Proteomics in liver fibrosis is more than meets the eye

Mapping Novel Biomarkers of Liver Injury by Tissue Proteomic Analysis

Liver damage is a dynamic process, and evaluation of liver injury degree is the key step in disease diagnosis. However, few common markers among different types of liver injury have been reported. Herein, we generated three liver injury mouse models, including Con A-induced, CCl₄-injected, and subjected bile duct ligation mouse models, to simulate different types of liver damage in humans and then performed a label-free mass spectrometry to identify differentially expressed proteins in liver tissues. Interestingly, two proteins, G3BP and ABCC6, were conserved regulated in different liver injury models and are proposed to be biomarkers in liver injury, with G3BP upregulated and ABCC6 downregulated. Overall, our study identified two novel biomarkers of liver injury, and they might be used as potential drug targets of liver damage research studies.

Proteomic profiling of hepatic stellate cells in alcohol liver fibrosis reveals proteins involved in collagen production

BACKGROUND

Hepatic stellate cell (HSC) activation has central functions in alcohol-induced liver fibrosis. Proteins of HSCs in alcoholic liver fibrosis (ALF) are still not completely understood. Here, we performed a proteomic study to discover proteins related to ALF using HSCs isolated from a rat model.

METHODS

Sprague-Dawley rats were fed with ethanol for 2 or 6 weeks. Liver histology was assessed using Sirius red and Oil red O staining. HSCs were enriched by using Percoll density gradient centrifugation, and analyzed using flow cytometry. Proteins extracted from HSCs were separated using two-dimensional electrophoresis (2DE). Differentially expressed proteins were identified using liquid chromatography-mass spectrometry (LC-MS). The characteristics of the differentially expressed proteins were analyzed using the UniProtKB database and STRING software. The mRNA levels of two differentially expressed proteins were analyzed using real-time RT-PCR, of which NADH dehydrogenase (ubiquinone) flavoprotein 2, mitochondrial (Ndufv2) was further investigated using Western blot (WB) and immunohistochemical analysis in the ALF model and human liver tissues. The relationship between Ndufv2 and alcohol stimulation was evaluated using WB. Next, Ndufv2 was knocked-down by shRNA in the HSC-T6 cell line. Three genes (encoding collagen, metalloproteinase inhibitor 1 [TIMP-1], and α-smooth muscle actin [a-SMA]) related to HSC activation were detected.

RESULTS

An ALF model was successfully established, with a liver fibrosis score of 1-2 (S1-2), and some big fat vacuoles development. Twenty-one non-abundant proteins with more than a 2-fold difference were identified using mass spectrometry, including 7 upregulated and 14 downregulated proteins. These differential proteins are a response to antigen presentation, mitochondrial metabolism, ethanol, and collagen degradation. Among them, two upregulated proteins (Ndufv2 and ATP synthase subunit alpha, mitochondrial [ATP5a1]) were involved in mitochondrial metabolism in ALF, and showed concurrent changes in mRNA and protein levels. Ndufv2 was upregulated in HSCs, as shown by WB, in non-parenchymal cells (NPCs) in the rat model and human liver tissues, and detected using immunohistochemistry. Ndufv2 was also upregulated after alcohol stimulation. Following Ndufv2 knockdown, collagen, TIMP-1, and α-SMA were downregulated compared with that in the controls.

CONCLUSIONS

A proteomic study was performed to discover proteins related to ALF in HSCs isolated from a rat model. Twenty-one differentially expressed proteins were identified, including proteins involved in mitochondrial metabolism and antigen presentation. Ndufv2, an upregulated protein in ALF, might be involved in ALF through regulating the production of fibrosis factors.

Metabolic Signature of Hepatic Fibrosis: From Individual Pathways to Systems Biology

Hepatic fibrosis is a major cause of morbidity and mortality worldwide, as it ultimately leads to cirrhosis, which is estimated to affect up to 2% of the global population. Hepatic fibrosis is confirmed by liver biopsy, and the erroneous nature of this technique necessitates the search for noninvasive alternatives. However, current biomarker algorithms for hepatic fibrosis have many limitations. Given that the liver is the largest organ and a major metabolic hub in the body, probing the metabolic signature of hepatic fibrosis holds promise for the discovery of new markers and therapeutic targets. Regarding individual metabolic pathways, accumulating evidence shows that hepatic fibrosis leads to alterations in carbohydrate metabolism, as aerobic glycolysis is aggravated in activated hepatic stellate cells (HSCs) and the whole fibrotic liver; in amino acid metabolism, as Fischer’s ratio (branched-chain amino acids/aromatic amino acids) decreases in patients with hepatic fibrosis; and in lipid metabolism, as HSCs lose vitamin A-containing lipid droplets during transdifferentiation, and cirrhotic patients have decreased serum lipids. The current review also summarizes recent findings of metabolic alterations relevant to hepatic fibrosis based on systems biology approaches, including transcriptomics, proteomics, and metabolomics in vitro, in animal models and in humans.

Annexin A2 promotes liver fibrosis by mediating von Willebrand factor secretion

BACKGROUND

Liver fibrosis can lead to cirrhosis and hepatocellular carcinoma if not treated in the early stages. The molecular mechanisms of the pathogenesis of hepatic fibrosis remain unclear.

AIM

To identify the molecules involved in the pathogenesis of liver fibrosis and to investigate the potential effect and mechanism of Annexin A2 up-regulation during liver fibrosis progression.

METHODS

Twenty Sprague-Dawley rats were divided into two groups: the carbon tetrachloride (CCl₄)-induced liver fibrosis group and the normal control group. Hematoxylin and eosin staining or Masson Trichrome staining and enzyme-linked immunosorbent assay were applied to assess the degree of liver damage and fibrosis in rats with CCl₄-induced liver fibrosis. Liver tissue protein profiles were analyzed using iTRAQ and mass spectrometry. RT-PCR and western blotting analyses were employed to validate differentially expressed proteins. Small interfering RNA-based silencing was performed to study the function of Annexin A2.

RESULTS

Twelve weeks after CCl₄ injection, significant body weight changes and liver injury and liver fibrosis were observed in rats. In addition, 130 proteins were differentially expressed in the liver fibrosis group. Overexpression of Annexin A2 was confirmed by RT-PCR and Western blotting analysis. Silencing of Annexin A2 expression in HepG2 and LX-2 cells significantly reduced the secretion of von Willebrand factor (vWF).

CONCLUSION

Annexin A2 promotes liver fibrosis by mediating vWF secretion, which can be used to mitigate the progression of liver fibrosis.

Discovery of novel biomarker candidates for liver fibrosis in hepatitis C patients: a preliminary study

Background

Liver biopsy is the reference standard for assessing liver fibrosis and no reliable non-invasive diagnostic approach is available to discriminate between the intermediate stages of fibrosis. Therefore suitable serological biomarkers of liver fibrosis are urgently needed. We used proteomics to identify novel fibrosis biomarkers in hepatitis C patients with different degrees of liver fibrosis.

Methodology/Principal Findings

Proteins in plasma samples from healthy control individuals and patients with hepatitis C virus (HCV) induced cirrhosis were analysed using a proteomics technique: two dimensional gel electrophoresis (2-DE). This technique separated the proteins in plasma samples of control and cirrhotic patients and by visualizing the separated proteins we were able to identify proteins which were increasing or decreasing in hepatic cirrhosis. Identified markers were validated across all Ishak fibrosis stages and compared to the markers used in FibroTest, Enhanced Liver Fibrosis (ELF) test, Hepascore and FIBROSpect by Western blotting. Forty four candidate biomarkers for hepatic fibrosis were identified of which 20 were novel biomarkers of liver fibrosis. Western blot validation of all candidate markers using plasma samples from patients across all Ishak fibrosis scores showed that the markers which changed with increasing fibrosis most consistently included lipid transfer inhibitor protein, complement C3d, corticosteroid-binding globulin, apolipoprotein J and apolipoprotein L1. These five novel fibrosis markers which are secreted in blood showed a promising consistent change with increasing fibrosis stage when compared to the markers used for the FibroTest, ELF test, Hepascore and FIBROSpect. These markers will be further validated using a large clinical cohort.

Conclusions/Significance

This study identifies 20 novel fibrosis biomarker candidates. The proteins identified may help to assess hepatic fibrosis and eliminate the need for invasive liver biopsies.

Usefulness of a novel serum proteome-derived index FI-PRO (fibrosis-protein) in the prediction of fibrosis in chronic hepatitis C

BACKGROUND

Liver biopsy is an imperfect standard for the assessment of chronic hepatitis C liver fibrosis. In this study, the diagnostic role of proteome-derived protein markers and the usefulness of a protein-based index were assessed.

METHODS

Characteristics, clinical biochemistry, and protein markers of patients with chronic hepatitis C from a study (n=62) and validation group (n=73) were statistically assessed according to fibrosis severity. Multivariate models were built using linear discriminant analysis for the prediction of minor fibrosis (F0-F1), moderate fibrosis (F2-F3), and cirrhosis (F4). The best model was validated and diagnostic performance was compared with the aspartate aminotransferase-to-platelet ratio index based on their receiver operator characteristic curves.

RESULTS

Statistical analysis resulted in significant outcomes for both clinical and protein markers. The best multivariate model was based on four protein markers: α-2-macroglobulin (A2M), haptoglobin, hemopexin, and galectin-3-binding protein. A2M and hemopexin were the primary predictors according to this model. A novel index A2M/hemopexin [fibrosis-protein (FI-PRO) index] showed a diagnostic performance rate of 0.80-0.92 for the detection of significant fibrosis (F2-F4) and advanced fibrosis (F3-F4) in the validation group, which was better compared with aspartate aminotransferase-to-platelet ratio index. FI-PRO had an overall positive predictive value of 86% for significant fibrosis and a negative predictive value of at least 90% for advanced fibrosis.

CONCLUSION

Proteome-derived protein markers were successfully implemented in clinical diagnosis of hepatitis C fibrosis, which resulted in the FI-PRO index. The efficiency and usability of FI-PRO should be validated in large-scale, prospective studies.

Plasma membrane proteome analysis of the early effect of alcohol on liver: implications for alcoholic liver disease

In humans, the over-consumption of alcohol can lead to serious liver disease. To examine the early effects of alcohol on liver disease, rats were given sufficient ethanol to develop liver cirrhosis. Rats before the onset of fibrosis were studied in this work. Plasma membranes (PM) of liver were extracted by twice sucrose density gradient centrifugation. The proteome profiles of PM from ethanol-treated rats and the controls were analyzed using two-dimensional gel electrophoresis (2-DE) and isobaric tag for relative and absolute quantitation (iTRAQ) technology. Ethanol treatment altered the amount of 15 different liver proteins: 10 of them were detected by 2-DE and 5 by iTRAQ. Keratin 8 was detected by both methods. Gene ontology analysis of these differentially detected proteins indicated that most of them were involved in important cell functions such as binding activity (including ion, DNA, ATP binding, etc.), cell structure, or enzyme activity. Among these, annexin A2, keratin 8, and keratin 18 were further verified using western blot analysis and annexin A2 was verified by immunohistochemistry. Our results suggested that alcohol has the potential to affect cell structure, adhesion and enzyme activity by altering expression levels of several relevant proteins in the PM. To the best of our knowledge, this is the first time to study the effect of alcohol on the liver PM proteome and it might be helpful for understanding the possible mechanisms of alcohol-induced liver disease.

Galectin-3-binding protein: a serological and histological assessment in accordance with hepatitis C-related liver fibrosis

OBJECTIVES

Invasive liver biopsy is the current method for the assessment of liver fibrosis. In search of noninvasive alternatives, galectin-3-binding protein (G3BP) was introduced as a candidate-marker of hepatitis C-related fibrosis based on serum proteomics. We investigated the role of G3BP as a single-marker of significant fibrosis and cirrhosis by serology and histology and studied the effect of glycosylation on antibody-affinity in hepatitis C and alcoholic cirrhosis.

METHODS

Sera and available biopsies of hepatitis C patients with various fibrosis-grades and patients with alcoholic cirrhosis were used for G3BP-measurements by enzyme-linked immunosorbent assay and immunohistochemistry, respectively. Glycosylation-effect was analyzed by western blot. Data was analyzed in accordance to fibrosis.

RESULTS

G3BP-levels (mean+/-standard deviation) were increased during cirrhosis (22.7+/-10.1 microg/ml) compared to mild (11.3+/-6.4 microg/ml) and moderate fibrosis (13.4+/-8.3 microg/ml) (P<0.001; P=0.004, respectively). Receiver operator characteristic curves showed areas under the curve of 0.68, 0.75 and 0.81 for detection of significant fibrosis, severe fibrosis, and cirrhosis, respectively. Similar findings in hepatic G3BP expression were obtained, in which cirrhosis was associated with diffuse, parenchymal expression (P=0.002). The observed difference between hepatitis C and alcoholic cirrhosis (13.5+/-9.0 microg/ml) (P=0.009) could not be explained by glycosylation.

CONCLUSION

Our recent findings confirm our initial proteome results on serological and histological level as well as the role of G3BP as a marker of hepatitis C-related fibrosis, especially cirrhosis. Implication of this protein in future multi-marker study should be considered.

Subcellular proteome analysis unraveled annexin A2 related to immune liver fibrosis

It is important to study the mechanism of liver fibrogenesis, and find new non-invasive biomarkers. In this study, we used subcellular proteomic technology to study the plasma membrane (PM) proteins related to immune liver fibrosis and search for new non-invasive biomarkers. A rat liver fibrosis model was induced by pig serum injection. The liver fibrogenesis from stage (S) S0-1, S2, S3-4, and S4 was detected by Masson staining and HE staining in this rat model after 2, 4, 6, and 8 weeks of treatment. The liver PM was enriched and analyzed using subcellular proteomic technology. The differentially expressed proteins were verified by Western blotting, immunohistochemistry, and ELISA. PM with 149-fold purification was obtained and 22 differentially expressed proteins were identified. Of which, annexin A2 (ANXA2) was detected to be increased obviously in S4 compared with S0-1, and verified by Western blotting of rat liver tissue and immunohistochemistry of rat and human liver tissue. The expression of ANXA2 in human plasma with S1-2 was also found to be up-regulated for 1.4-fold than that in S0. Furthermore, ANXA2 was detected to translocate from nuclear membrane and cytosol to PM as HBV stimulation through immunocytochemical analysis in vitro. This study identified 22 differentially expressed proteins related to liver fibrosis, and verified a potential biomarker (ANXA2) for non-invasive diagnosis of immune liver fibrosis. To our knowledge, it was the first time to dynamically study the proteins related to liver fibrosis and select biomarkers for liver fibrosis diagnosis through PM proteome research.

Proteomic approaches in the search for biomarkers of liver fibrosis

Chronic liver diseases (CLDs) can cause progressive hepatic fibrosis culminating in cirrhosis. Fibrosis staging requires liver biopsy, which is invasive, expensive and frequently poorly tolerated by patients. Serum-based panels of fibrosis biomarkers have been developed as alternatives to biopsy. Recent advances in high-throughput proteomic methods have the potential to optimise combinations of biomarkers for the diagnosis of liver fibrosis. Here, we review the key recent developments in the field of proteomics and their application to this important clinical question. We critically discuss the challenges and priorities for future research that are of critical importance to clinical hepatology.

Proteomics and liver fibrosis: identifying markers of fibrogenesis

Chronic hepatic disease damages the liver and the resulting wound-healing process might lead to liver fibrosis and subsequent cirrhosis development. Fibrosis is the excessive deposition of extracellular matrix (ECM) in the tissue as consequence of chronic liver damage. The fibrotic response triggers almost all of the complications of end-stage liver disease, including portal hypertension, ascites, encephalopathy, synthetic dysfunction and impaired metabolic capacity. Thus, efforts to understand and attenuate fibrosis have direct clinical implications. Reliable, accurate, disease-specific, noninvasive biomarkers of fibrosis and fibrogenesis in order to prevent or minimize the impact of the chronic liver disease progression are a critical need. This review aims to provide an overview of the possibilities that proteome technology can offer to the knowledge, diagnosis and prognosis of liver fibrosis.

The HCV serum proteome: a search for fibrosis protein markers

Liver fibrosis/cirrhosis is a serious health issue in hepatitis C virus (HCV-) infected patients and is currently diagnosed by the invasive liver biopsy. The aim of this study was to find useful fibrosis markers in HCV-patients' sera of different fibrosis degrees (METAVIR F0-F4) based on proteomics. Serum proteome profiles were created by two-dimensional gel electrophoresis. Profiles were analysed between different degrees of fibrosis (F0-F4) and between early (F0F1) and late (F2F3F4) fibrosis by univariate analyses (P <or= 0.05). Differentially expressed proteins were subsequently identified by mass spectrometry. Mac-2-binding protein, alpha-2-macroglobulin and hemopexin were increased in F4 opposite F0/F1. A-1-antitrypsin, leucine-rich alpha-2-glycoprotein and fetuin-A were decreased in F4 opposite F0/F1. Late fibrosis was characterized by an increase in Mac-2-binding protein, alpha-2-macroglobulin and alpha-1B-glycoprotein expression and a decrease in haptoglobin expression. Mac-2-binding protein expression was confirmed by dot blot assay and enzyme-linked immunosorbent assay in a secondary population. In conclusion, serum proteome analysis enabled the detection/identification of existing and new candidate markers in line with fibrosis progression in HCV-patients.