Proteomic Differences Between Hepatocellular Carcinoma and Nontumorous Liver Tissue Investigated by a Combined Gel-based and Label-free Quantitative Proteomics Study

Proteomics-based clinical studies have been shown to be promising strategies for the discovery of novel biomarkers of a particular disease. Here, we present a study of hepatocellular carcinoma (HCC) that combines complementary two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography (LC-MS)-based approaches of quantitative proteomics. In our proteomic experiments, we analyzed a set of 14 samples (7 × HCC versus 7 × nontumorous liver tissue) with both techniques. Thereby we identified 573 proteins that were differentially expressed between the experimental groups. Among these, only 51 differentially expressed proteins were identified irrespective of the applied approach. Using Western blotting and immunohistochemical analysis the regulation patterns of six selected proteins from the study overlap (inorganic pyrophosphatase 1 (PPA1), tumor necrosis factor type 1 receptor-associated protein 1 (TRAP1), betaine-homocysteine S-methyltransferase 1 (BHMT)) were successfully verified within the same sample set. In addition, the up-regulations of selected proteins from the complements of both approaches (major vault protein (MVP), gelsolin (GSN), chloride intracellular channel protein 1 (CLIC1)) were also reproducible. Within a second independent verification set (n = 33) the altered protein expression levels of major vault protein and betaine-homocysteine S-methyltransferase were further confirmed by Western blots quantitatively analyzed via densitometry. For the other candidates slight but nonsignificant trends were detectable in this independent cohort. Based on these results we assume that major vault protein and betaine-homocysteine S-methyltransferase have the potential to act as diagnostic HCC biomarker candidates that are worth to be followed in further validation studies.Hepatocellular carcinoma (HCC)¹ currently is the fifth most common malignancy worldwide with an annual incidence up to 500 per 100,000 individuals depending on the geographic region investigated. Whereas 80% of new cases occur in developing countries, the incidence increases in industrialized nations including Western Europe, Japan, and the United States (1). To manage patients with HCC, tumor markers are very important tools for diagnosis, indicators of disease progression, outcome prediction, and evaluation of treatment efficacy. Several tumor markers have been reported for HCC, including α-fetoprotein (AFP) (2), Lens culinaris agglutinin-reactive fraction of AFP (AFP-L3) (3), and des-γ-carboxyl prothrombin (DCP) (4). However, none of these tumor markers show 100% sensitivity or specificity, which calls for new and better biomarkers.To identify novel biomarkers of HCC, many clinical studies using “omics”-based methods have been reported over the past decade (5–6). In particular, the proteomics-based approach has turned out to be a promising one, offering several quantification techniques to reveal differences in protein expression that are caused by a particular disease. In most studies, the well-established 2D-DIGE technique has been applied for protein quantification followed by identification via mass spectrometry (7–15). Even if the quantification is very accurate and sensitive in this gel-based approach, the relatively high amount of protein sample necessary for protein identification is the major disadvantage of this technique. Several mass-spectrometry-based quantitative studies using labeling-techniques like SILAC (stable isotope labeling by amino acids in cell culture) or iTRAQ (isobaric tags for relative and absolute quantification) have also been carried out for biomarker discovery of HCC (16–18). Here, the concomitant protein quantification and identification in a mass spectrometer allows high-throughput analyses. However, such experiments imply additional labeling reactions (in case of iTRAQ) or are limited to tissue culture systems (in case of SILAC). In the latter case, one can overcome the limitation by using the isotope-labeled proteins obtained from tissue culture as an internal standard added to a corresponding tissue sample. This approach is known as CDIT (culture-derived isotope tags) and was applied in a HCC study, very recently (19). Label-free proteomics approaches based on quantification by ion-intensities or spectral counting offer another possibility for biomarker discovery. These approaches are relatively cheap compared with the labeling approaches, because they do not require any labeling reagents and furthermore they allow for high-throughput and sensitive analyses in a mass spectrometer. A quantitative study of HCC using spectral counting has been reported (20), whereas to our knowledge an ion-intensity-based study has not been performed yet. Apart from these quantification strategies, protein alterations in HCC have been studied by MALDI imaging, as well. Here, the authors could show that based on its proteomic signature, hepatocellular carcinoma can be discriminated with high accuracy from liver metastasis samples or other cancer types (21) as well as liver cirrhosis (22). Based on these results, it could be assumed that MALDI imaging might be a promising alternative to standard histological methods in the future.Here, we report a quantitative proteomic study that combines two different techniques, namely the well-established 2D-DIGE approach and a label-free ion-intensity-based quantification via mass spectrometry and liquid chromatography. To our knowledge this is the first time such a combined study was performed with regard to hepatocellular carcinoma. By comparing the results of both studies, we aim to identify high-confident biomarker candidates of HCC, as gel- and LC-MS-based techniques are complementary. To verify the differential protein expressions detected in our proteomic studies we performed additional immunological verifications for selected proteins within two different sample sets (Fig. 1).Open in a separate windowFig. 1.Schematic representation of the applied workflow.     

Adenine-dependent growth of marine yeast,Rhodotorula glutinis var.salinaria under sodium chloride-hypertonic condition

Nitrate and ammonium were shown to alter the growth ofRhodotorula glutinis var.salinaria in saline and non-saline media. In saline medium in which ammonium was the sole nitrogen source, ammonium inhibited growth in the presence of molybdate ions. Detailed comparisons of the growth in saline and non-saline media when nitrate was supplemented in the presence of molybdate ions showed that differences in utilizability of purine bases of nucleic acid were responsible for the differences in growth,i.e. adenine increased the growth in such saline medium, but decreased it in non-saline medium. There was not such a specific requirement for adenine in saline medium in the presence of molybdate ions when nitrate was substituted for ammonium as the sole nitrogen source. It was suggested that adenine might provide the necessary skeleton of nucleic acid for serving nitrate reduction in saline medium.     

Fibrinolysis: Its initiation and regulation

Fibrinolytic system is one of the major proteolytic pathways in vivo and primarily responsible for dissolution of thrombi. Two enzymes are primarily involved in this proteolytic system; plasminogen activator (PA) and plasmin. Plasmin is formed by a limited proteolysis of plasminogen by PA, which is mainly synthesized by and secreted from vascular endothelial cells. This proteolytic process proceeds physiologically only on the surface of fibrin. Thus, initiation and progression of the fibrinolytic process depend on the function of endothelial cells and fibrin formation. Endothelial cells may also synthesize and excrete PA inhibitor (PAI) which inhibits immediately, PA once released. The rates of synthesis and excretion of PA and PAI by endothelial cells are regulated by various factors. Among them, thrombin stimulates the release of PA whereas activated protein C may decrease the release of PAI. Thus, both enzymes enhance fibrinolytic potential. PA which has escaped from inhibition by PAI binds to fibrin. ₂-Plasmin inhibitor (₂PI) inhibits the binding of plasminogen to fibrin, thereby suppressing this fibrin-associated plasminogen activation. A part of ₂PI is cross-linked to fibrin by activated factor XIII when fibrin is formed, and the ₂PI thus cross-linked to fibrin inhibits in situ plasmin formed on fibrin. Thus, ₂PI as well as PAI plays a central role in inhibition of fibrinolysis.     

Pleistocene rapid uplift of the Himalayan frontal ranges recorded in the Kathmandu and Siwalik basins

Core-drilling project carried out in the southern margin of the Kathmandu Basin revealed that muddy debris flow deposits dammed up the Proto-Bagmati river to form the Paleo-Kathmandu Lake during the Jaramillo subchron from 1.07 to 0.97 Ma. Subsequent deposition of the alluvial fanglomerate, derived from the uplifting Mahabharat Range to the south, raised the dam deepening the lake-water. After 1 Ma, in the southern part of the basin, palaeo-current directions changed from southward to northward and deposition of gneissose and granitic detritus are replaced by meta-sediments derived from the Mahabharat Range.During the same time, at about 1 Ma, the boulder conglomerates were deposited on top of the Siwalik Group as piggy-back basins in front of an intra-basinal high, along the Main Dung Thrust in Nepal and NW India. Onset of movement of the Main Dung Thrust is dated back to 3 to 2.4 Ma [Mugnier, J.L., Huyge, P., Leturmy, P., Jouanne, F., 2003, Episodicity and rates of thrust-sheet motion in the Himalayas, Western Nepal. Am. Assoc. Petrol. Geol., Mem. 82, 1-24]. The Main Frontal Thrust is most active at present suggesting that imbricated structure of the Siwalik Group was formed by convergence of the Indian plate during the last 3 myr. The accretionary wedge of the Siwalik Group, stacked beneath the Main Boundary Thrust, might have started to jack up the frontal range of the Lesser Himalaya since 1 Ma.Coeval uplift and erosion of the frontal range of the Lesser Himalaya and the intra-basinal high in the Siwalik since 1 Ma are possible causes of an abrupt increase in both sedimentation rate and grain size of detrital quartz, and changes in composition of clay minerals, recorded in the sediments of the Bengal Deep Sea Fan at 0.9 Ma.     

Characterization of acute and latent herpes simplex virus infection of dorsal root ganglia in rats.

The characteristics of HSV type-1 infection following subcutaneous inoculation in the dorsum of one hind paw of Sprague-Dawley rats were studied to determine whether infection in rats might more closely parallel the infection in man than is seen in other animals. The serologic and virologic characteristics of acute and latent ganglion infection conformed to those of human infection. Immunohistochemical studies suggested that sensory ganglion infection arose via centripetal axonal migration of virus as is hypothesized in man. In rat, small type B neuronal cell bodies appeared central to the maintenance of latent infection and reactivation observed during cocultivation of lumbar ganglia. Acute and latent lumbar sensory ganglion infection in rats after subcutaneous hind paw injection of HSV-1 appears to be another suitable model of this infection in man.     

Role of O-Methyltransferase in the Lignification of Bamboo

Characterization of S-adenosylmethionine: catechol O-methyltransferase (EC. 2. 1. 1.6) isolated from bamboo shoot was carried out. Ferulic and sinapic acids which are believed to be lignin precursors are formed by the mediation of the enzyme, and the enzyme activity increased progressively during the lignification of bamboo shoots. Evidences suggest that this enzyme may contribute to the synthesis of lignin precursors.