preservation of hepatic ATP contents. However, the precise molecular mechanisms of these events remain poorly elucidated. In this study, liver proteomes of the mice subjected to I/R injury pretreated with or without IPC were analyzed using 2-DE combined with MALDI-TOF/TOF mass analysis. Twenty proteins showing more than 1.5-fold difference were identified in the livers upon I/R injury. Among these proteins, four proteins were further regulated by IPC when compared with nonpretreated controls. One of these proteins, ATP synthase beta subunit (ATP5beta) catalyzes the rate-limiting step of ATP formation. The expression level of ATP5beta, which was further validated by Western blot analysis, was significantly decreased upon I/R injury while turned over by IPC pretreatment. Change pattern of hepatic ATP corresponded with that of ATP5beta expression, indicating that increasing hepatic ATP5beta expression might be a reason for ATP-preserving effect of IPC. In summary, this study provided new clues for understanding the mechanisms of IPC against I/R injury. The protective role of ATP5beta might give evidences for developing new therapeutic approaches against hepatic I/R injury.

Transcriptome and proteome analysis of osteocytes treated with nitrogen-containing bisphosphonates

We combined high-throughput screening of differential mRNAs with mass spectrometric characterization of proteins obtained from osteocytes untreated and treated with Risedronate. Microarray analysis revealed, upon treatment, a marked upregulation of messengers encoding zinc-proteins. MS analysis identified 84 proteins in the osteocytes proteome map. Risedronate affected the expression of 10 proteins, associated with cytoskeleton, stress-response and metabolism. Data validated using gel imaging in combination with the GLaD post digestion isotopic labeling method provide the molecular basis for understanding the role of bisphosphonates as antiapoptotic drugs for osteocytes.

APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process

APE1/Ref-1 (hereafter, APE1), a DNA repair enzyme and a transcriptional coactivator, is a vital protein in mammals. Its role in controlling cell growth and the molecular mechanisms that fine-tune its different cellular functions are still not known. By an unbiased proteomic approach, we have identified and characterized several novel APE1 partners which, unexpectedly, include a number of proteins involved in ribosome biogenesis and RNA processing. In particular, a novel interaction between nucleophosmin (NPM1) and APE1 was characterized. We observed that the 33 N-terminal residues of APE1 are required for stable interaction with the NPM1 oligomerization domain. As a consequence of the interaction with NPM1 and RNA, APE1 is localized within the nucleolus and this localization depends on cell cycle and active rRNA transcription. NPM1 stimulates APE1 endonuclease activity on abasic double-stranded DNA (dsDNA) but decreases APE1 endonuclease activity on abasic single-stranded RNA (ssRNA) by masking the N-terminal region of APE1 required for stable RNA binding. In APE1-knocked-down cells, pre-rRNA synthesis and rRNA processing were not affected but inability to remove 8-hydroxyguanine-containing rRNA upon oxidative stress, impaired translation, lower intracellular protein content, and decreased cell growth rate were found. Our data demonstrate that APE1 affects cell growth by directly acting on RNA quality control mechanisms, thus affecting gene expression through posttranscriptional mechanisms.

Oxidative inactivation of key mitochondrial proteins leads to dysfunction and injury in hepatic ischemia reperfusion

BACKGROUND & AIMS

Ischemia-reperfusion (I/R) is a major mechanism of liver injury following hepatic surgery or transplantation. Despite numerous reports on the role of oxidative/nitrosative stress and mitochondrial dysfunction in hepatic I/R injury, the proteins that are oxidatively modified during I/R damage are poorly characterized. This study was aimed at investigating the oxidatively modified proteins underlying the mechanism for mitochondrial dysfunction in hepatic I/R injury. We also studied the effects of a superoxide dismutase mimetic/peroxynitrite scavenger metalloporphyrin (MnTMPyP) on oxidatively modified proteins and their functions.

METHODS

The oxidized and/or S-nitrosylated mitochondrial proteins from I/R-injured mouse livers with or without MnTMPyP pretreatment were labeled with biotin-N-maleimide, purified with streptavidin-agarose, and resolved by 2-dimensional gel electrophoresis. The identities of the oxidatively modified proteins were determined using mass spectrometric analysis. Liver histopathology, serum transaminase levels, nitrosative stress markers, and activities of oxidatively modified mitochondrial proteins were measured.

RESULTS

Comparative 2-dimensional gel analysis revealed markedly increased numbers of oxidized and S-nitrosylated mitochondrial proteins following hepatic I/R injury. Many key mitochondrial enzymes involved in cellular defense, fat metabolism, energy supply, and chaperones were identified as being oxidatively modified proteins. Pretreatment with MnTMPyP attenuated the I/R-induced increased serum transaminase levels, histologic damage, increased inducible nitric oxide synthase expression, and S-nitrosylation and/or nitration of various key mitochondrial proteins. MnTMPyP pretreatment also restored I/R-induced suppressed activities of mitochondrial aldehyde dehydrogenase, 3-ketoacyl-CoA thiolases, and adenosine triphosphate synthase.

CONCLUSIONS

These results suggest that increased nitrosative stress is critically important in promoting S-nitrosylation and nitration of various mitochondrial proteins, leading to mitochondrial dysfunction with decreased energy supply and increased hepatic injury.

Gene expression profiling of human liver transplants identifies an early transcriptional signature associated with initial poor graft function

Liver ischemia-reperfusion injury occurring in orthotopic liver transplantation (OLT) may be responsible for early graft failure. Molecular mechanisms underlying initial poor graft function (IPGF) have been poorly documented in human. The purpose of this study was to identify the major transcriptional alterations occurring in human livers during OLT. Twenty-one RNA extracts derived from liver transplant biopsies taken after graft reperfusion were compared with 7 RNA derived from normal control livers. Three hundred seventy-one genes were significantly modulated and classified in molecular pathways relevant to liver metabolism, inflammatory response, cell proliferation and liver protection. Grafts were then subdivided into two groups based on their peak levels of serum aspartate amino transferase within 72 h after OLT (group 1, non-IPGF: 14 patients; group 2, IPGF: 7 patients). The two corresponding data sets were compared using a supervised prediction method. A new set of genes able to correctly classify 71% of the patients was defined. These genes were functionally associated with oxidative stress, inflammation and inhibition of cell proliferation. This study provides a comprehensive picture of the transcriptional events associated with human OLT and IPGF. We anticipate that such alterations provide a framework for the elucidation of the molecular mechanisms leading to IPGF.

Proteomic profiling of human liver biopsies: hepatitis C virus-induced fibrosis and mitochondrial dysfunction

Liver biopsies from hepatitis C virus (HCV)-infected patients offer the unique opportunity to study human liver biology and disease in vivo. However, the low protein yields associated with these small samples present a significant challenge for proteomic analysis. In this study we describe the application of an ultrasensitive proteomics platform for performing robust quantitative proteomic studies on microgram amounts of HCV-infected human liver tissue from 15 patients at different stages of fibrosis. A high-quality liver protein database containing 5,920 unique protein identifications supported high throughput quantitative studies using (16)O/(18)O stable isotope labeling in combination with the accurate mass and time (AMT) tag approach. A total of 1,641 liver biopsy proteins were quantified, and analysis of variance (ANOVA) identified 210 proteins exhibiting statistically significant differences associated with fibrosis stage. Hierarchical clustering showed that biopsies representative of later fibrosis stages (for example, Batts-Ludwig stages 3-4) exhibited a distinct protein expression profile, indicating an apparent down-regulation of many proteins when compared with samples from earlier fibrosis stages (for example, Batts-Ludwig stages 0-2). Functional analysis of these signature proteins suggests that impairment of key mitochondrial processes including fatty acid oxidation and oxidative phosphorylation, and response to oxidative stress and reactive oxygen species occurs during advanced stage 3 to 4 fibrosis.

CONCLUSION

The results reported here represent a significant advancement in clinical proteomics providing to our knowledge, the first demonstration of global proteomic alterations accompanying liver disease progression in patients chronically infected with HCV. Our findings contribute to a generally emerging theme associating oxidative stress and hepatic mitochondrial dysfunction with HCV pathogenesis.

Oxidized transthyretin in amniotic fluid as an early marker of preeclampsia

Preeclampsia is a pregnancy-specific hypertensive syndrome and a major cause of maternal and fetal morbidity and mortality. At the present time, no reliable screening tests to identify women at risk are available. We have compared the amniotic fluids (AF) proteomic maps of five preeclamptic patients with those of five controls. The analysis was carried out by two-dimensional electrophoresis followed by peptide mapping and tandem mass spectrometric analysis. Besides the implementation of the previously published AF proteomic maps, our results show that transthyretin (TTR), the protein responsible for transporting both the thyroid hormone tyroxine and the retinol binding protein, is present in the AF of both preeclamptic and control women as a mixture of dimeric and post-translationally modified monomeric forms. Although the nature of these forms is similar in both groups, the preeclamptic women showed a significant increase in the amount of monomeric proteins with respect to the control group. Since the TTR monomeric forms are the results of different oxidizing reactions, we hypothesize that the higher oxidative stress in preeclampsia is the major destabilizing factor of the TTR functional dimeric form in the preeclamptic women.