A dynamic plasma membrane proteome analysis of alcohol-induced liver cirrhosis

Proteomic analysis of alcohol-associated hepatitis reveals glycoprotein NMB (GPNMB) as a novel hepatic and serum biomarker

Alcohol consumption remains a leading cause of liver disease worldwide, resulting in a complex array of hepatic pathologies, including steatosis, steatohepatitis, and cirrhosis. Individuals who progress to a rarer form of alcohol-associated liver disease (ALD), alcohol-associated hepatitis (AH), require immediate life-saving intervention in the form of liver transplantation. Rapid onset of AH is poorly understood and the metabolic mechanisms contributing to the progression to liver failure remain undetermined. While multiple mechanisms have been identified that contribute to ALD, no cures exist and mortality from AH remains high. To identify novel pathways associated with AH, our group utilized proteomics to investigate AH-specific biomarkers in liver explant tissues. The goal of the present study was to determine changes in the proteome as well as epigenetic changes occurring in AH. Protein abundance and acetylomic analyses were performed utilizing nHPLC-MS/MS, revealing significant changes to proteins associated with metabolic and inflammatory fibrosis pathways. Here, we describe a novel hepatic and serum biomarker of AH, glycoprotein NMB (GPNMB). The anti-inflammatory protein GPNMB was significantly increased in AH explant liver and serum compared to healthy donors by 50-fold and 6.5-fold, respectively. Further, bioinformatics analyses identified an AH-dependent decrease in protein abundance across fatty acid degradation, biosynthesis of amino acids, and carbon metabolism. The greatest increases in protein abundance were observed in pathways for focal adhesion, lysosome, phagosome, and actin cytoskeleton. In contrast with the hyperacetylation observed in murine models of ALD, protein acetylation was decreased in AH compared to normal liver across fatty acid degradation, biosynthesis of amino acids, and carbon metabolism. Interestingly, immunoblot analysis found epigenetic marks were significantly increased in AH explants, including Histone H3K9 and H2BK5 acetylation. The increased acetylation of histones likely plays a role in the altered proteomic profile observed, including increases in GPNMB. Indeed, our results reveal that the AH proteome is dramatically impacted through unanticipated and unknown mechanisms. Understanding the origin and consequences of these changes will yield new mechanistic insight for ALD as well as identify novel hepatic and serum biomarkers, such as GPNMB.

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.

Annexin A6 protein is downregulated in human hepatocellular carcinoma

Annexin A6 (AnxA6) is a lipid-binding protein highly expressed in the liver, regulating cholesterol homeostasis and signaling pathways with a role in liver physiology. Here, we analyzed whether hepatic AnxA6 levels are affected by pathological conditions that are associated with liver dysfunction and liver injury. AnxA6 levels in the fatty liver of mice fed a high-fat diet, in ob/ob and db/db animals and in human fatty liver are comparable to controls. Similarly, AnxA6 levels appear unaffected in murine nonalcoholic steatohepatitis and human liver fibrosis. Accordingly, adiponectin, lysophosphatidylcholine, palmitate, and TGFbeta, all of which have a role in liver injury, do not affect AnxA6 expression in human hepatocytes. Likewise, adiponectin and IL8 do not alter AnxA6 levels in primary human hepatic stellate cells. However, in hepatic tumors of 18 patients, AnxA6 protein levels are substantially reduced compared to nontumorous tissues. AnxA6 mRNA is even increased in the tumors suggesting that posttranscriptional mechanisms are involved herein. Lipidomic analysis shows trends toward elevated cholesteryl ester and sphingomyelin in the tumor samples, yet the ratio of tumor to nontumorous AnxA6 does not correlate with these lipids. The current study shows that AnxA6 is specifically reduced in human hepatocellular carcinoma suggesting a role of this protein in hepatocarcinogenesis.

Hepatic proteomic analysis revealed altered metabolic pathways in insulin resistant Akt1(+/-)/Akt2(-/-) mice

OBJECTIVE

The aim of this study was to identify liver proteome changes in a mouse model of severe insulin resistance and markedly decreased leptin levels.

METHODS

Two-dimensional differential gel electrophoresis was utilized to identify liver proteome changes in AKT1(+/-)/AKT2(-/-) mice. Proteins with altered levels were identified with tandem mass spectrometry. Ingenuity Pathway Analysis was performed for the interpretation of the biological significance of the observed proteomic changes.

RESULTS

11 proteins were identified from 2 biological replicates to be differentially expressed by a ratio of at least 1.3 between age-matched insulin resistant (Akt1(+/-)/Akt2(-/-)) and wild type mice. Albumin and mitochondrial ornithine aminotransferase were detected from multiple spots, which suggest post-translational modifications. Enzymes of the urea cycle were common members of top regulated pathways.

CONCLUSION

Our results help to unveil the regulation of the liver proteome underlying altered metabolism in an animal model of severe insulin resistance.

Multifactorial comparative proteomic study of cytochrome P450 2E1 function in chronic alcohol administration

With the use of iTRAQ technique, a multifactorial comparative proteomic study can be performed. In this study, to obtain an overview of ethanol, CYP2E1 and gender effects on liver injury and gain more insight into the underlying molecular mechanism, mouse liver proteomes were quantitatively analyzed using iTRAQ under eight conditions including mice of different genders, wild type versus CYP2E1 knockout, and normal versus alcohol diet. A series of statistical and bioinformatic analyses were explored to simplify and clarify multifactorial comparative proteomic data. First, with the Principle Component analysis, six proteins, CYP2E1, FAM25, CA3, BHMT, HIBADH and ECHS1, involved in oxidation reduction, energy and lipid metabolism and amino acid metabolism, were identified as the most differentially expressed gene products across all of the experimental conditions of our chronic alcoholism model. Second, hierarchical clustering analysis showed CYP2E1 knockout played a primary role in the overall differential protein expression compared with ethanol and gender factors. Furthermore, pair-wise multiple comparisons have revealed that the only significant expression difference lied in wild-type and CYP2E1 knockout mice both treated with ethanol. Third, K-mean clustering analysis indicated that the CYP2E1 knockout had the reverse effect on ethanol induced oxidative stress and lipid oxidation. More importantly, IPA analysis of proteomic data inferred that the gene expressions of two upstream regulators, NRF2 and PPARα, regulated by chronic alcohol feeding and CYP2E1 knockout, are involved in ethanol induced oxidative stress and lipid oxidation. The present study provides an effectively comprehensive data analysis strategy to compare multiple biological factors, contributing to biochemical effects of alcohol on the liver. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with data set identifier of PXD000635.