New application of a subcellular fractionation method to kidney and testis for the determination of conjugated linoleic acid in selected cell organelles of healthy and cancerous human tissues

Subcellular metabolomics: Isolation, measurement, and applications

Metabolomics, a technique that profiles global small molecules in biological samples, has been a pivotal tool for disease diagnosis and mechanism research. The sample type in metabolomics covers a wide range, including a variety of body fluids, tissues, and cells. However, little attention was paid to the smaller, relatively independent partition systems in cells, namely the organelles. The organelles are specific compartments/places where diverse metabolic activities are happening in an orderly manner. Metabolic disorders of organelles were found to occur in various pathological conditions such as inherited metabolic diseases, diabetes, cancer, and neurodegenerative diseases. However, at the cellular level, the metabolic outcomes of organelles and cytoplasm are superimposed interactively, making it difficult to describe the changes in subcellular compartments. Therefore, characterizing the metabolic pool in the compartmentalized system is of great significance for understanding the role of organelles in physiological functions and diseases. So far, there are very few research articles or reviews related to subcellular metabolomics. In this review, subcellular fractionation and metabolite analysis methods, as well as the application of subcellular metabolomics in the physiological and pathological studies are systematically reviewed, as a practical reference to promote the continued advancement in subcellular metabolomics.

Subcellular Fractionation from Fresh and Frozen Gastrointestinal Specimens

The purpose of this protocol is to fractionate human intestinal tissue obtained by endoscopy into nuclear and cytoplasmic compartments for the localization analysis of specific proteins or protein complexes in different tissue states (i.e., healthy vs. disease). This method is useful for the fractionation of both fresh and frozen intestinal tissue samples; it is easily accessible for all laboratories and not time consuming.

Targeting mammalian organelles with internalizing phage (iPhage) libraries

Techniques that are largely used for protein interaction studies and the discovery of intracellular receptors, such as affinity-capture complex purification and the yeast two-hybrid system, may produce inaccurate data sets owing to protein insolubility, transient or weak protein interactions or irrelevant intracellular context. A versatile tool for overcoming these limitations, as well as for potentially creating vaccines and engineering peptides and antibodies as targeted diagnostic and therapeutic agents, is the phage-display technique. We have recently developed a new technology for screening internalizing phage (iPhage) vectors and libraries using a ligand/receptor-independent mechanism to penetrate eukaryotic cells. iPhage particles provide a unique discovery platform for combinatorial intracellular targeting of organelle ligands along with their corresponding receptors and for fingerprinting functional protein domains in living cells. Here we explain the design, cloning, construction and production of iPhage-based vectors and libraries, along with basic ligand-receptor identification and validation methodologies for organelle receptors. An iPhage library screening can be performed in ∼8 weeks.

Protein kinase C beta mediates CD40 ligand-induced adhesion of monocytes to endothelial cells

Accumulating evidence supports the early involvement of monocyte/macrophage recruitment to activated endothelial cells by leukocyte adhesion molecules during atherogenesis. CD40 and its ligand CD40L are highly expressed in vascular endothelial cells, but its impact on monocyte adhesion and the related molecular mechanisms are not fully understood. The present study was designed to evaluate the direct effect of CD40L on monocytic cell adhesion and gain mechanistic insight into the signaling coupling CD40L function to the proinflammatory response. Exposure of cultured human aortic endothelial cells (HAECs) to clinically relevant concentrations of CD40L (20 to 80 ng/mL) dose-dependently increased human monocytic THP-1 cells to adhere to them under static condition. CD40L treatment induced the expression of vascular cell adhesion molecule-1 (VCAM-1) mRNA and protein expression in HAECs. Furthermore, exposure of HAECs to CD40L robustly increased the activation of protein kinase C beta (PKCβ) in ECs. A selective inhibitor of PKCβ prevented the rise in VCAM-1 and THP-1 cell adhesion to ECs. Moreover, stimulation of ECs to CD40L induced nuclear factor-κB (NF-κB) activation. PKCβ inhibition abolished CD40L-induced NF-κB activation, and NF-κB inhibition reduced expression of VCAM-1, each resulting in reduced THP-1 cell adhesion. Our findings provide the evidence that CD40L increases VCAM-1 expression in ECs by activating PKCβ and NF-κB, suggesting a novel mechanism for EC activation. Finally, administration of CD40L resulted in PKCβ activation, increased VCAM-1 expression and activated monocytes adhesiveness to HAECs, processes attenuated by PKCβ inhibitor. Therefore, CD40L may contribute directly to atherogenesis by activating ECs and recruiting monocytes to them.

Characterization of in vitro glucuronidation clearance of a range of drugs in human kidney microsomes: comparison with liver and intestinal glucuronidation and impact of albumin

Previous studies have shown the importance of the addition of albumin for characterization of hepatic glucuronidation in vitro; however, no reports exist on the effects of albumin on renal or intestinal microsomal glucuronidation assays. This study characterized glucuronidation clearance (CL(int, UGT)) in human kidney, liver, and intestinal microsomes in the presence and absence of bovine serum albumin (BSA) for seven drugs with differential UDP-glucuronosyltransferase (UGT) 1A9 and UGT2B7 specificity, namely, diclofenac, ezetimibe, gemfibrozil, mycophenolic acid, naloxone, propofol, and telmisartan. The impact of renal CL(int, UGT) on accuracy of in vitro-in vivo extrapolation (IVIVE) of glucuronidation clearance was investigated. Inclusion of 1% BSA for acidic drugs and 2% for bases/neutral drugs in incubations was found to be suitable for characterization of CL(int, UGT) in different tissues. Although BSA increased CL(int, UGT) in all tissues, the extent was tissue- and drug-dependent. Scaled CL(int, UGT) in the presence of BSA ranged from 2.22 to 207, 0.439 to 24.4, and 0.292 to 23.8 ml · min(-1) · g tissue(-1) in liver, kidney, and intestinal microsomes. Renal CL(int, UGT) (per gram of tissue) was up to 2-fold higher in comparison with that for liver for UGT1A9 substrates; in contrast, CL(int, UGT) for UGT2B7 substrates represented approximately one-third of hepatic estimates. Scaled renal CL(int, UGT) (in the presence of BSA) was up to 30-fold higher than intestinal glucuronidation for the drugs investigated. Use of in vitro data obtained in the presence of BSA and inclusion of renal clearance improved the IVIVE of glucuronidation clearance, with 50% of drugs predicted within 2-fold of observed values. Characterization and consideration of kidney CL(int, UGT) is particularly important for UGT1A9 substrates.

Anthocyanin inhibits high glucose-induced hepatic mtGPAT1 activation and prevents fatty acid synthesis through PKCζ

Mitochondrial acyl-CoA:glycerol-sn-3-phosphate acyltransferase 1 (mtGPAT1) controls the first step of triacylglycerol (TAG) synthesis and is critical to the understanding of chronic metabolic disorders such as primary nonalcoholic fatty liver disease (NAFLD). Anthocyanin, a large group of polyphenols, was negatively correlated with hepatic lipid accumulation, but its impact on mtGPAT1 activity and NAFLD has yet to be determined. Hepatoma cell lines and KKAy mice were used to investigate the impact of anthocyanin on high glucose-induced mtGPAT1 activation and hepatic steatosis. Treatment with anthocyanin cyanidin-3-O-β-glucoside (Cy-3-g) reduced high glucose-induced GPAT1 activity through the prevention of mtGPAT1 translocation from the endoplasmic reticulum to the outer mitochondrial membrane (OMM), thereby suppressing intracellular de novo lipid synthesis. Cy-3-g treatment also increased protein kinase C ζ phosphorylation and membrane translocation in order to phosphorylate the mtF0F1-ATPase β-subunit, reducing its enzymatic activity and thus inhibiting mtGPAT1 activation. In vivo studies further showed that Cy-3-g treatment significantly decreases hepatic mtGPAT1 activity and its presence in OMM isolated from livers, thus ameliorating hepatic steatosis in diabetic KKAy mice. Our findings reveal a novel mechanism by which anthocyanin regulates lipogenesis and thereby inhibits hepatic steatosis, suggesting its potential therapeutic application in diabetes and related steatotic liver diseases.

Influence of diet enriched with conjugated linoleic acids on their distribution in tissues of rats with DMBA induced tumors

Backround

Conjugated linoleic acids (CLA) are a group of positional and geometric isomers of linoleic acid with proven beneficial influence on health. They show e.g. anticarcinogenic, antiobesity, and antiatherogenic effect. Milk, dairy products and meat of poligastric animals are their most valuable dietary sources, with cis-9, trans-11 CLA (RA - rumenic acid) being the predominant isomer. Dietary supplements with CLA became very popular, mainly among the overweight and bodybuilders.

The aim of this study was to examine the influence of the food supplements with conjugated linoleic acid on carcinogenesis in female Sprague-Dawley rats and evaluation of CLA and other fatty acids distribution in their bodies.

Animals were divided into four groups depending on the diet supplementation (oil or Bio-C.L.A. (Pharma Nord Denmark) given intragastrically) and presence or absence of carcinogenic agent (7,12-dimethylbenz[a]antharcene). Animals were decapitated at 21st week of experiment and serum and microsomes were extracted.

Results and conclusions

The mammary tumours (adenocarcinoma) occurred in groups treated with DMBA. Diet enriched with CLA decreased the cancer morbidity (67% in Bio-C.L.A. compared to 88% in oil) and delayed the cancer induction (p = 0.0018). There were no differences in body and organs weight.

The supplement used in the study was a mixture of several fatty acids with the greatest proportion of CLA isomers: trans-10, cis-12 (33%) and cis-9, trans-11 (31%). Both of them were present in tissues but the content of rumenic acid was greater. Dietary supplementation had also significant impact on other fatty acids content, both in serum and in microsomes.

Identification of a structural motif in the tumor-suppressive protein GRIM-19 required for its antitumor activity

We have previously isolated GRIM-19, a novel growth suppressor, using a genetic method. GRIM-19 ablates cell growth by inhibiting the transcription factor signal transducer and activator of transcription 3 (STAT3). Up-regulation of STAT3 and growth promotion were observed in a number of human tumors. Although the tumor-suppressive actions of GRIM-19 are known, the structural elements required for its antitumor actions are not understood. Mutational and protein sequence analyses identified a motif in the N terminus of GRIM-19 that exhibited similarity to certain RNA viral proteins. We show that disruption of specific amino acids within this motif cripples the antitumor actions of GRIM-19. These mutants fail to interact with STAT3 efficiently and consequently do not inhibit growth-promoting gene expression. More importantly, we show that a clinically observed mutation in the N terminus of GRIM-19 also weakened its interaction with STAT3 and antitumor action. Together, these studies identify a major role for the N terminus of GRIM-19 in mediating its tumor-suppressive actions.

Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

Placental abnormalities are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ∼5% of all pregnancies. An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities, but there have been no systematic attempts to assess their molecular similarities or differences. We collected protein and mRNA expression data through shot-gun proteomics and microarray expression analysis of the highly vascular exchange region, microdissected from the human and mouse near-term placenta. Over 7000 ortholog genes were detected with 70% co-expressed in both species. Close to 90% agreement was found between our human proteomic results and 1649 genes assayed by immunohistochemistry for expression in the human placenta in the Human Protein Atlas. Interestingly, over 80% of genes known to cause placental phenotypes in mouse are co-expressed in human. Several of these phenotype-associated proteins form a tight protein–protein interaction network involving 15 known and 34 novel candidate proteins also likely important in placental structure and/or function. The entire data are available as a web-accessible database to guide the informed development of mouse models to study human disease.

APE1/Ref-1 promotes the effect of angiotensin II on Ca2+ -activated K+ channel in human endothelial cells via suppression of NADPH oxidase

The effects of angiotensin II (Ang II) on whole-cell large conductance Ca(2+)-activated K(+) (BK(Ca)) currents was investigated in control and Apurinic/apyrimidinic endonuclease1/redox factor 1 (APE1/Ref-1)-overexpressing human umbilical vein endothelial cells (HUVECs). Ang II blocked the BK(Ca) current in a dose-dependent fashion, and this inhibition was greater in APE1/Ref-1-overexpressing HUVECs than in control HUVECs (half-inhibition values of 102.81+/-9.54 nM and 11.34+/-0.39 nM in control and APE1/Ref-1-overexpressing HUVECs, respectively). Pretreatment with the NADPH oxidase inhibitor diphenyleneiodonium (DPI) or knock down of NADPH oxidase (p22 phox) using siRNA increased the inhibitory effect of Ang II on the BK(Ca) currents, similar to the effect of APE1/Ref-1 overexpression. In addition, application of Ang II increased the superoxide and hydrogen peroxide levels in the control HUVECs but not in APE1/Ref-1-overexpressing HUVECs. Furthermore, direct application of hydrogen peroxide increased BK(Ca) channel activity. Finally, the inhibitory effect of Ang II on the BK(Ca) current was blocked by an antagonist of the Ang II type 1 (AT(1)) receptor in both control and APE1/Ref-1-overexpressing HUVECs. From these results, we conclude that the inhibitory effect of Ang II on BK(Ca) channel function is NADPH oxidase-dependent and may be promoted by APE1/Ref-1.

Phosphorylation of LKB1 at serine 428 by protein kinase C-zeta is required for metformin-enhanced activation of the AMP-activated protein kinase in endothelial cells

BACKGROUND

Metformin, one of most commonly used antidiabetes drugs, is reported to exert its therapeutic effects by activating AMP-activated protein kinase (AMPK); however, the mechanism by which metformin activates AMPK is poorly defined. The objective of the present study was to determine how metformin activates AMPK in endothelial cells.

METHODS AND RESULTS

Exposure of human umbilical vein endothelial cells or bovine aortic endothelial cells to metformin significantly increased AMPK activity and the phosphorylation of both AMPK at Thr172 and LKB1 at Ser428, an AMPK kinase, which was paralleled by increased activation of protein kinase C (PKC)-zeta, as evidenced by increased activity, phosphorylation (Thr410/403), and nuclear translocation of PKC-zeta. Consistently, either pharmacological or genetic inhibition of PKC-zeta ablated metformin-enhanced phosphorylation of both AMPK-Thr172 and LKB1-Ser428, suggesting that PKC-zeta might act as an upstream kinase for LKB1. Furthermore, adenoviral overexpression of LKB1 kinase-dead mutants abolished but LKB1 wild-type overexpression enhanced the effects of metformin on AMPK in bovine aortic endothelial cells. In addition, metformin increased the phosphorylation and nuclear export of LKB1 into the cytosols as well as the association of AMPK with LKB1 in bovine aortic endothelial cells. Similarly, overexpression of LKB1 wild-type but not LKB1 S428A mutants (serine replaced by alanine) restored the effects of metformin on AMPK in LKB1-deficient HeLa-S3 cells, suggesting that Ser428 phosphorylation of LKB1 is required for metformin-enhanced AMPK activation. Moreover, LKB1 S428A, like kinase-dead LKB1 D194A, abolished metformin-enhanced LKB1 translocation as well as the association of LKB1 with AMPK in HeLa-S3 cells. Finally, inhibition of PKC-zeta abolished metformin-enhanced coimmunoprecipitation of LKB1 with both AMPKalpha1 and AMPKalpha2.

CONCLUSIONS

We conclude that PKC-zeta phosphorylates LKB1 at Ser428, resulting in LKB1 nuclear export and hence AMPK activation.

Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics

We have shown that sample fractionation is an effective method for increasing the detection coverage of the proteome of complex samples, such as organs, by mass-spectrometric techniques. Further fractionating a sample based on subcellular compartments can generate molecular information on the state of a tissue and the distribution of its protein components. Although many methods exist for fractionating proteins, the method described here can capture the majority of subcellular fractions simultaneously at reasonable purity. The scalability of this method makes it amenable to small samples, such as embryonic tissues, in addition to larger tissues. The protocol described is for the general fractionation and extraction of proteins from organs or tissues for subsequent analysis by mass spectrometry. It uses differential centrifugation in density gradients to isolate nuclear, cytosolic, mitochondrial and mixed microsomal (Golgi, endoplasmic reticulum, other vesicles and plasma membrane) fractions. Once the fractions are isolated, they are extracted for protein and the samples can then be frozen for processing and analysis at a later date. The procedure can typically be completed in 5 h.

Recent advances in protein profiling of tissues and tissue fluids

Creating protein profiles of tissues and tissue fluids, which contain secreted proteins and peptides released from various cells, is critical for biomarker discovery as well as drug and vaccine target selection. It is extremely difficult to obtain pure samples from tissues or tissue fluids, however, and identification of complex protein mixtures is still a challenge for mass spectrometry analysis. Here, we summarize recent advances in techniques for extracting proteins from tissues for mass spectrometry profiling and imaging. We also introduce a novel technique using a capillary ultrafiltration (CUF) probe to enable in vivo collection of proteins from the tissue microenvironment. The CUF probe technique is compared with existing sampling techniques, including perfusion, saline wash, fine-needle aspiration and microdialysis. In this review, we also highlight quantitative mass spectrometric proteomic approaches with, and without, stable-isotope labels. Advances in quantitative proteomics will significantly improve protein profiling of tissue and tissue fluid samples collected by CUF probes.

IF(1) distribution in HepG2 cells in relation to ecto-F(0)F (1)ATPsynthase and calmodulin

F(0)F(1)ATPsynthase is now known to be expressed as a plasma membrane receptor for several extracellular ligands. On hepatocytes, ecto-F(0)F(1)ATPsynthase binds apoA-I and triggers HDL endocytosis concomitant with ATP hydrolysis. Considering that inhibitor protein IF(1) was shown to regulate the hydrolytic activity of ecto-F(0)F(1)ATPsynthase and to interact with calmodulin (CaM) in vitro, we investigated the subcellular distributions of IF(1), calmodulin (CaM), OSCP and beta subunits of F(0)F(1)ATPsynthase in HepG2 cells. Using immunofluorescence and Western blotting, we found that around 50% of total cellular IF(1) is localized outside mitochondria, a relevant amount of which is associated to the plasma membrane where we also found Ca(2+)-CaM, OSCP and beta. Confocal microscopy showed that IF(1) colocalized with Ca(2+)-CaM on plasma membrane but not in mitochondria, suggesting that Ca(2+)-CaM may modulate the cell surface availability of IF(1) and thus its ability to inhibit ATP hydrolysis by ecto-F(0)F(1)ATPsynthase. These observations support a hypothesis that the IF(1)-Ca(2+)-CaM complex, forming on plasma membrane, functions in the cellular regulation of HDL endocytosis by hepatocytes.

Ability of a small, basic protein isolated from Russell's viper venom (Daboia russelli russelli) to induce renal tubular necrosis in mice

Russell's viper venom (RVV) induced acute renal failure involves both direct and indirect nephrotoxic actions where the specific component/s are yet to be identified. A basic cytotoxin of 7.2kDa (RVV-7) has been identified as potential nephrotoxin. Autoradiographic experiments demonstrated that only RVV-7 among RVV toxins binds specifically to mice kidney membrane. Homogeneous preparation of RVV-7 confirmed its necrotic cell killing property having EC(50) of 4.79+/-3.28microM. Tissue distribution kinetics of RVV-7 in mice showed its higher localization in kidney compared to blood and liver. Role of inherent factor responsible for its localization in kidney was assessed after chemical inactivation of its cytotoxic activity. Cytotoxicity was neutralized by histidine modification but consequent alteration of in vivo distribution was insignificant. Classical concept of glomerular capillary wall (GCW) permselectivity barrier denotes that apart from size selectivity, GCW also restricts anionic proteins from filtration. Reducing the pI of RVV-7 by chemical manipulation of its surface positive charges resulted to decreased accumulation in kidney. Histological observations of kidney from mice treated in vivo with RVV-7 showed degenerated tubular epithelium. These findings indicate that basic character and small size of RVV-7 are favorable for its rapid accumulation in kidney leading to necrotic destruction of tubular epithelium.

Sample preparation project for the subcellular proteome of mouse liver

Organelle proteome has become one of the most important fields of proteomics, and the subcellular fractionation with high purity and yield has always been a challenge for cell biologists and also for the Human Liver Proteome Project (HLPP). The liver of a C57BL/6J mouse was chosen as the model to find the optimum method for subcellular preparation. The method we selected could obtain the multiple fractions including plasma membrane, mitochondria, nucleus, ER, and cytosol from a single homogenate. With the same procedure, it is for the first time that the preparation method of frozen homogenized livers was compared with that of the fresh livers and frozen livers. We systematically evaluated the purity, efficiency, and integrity by protein yield, immunoblotting, and transmission electron microscopy. Taken together, the method of multiple fractions from a single tissue is effective enough for subcellular fractionation of mouse liver. We give a selective sample preparation method for frozen homogenized livers, for rare clinical samples, which cannot easily be used for subcellular separation immediately. But the frozen livers are not recommended for organelles isolation. This result is especially useful for sample preparation of human liver for subcellular fractionation of HLPP.

Distribution of polyunsaturated fatty acids including conjugated linoleic acids in total and subcellular fractions from healthy and cancerous parts of human kidneys

Differences in the FA composition of subcellular fractions from healthy and cancerous kidney tissues from the same patients were examined. Only minor differences in CLA content were found between the healthy and the cancerous tissue portions. Regarding the distribution pattern, CLA incorporation into nuclei and cytosol was significantly higher than incorporation into plasma membranes and mitochondria, which could be correlated to the neutral lipid content of these fractions. The subcellular distribution pattern of CLA was similar to that observed with monounsaturated FA but unlike that found with 18:2n-6, which underlines the different physiological properties of CLA and 18:2n-6. Because PUFA have been suggested to have an effect on cancer risk, the contents of n-3 and n-6 PUFA were determined in kidney and renal cell carcinoma (RCC). The 18:2n-6 content and delta5 desaturase activity were significantly lower, and the 18:3n-6, 20:3n-6, and 20:5n-3 contents and delta6 desaturase activity were significantly higher in RCC than in healthy renal tissue, indicating a changed PUFA metabolism in RCC. Previous research has suggested that CLA inhibits the elongation and desaturation of 18:2n-6 into 20:4n-6. In that case, one might speculate that a diet enriched in CLA would be a useful tool in preventing RCC. However, the involvement of CLA in preventing renal cancer could not be demonstrated definitively from the design of this experiment. Further understanding of the cause and/or consequence of the difference in FA metabolism may lead to a better understanding of RCC.

Distribution of conjugated linoleic acid in total and subcellular fractions from normal and cancerous parts of human testes

The objective of the present study was to examine differences in the fatty acid composition of subcellular fractions from normal and cancerous parts of human testes. The conjugated linoleic acid (CLA) content was significantly higher in total testicular carcinoma (TC), but significantly lower in the mitochondrial fraction of TC in comparison to normal testicular tissue. The subcellular distribution pattern of CLA was similar to that of monounsaturated fatty acids, but different to that of 18:2n-6 (linoleic acid), underlining the different physiological properties of CLA and 18 : 2n-6. Because polyunsaturated fatty acids (PUFAs) have been suggested to have an effect on cancer risk and previous research has found that CLA inhibits the metabolism of 18 : 2n-6 into 20 : 4n-6, the contents of n-6 and n-3 PUFAs were determined. Significant differences were observed for 18 : 2n-6, 18 : 3n-3, 20 : 5n-3, and 22 : 6n-3, with 18 : 2n-6, 18 : 3n-3, and 20 : 5n-3 contents being higher and 22 : 6n-3 content being lower in TC than in normal testicular tissue. These results indicate a changed availability of substrates for the cyclooxygenase (COX) or lipooxygenase (LOX) pathways generating eicosanoids. Although not statistically significant, the reduced content of 20 : 4n-6 shown in this study might be due to an increased metabolism of this fatty acid into eicosanoids.