Liver-specific Deficiency of Serine Palmitoyltransferase Subunit 2 Decreases Plasma Sphingomyelin and Increases Apolipoprotein E Levels

Sphingomyelin (SM) is one of the major lipid components of plasma lipoproteins. Serine palmitoyltransferase (SPT) is the key enzyme in SM biosynthesis. Mice totally lacking in SPT are embryonic lethal. The liver is the major site for plasma lipoprotein biosynthesis, secretion, and degradation, and in this study we utilized a liver-specific knock-out approach for evaluating liver SPT activity and also its role in plasma SM and lipoprotein metabolism. We found that a deficiency of liver-specific Sptlc2 (a subunit of SPT) decreased liver SPT protein mass and activity by 95 and 92%, respectively, but had no effect on other tissues. Liver Sptlc2 deficiency decreased plasma SM levels (in both high density lipoprotein and non-high density lipoprotein fractions) by 36 and 35% (p < 0.01), respectively, and increased phosphatidylcholine levels by 19% (p < 0.05), thus increasing the phosphatidylcholine/SM ratio by 77% (p < 0.001), compared with controls. This deficiency also decreased SM levels in the liver by 38% (p < 0.01) and in the hepatocyte plasma membranes (based on a lysenin-mediated cell lysis assay). Liver-specific Sptlc2 deficiency significantly increased hepatocyte apoE secretion and thus increased plasma apoE levels 3.5-fold (p < 0.0001). Furthermore, plasma from Sptlc2 knock-out mice had a significantly stronger potential for promoting cholesterol efflux from macrophages than from wild-type mice (p < 0.01) because of a greater amount of apoE in the circulation. As a result of these findings, we believe that the ability to control liver SPT activity could result in regulation of lipoprotein metabolism and might have an impact on the development of atherosclerosis.Sphingomyelin (SM),² an amphipathic phospholipid located in the surface monolayer of all classes of plasma lipoproteins (LDL/very low density lipoprotein, 70–75%; HDL, 25–30%) (1), has significant effects on lipoprotein metabolism.A number of studies indicate that plasma SM levels influence the metabolism of apoB-containing lipoproteins. It has been reported that SM, but not cholesterol, significantly inhibits triglyceride lipolysis by lipoprotein lipase (2, 3). It has also been found that SM in lipoproteins delays remnant clearance by decreasing the binding of apoE to cell membrane receptors (4).Plasma SM levels also influence high density lipoprotein (HDL) metabolism. There have been reports that SM affects the structure of discoidal and spherical HDL (5). SM can inhibit lecithin-cholesterol acyltransferase by decreasing its binding to HDL (6). A negative correlation between the SM content of HDL and lecithin-cholesterol acyltransferase activity was observed in studies with proteoliposomes or reconstituted HDL (7). SM-rich recombinant HDL can inhibit scavenger receptor class B type I-mediated cholesterol ester-selective uptake in HepG2 cells (8).It is known that subendothelial retention and aggregation of atherogenic lipoproteins play an important role in atherogenesis (9). LDL extracted from human atherosclerotic lesions is highly enriched in SM than in plasma LDL (10–13). LDL retained in atherosclerotic lesions is acted on by an arterial wall sphingomyelinase, which promotes aggregation by converting SM to ceramide (10–12). Sphingomyelinase deficiency diminishes lipoprotein retention within early atheromata and prevents lesion progression (14). The ratio of SM to PC is increased 5-fold in very low density lipoprotein from hypercholesterolemic rabbits (15). ApoE knock-out (KO) mice are a well known atherogenic model. It has been shown that plasma SM levels in these mice are 4-fold higher than in WT animals (16), and this may contribute to increased atherosclerosis (17, 18). It has also been shown that in humans, higher plasma SM levels and SM/PC ratios are independent risk factors for coronary heart disease (19, 20). All these data suggest that plasma SM plays a critical role in the development of atherosclerosis.The interaction of SM, cholesterol, and glycosphingolipids drives the formation of plasma membrane rafts (21). These rafts, formed in the Golgi apparatus, are targeted to the plasma membranes, where they are thought to exist as islands within the sea of bulk membrane. Although there is disagreement as to their content, rafts are considered in most reports to include about 3500 lipid molecules and 30 proteins (22). As much as 65% of the total cellular SM is located in these rafts (23). Manipulation of membrane SM levels by sphingomyelinase can alter lipid raft composition, thus modifying cell function. For example, cholesterol efflux from macrophage foam cells, a key step in reverse cholesterol transport, requires trafficking of cholesterol from intracellular sites to the plasma membranes. Sphingomyelinase deficiency decreases cholesterol efflux through promoting cholesterol sequestration by SM (24).The biochemical synthesis of SM occurs through the actions of serine palmitoyl-CoA transferase (SPT), 3-ketosphinganine reductase, ceramide synthase, dihydroceramide desaturase, and sphingomyelin synthase. Located in the endoplasmic reticulum membranes, SPT is the rate-limiting enzyme in the pathway (25). Mammalian SPT contains two subunits, Sptlc1 and Sptlc2, encoding 53- and 63-kDa proteins, respectively (26, 27). Data from in vivo and in vitro studies suggest that each subunit is stabilized by forming a dimer (or possibly larger multimer) with the other (28). Another subunit, Sptlc3, has been reported (29), and it is important that its functions be further characterized.Mice totally lacking Sptlc1 or Sptlc2 are embryonic lethal (30). Because the liver is the major site for plasma lipoprotein biosynthesis, secretion, and degradation, we utilized a liver-specific knock-out approach for evaluating liver SPT activity and its role in plasma SM and lipoprotein metabolism. We found that Sptlc2 deficiency in the liver decreases plasma SM and increases apoE levels.     

Multi-dimensional Co-separation Analysis Reveals Protein–Protein Interactions Defining Plasma Lipoprotein Subspecies

The distribution of circulating lipoprotein particles affects the risk for cardiovascular disease (CVD) in humans. Lipoproteins are historically defined by their density, with low-density lipoproteins positively and high-density lipoproteins (HDLs) negatively associated with CVD risk in large populations. However, these broad definitions tend to obscure the remarkable heterogeneity within each class. Evidence indicates that each class is composed of physically (size, density, charge) and compositionally (protein and lipid) distinct subclasses exhibiting unique functionalities and differing effects on disease. HDLs in particular contain upward of 85 proteins of widely varying function that are differentially distributed across a broad range of particle diameters. We hypothesized that the plasma lipoproteins, particularly HDL, represent a continuum of phospholipid platforms that facilitate specific protein–protein interactions. To test this idea, we separated normal human plasma using three techniques that exploit different lipoprotein physicochemical properties (gel filtration chromatography, ionic exchange chromatography, and preparative isoelectric focusing). We then tracked the co-separation of 76 lipid-associated proteins via mass spectrometry and applied a summed correlation analysis to identify protein pairs that may co-reside on individual lipoproteins. The analysis produced 2701 pairing scores, with the top hits representing previously known protein–protein interactions as well as numerous unknown pairings. A network analysis revealed clusters of proteins with related functions, particularly lipid transport and complement regulation. The specific co-separation of protein pairs or clusters suggests the existence of stable lipoprotein subspecies that may carry out distinct functions. Further characterization of the composition and function of these subspecies may point to better targeted therapeutics aimed at CVD or other diseases.Lipoproteins are circulating emulsions of protein and lipid that play important roles, both positive and negative, in cardiovascular disease (CVD).¹ Historically defined by their density as separated by ultracentrifugation, the major lipoprotein classes include the neutral lipid ester-rich very low-density and low-density lipoproteins (VLDLs and LDLs, respectively), which function to transport triglyceride and cholesterol from the liver to the peripheral tissues. Significant epidemiological evidence, in vitro studies, animal experiments, and human clinical trials have shown that high-LDL cholesterol is a bona fide causative factor in CVD (1). In contrast, protein- and phospholipid-rich high-density lipoproteins (HDLs) are thought to mediate the reverse transport of cholesterol from the periphery to the liver for catabolism and to perform anti-oxidative and anti-inflammatory functions (reviewed in Refs. 2 and 3). A host of human epidemiology and animal studies indicate that HDLs are atheroprotective (4). However, recent clinical trials of therapeutics that generically raise HDL, at least as measured by its cholesterol levels, have failed to confer the expected CVD protections (5–7).Although these traditional density-centric definitions have been used for nearly 40 years, accumulating evidence indicates that they are not particularly reflective of lipoprotein compositional and functional complexity. With respect to most physical traits (size, charge, lipid content, protein content, etc.), one can demonstrate significant heterogeneity within each density class. This suggests that particle subspecies exist with unique functions and effects on disease. For example, LDL can be resolved into large, buoyant and small, dense forms (8), with subjects carrying more cholesterol in the small, dense LDL exhibiting a greater CVD risk (9). HDL is particularly noted for heterogeneity, as it can be separated into numerous subfractions by density (10), diameter (11), charge (12), and major apolipoprotein content (13). Most strikingly, recent applications of soft-ionization mass spectrometry (MS) have identified upward of 85 HDL proteins with functions that go well beyond the structural apolipoproteins, lipid transport proteins, and lipid-modifying enzymes known from previous biochemical studies (14, 15). Many of these proteins imply functions as diverse as complement regulation, acute phase response, protease inhibition, and innate immunity (16). Individual HDL subspecies can apparently draw from this palette of proteins to produce distinct particles of distinct function. One well-defined HDL subfraction, termed trypanosome lytic factor, contains apolipoprotein apoA-I, haptoglobin-related protein, and apoL-I. Working together, these proteins enter the trypanosome brucei brucei and kill it via lysosomal disruption (17). There are numerous other instances of on-particle protein cooperation in HDL related to CVD (reviewed in Ref. 15). Furthermore, two-dimensional electrophoresis studies by Asztalos and colleagues (18), as well as our own work (11, 19), strongly support the concept that certain apolipoproteins segregate among different HDL particles. These observations present the intriguing possibility that the phospholipids of HDLs act as an organizing platform that facilitates the assembly of specific protein complexes (20). Such subspecies could have important functional implications in the context of CVD protection, inflammation, or even innate immune function. Furthermore, this subspeciation may explain why therapeutics that raise HDL cholesterol levels across the board have not yet shown promise with regard to CVD.To address this hypothesis, we began to think of lipoproteins as a continuum of phospholipid platforms that support the assembly of specific protein complexes analogous to those in cells that perform coordinated biological functions (i.e. ribosomes, centrosomes, etc.). Two common methods for characterizing protein complexes are tandem affinity purification (21) and immunoprecipitation. Both rely on the specific pull-down of a target protein (by either an introduced affinity tag or an antibody) followed by the identification of co-precipitated proteins via MS. Unfortunately, tandem affinity purification strategies are impractical in humans, and we have found that immunoprecipitation experiments with human plasma lipoproteins result in a high false-positive rate due to the low abundance of most of these proteins, particularly those in HDLs. Therefore, we took an alternative approach called co-separation analysis, a method based on the principle that stable protein complexes can be identified by tracking their co-migration as they undergo biochemical separation by multiple orthogonal approaches (22). Native proteins are analyzed in an unbiased manner without affinity tags or antibodies, and purification to homogeneity is not necessary for the identification of putative protein complexes.Most current studies of the lipoprotein proteome utilize samples isolated via density ultracentrifugation because contaminating lipid-unassociated lipoproteins, which can be highly abundant and obscure the identification of targeted lipid-associated proteins, are thus removed prior to the analysis. In previous work, we characterized the use of a calcium silica hydrate (CSH) resin that allowed the specific isolation of phospholipid-associated proteins and their subsequent MS identification without ultracentrifugation (11). This advance enabled the use of a variety of non-density-based separation methods for the study of plasma lipoproteins. Here, we take advantage of this to analyze the proteome of human plasma lipoproteins separated via three separation techniques that exploit different physicochemical properties: (i) gel filtration chromatography (size), (ii) anion exchange chromatography (charge interaction), and (iii) isoelectric focusing. By tracking the co-migration of specific proteins across these separations (Fig. 1), we identified a host of putative protein pairings, including the previously known trypanosome lytic factor HDL fraction, for further biochemical verification and characterization.Open in a separate windowFig. 1.Overview of the multi-dimensional separation co-migration analysis used in this study (see “Experimental Procedures” for details).     

Requirement of Myosin Vb��Rab11a��Rab11-FIP2 Complex in Cholesterol-regulated Translocation of NPC1L1 to the Cell Surface

Niemann-Pick C1-like 1 (NPC1L1) plays a critical role in the enterohepatic absorption of free cholesterol. Cellular cholesterol depletion induces the transport of NPC1L1 from the endocytic recycling compartment to the plasma membrane (PM), and cholesterol replenishment causes the internalization of NPC1L1 together with cholesterol via clathrin-mediated endocytosis. Although NPC1L1 has been characterized, the other proteins involved in cholesterol absorption and the endocytic recycling of NPC1L1 are largely unknown. Most of the vesicular trafficking events are dependent on the cytoskeleton and motor proteins. Here, we investigated the roles of the microfilament and microfilament-associated triple complex composed of myosin Vb, Rab11a, and Rab11-FIP2 in the transport of NPC1L1 from the endocytic recycling compartment to the PM. Interfering with the dynamics of the microfilament by pharmacological treatment delayed the transport of NPC1L1 to the cell surface. Meanwhile, inactivation of any component of the myosin Vb·Rab11a·Rab11-FIP2 triple complex inhibited the export of NPC1L1. Expression of the dominant-negative mutants of myosin Vb, Rab11a, or Rab11-FIP2 decreased the cellular cholesterol uptake by blocking the transport of NPC1L1 to the PM. These results suggest that the efficient transport of NPC1L1 to the PM is dependent on the microfilament-associated myosin Vb·Rab11a·Rab11-FIP2 triple complex.Cholesterol homeostasis in human bodies is maintained through regulated cholesterol synthesis, absorption, and excretion. Intestinal cholesterol absorption is one of the major pathways to maintain cholesterol balance. NPC1L1 (Niemann-Pick C1-like protein 1), a polytopic transmembrane protein highly expressed in the intestine and liver, is required for dietary cholesterol uptake and biliary cholesterol reabsorption (1–4). Genetic or pharmaceutical inactivation of NPC1L1 significantly inhibits cholesterol absorption and confers the resistance to diet-induced hypercholesterolemia (1, 2, 4). Ezetimibe, an NPC1L1-specific inhibitor, is currently used to prevent and treat cardiovascular diseases (5).Human NPC1L1 contains 1,332 residues with 13 transmembrane domains (6). The third to seventh transmembrane helices constitute a conserved sterol-sensing domain (4, 7). NPC1L1 recycles between the endocytic recycling compartment (ERC)³ and the plasma membrane (PM) in response to the changes of cholesterol level (8). ERC is a part of early endosomes that is involved in the recycling of many transmembrane proteins. It is also reported that ERC is a pool for free cholesterol storage (9). When cellular cholesterol concentration is low, NPC1L1 moves from the ERC to the PM (8, 10). Under cholesterol-replenishing conditions, NPC1L1 and cholesterol are internalized together and transported to the ERC (8). Disruption of microfilament, depletion of the clathrin·AP2 complex, or ezetimibe treatment can impede the endocytosis of NPC1L1, thereby decreasing cholesterol internalization (8, 10, 11).The microfilament (MF) system, part of the cytoskeleton network, is required for multiple cellular functions such as cell shape maintenance, cell motility, mitosis, protein secretion, and endocytosis (12, 13). The major players in the microfilament system are actin fibers and motor proteins (14). Actin fibers form a network that serves as the tracks for vesicular transport (15, 16). Meanwhile, the dynamic assembly and disassembly of actin fibers and the motor proteins provides the driving force for a multitude of membrane dynamics including endocytosis, exocytosis, and vesicular trafficking between compartments (15, 16).Myosins are a large family of motor proteins that are responsible for actin-based mobility (14). Class V myosins (17, 18), comprising myosin Va, Vb, and Vc, are involved in a wide range of vesicular trafficking events in different mammalian tissues. Myosin Va is expressed mainly in neuronal tissues (19, 20), whereas myosins Vb and Vc are universally expressed with enrichment in epithelial cells (21, 22). Class V myosins are recruited to their targeting vesicles by small GTPase proteins (Rab) (23). Rab11a and Rab11 family-interacting protein 2 (Rab11-FIP2) facilitate the binding of myosin Vb to the cargo proteins of endocytic recycling vesicles (24–28).Myosin Vb binds Rab11a and Rab11-FIP2 through the C-terminal tail (CT) domain. The triple complex of myosin Vb, Rab11a, and Rab11-FIP2 is critical for endocytic vesicular transport and the recycling of many proteins including transferrin receptor (29), AMPA receptors (30), CFTR (28), GLUT4 (31, 32), aquaporin-2 (26), and β2-adrenergic receptors (33). The myosin Vb-CT domain (24) competes for binding to Rab11a and Rab11-FIP2 and functions as a dominant-negative form. Expression of the CT domain substantially impairs the transport of vesicles. Deficient endocytic trafficking is also observed in cells expressing the GDP-locked form of Rab11a (S25N) (34) or a truncated Rab11-FIP2, which competes for the rab11a binding (35).Here we investigated the roles of actin fibers and motor proteins in the cholesterol-regulated endocytic recycling of NPC1L1. Using pharmaceutical inactivation, dominant-negative forms, and an siRNA technique, we demonstrated that actin fibers and myosin Vb·Rab11a·Rab11-FIP2 triple complex are involved in the export of NPC1L1 to the PM and that this intact MF-associated triple complex is required for efficient cholesterol uptake. Characterization of the molecules involved in the recycling of NPC1L1 may shed new light upon the mechanism of cholesterol absorption.     

Identification of the Active Form of Endothelial Lipase, a Homodimer in a Head-to-Tail Conformation

Endothelial lipase (EL) is a member of a subfamily of lipases that act on triglycerides and phospholipids in plasma lipoproteins, which also includes lipoprotein lipase and hepatic lipase. EL has a tropism for high density lipoprotein, and its level of phospholipase activity is similar to its level of triglyceride lipase activity. Inhibition or loss-of-function of EL in mice results in an increase in high density lipoprotein cholesterol, making it a potential therapeutic target. Although hepatic lipase and lipoprotein lipase have been shown to function as homodimers, the active form of EL is not known. In these studies, the size and conformation of the active form of EL were determined. Immunoprecipitation experiments suggested oligomerization. Ultracentrifugation experiments showed that the active form of EL had a molecular weight higher than the molecular weight of a simple monomer but less than a dimer. A construct encoding a covalent head-to-tail homodimer of EL (EL-EL) was expressed and had similar lipolytic activity to EL. The functional molecular weights determined by radiation inactivation were similar for EL and the covalent homodimer EL-EL. We previously showed that EL could be cleaved by proprotein convertases, such as PC5, resulting in loss of activity. In cells overexpressing PC5, the covalent homodimeric EL-EL appeared to be more stable, with reduced cleavage and conserved lipolytic activity. A comparative model obtained using other lipase structures suggests a structure for the head-to-tail EL homodimer that is consistent with the experimental findings. These data confirm the hypothesis that EL is active as a homodimer in head-to-tail conformation.Three members of the triglyceride lipase family, lipoprotein lipase (LPL),³ hepatic lipase (HL), and endothelial lipase (EL), contribute to lipoprotein catabolism in the plasma compartment. They are all secreted proteins that bind to heparan sulfate proteoglycans on the luminal side of endothelial cells where they interact with their lipoprotein substrates. They have different specificities for lipoproteins, and all hydrolyze triglycerides and phosphatidylcholine at the sn-1 position, albeit with widely differing efficiencies (1). The preferred lipoprotein substrates for LPL are the triglyceride-rich lipoproteins, chylomicrons, and very low density lipoproteins; the triglyceride lipase activity of LPL is more than 100-fold greater than its phospholipase activity. The primary lipoprotein substrates for HL are chylomicron remnants, intermediate density lipoproteins, and large triglyceridase-enriched HDL; its triglyceride lipase activity is about 20-fold higher than its phospholipase activity. EL is much more active on HDL, and its phospholipase activity is quite similar to its triglyceride lipase activity.These three lipolytic enzymes share a number of structural features. By analogy to the crystal structure of pancreatic lipase (2), another member of the triglyceride lipase family, each has a clearly defined N-terminal and C-terminal structural domain, joined by a hinge region. They are all serine esterases with a catalytic triad of serine, aspartic acid, and histidine located in the N-terminal domain. The catalytic triad is covered by a lid domain that contributes to the preference for either triglyceride or phospholipid substrates (3–6). The C-terminal domain contributes to lipid binding and determines the preferences for binding to lipoproteins (7–12). The N-terminal portion of the EL molecule contains the active site of the enzyme. However, when this portion of the molecule is expressed without the C-terminal domain, it lacks enzymatic activity against phospholipid (13), triglyceride, and the more soluble micellar substrate tributyrin.⁴ Thus, the presence of the C-terminal domain is necessary for activity. All three enzymes are glycosylated to varying degrees, and two of the glycosylation sites (one each in the N- and C-terminal domains) are common to all three enzymes (14, 15). All three enzymes are also heparin-binding proteins, and regions that contribute to heparin binding are found in both the N- and C-terminal domains (16–18).EL and, to a lesser extent, LPL are subject to proteolytic cleavage by proprotein convertases at a prototypical RXKR site in the hinge region, but HL lacks the site and is not cleaved (19, 20). The catalytically active forms of both LPL and HL have been shown to be homodimers (18, 21–27), and in the case of LPL, the orientation of the subunits of the dimer has been shown to be head-to-tail (28–30). The present study tested the hypothesis that EL also functions as a head-to-tail dimer.     

Induction of the Cytoprotective Enzyme Heme Oxygenase-1 by Statins Is Enhanced in Vascular Endothelium Exposed to Laminar Shear Stress and Impaired by Disturbed Flow

In addition to cholesterol-lowering properties, statins exhibit lipid-independent immunomodulatory, anti-inflammatory actions. However, high concentrations are typically required to induce these effects in vitro, raising questions concerning therapeutic relevance. We present evidence that endothelial cell sensitivity to statins depends upon shear stress. Using heme oxygenase-1 expression as a model, we demonstrate differential heme oxygenase-1 induction by atorvastatin in atheroresistant compared with atheroprone sites of the murine aorta. In vitro, exposure of human endothelial cells to laminar shear stress significantly reduced the statin concentration required to induce heme oxygenase-1 and protect against H₂O₂-mediated injury. Synergy was observed between laminar shear stress and atorvastatin, resulting in optimal expression of heme oxygenase-1 and resistance to oxidative stress, a response inhibited by heme oxygenase-1 small interfering RNA. Moreover, treatment of laminar shear stress-exposed endothelial cells resulted in a significant fall in intracellular cholesterol. Mechanistically, synergy required Akt phosphorylation, activation of Kruppel-like factor 2, NF-E2-related factor-2 (Nrf2), increased nitric-oxide synthase activity, and enhanced HO-1 mRNA stability. In contrast, heme oxygenase-1 induction by atorvastatin in endothelial cells exposed to oscillatory flow was markedly attenuated. We have identified a novel relationship between laminar shear stress and statins, demonstrating that atorvastatin-mediated heme oxygenase-1-dependent antioxidant effects are laminar shear stress-dependent, proving the principle that biomechanical signaling contributes significantly to endothelial responsiveness to pharmacological agents. Our findings suggest statin pleiotropy may be suboptimal at disturbed flow atherosusceptible sites, emphasizing the need for more specific therapeutic agents, such as those targeting Kruppel-like factor 2 or Nrf2.The efficacy of 3-hydroxy-3-methylglutaryl-coenzyme A reductase antagonists (statins) in reducing low density lipoprotein cholesterol, cardiovascular morbidity, and mortality is widely recognized (1). The observation that beneficial actions of statins on vascular function are detectable prior to any fall in serum cholesterol, extend to normocholesterolemic patients and exceed those of other lipid-lowering drugs despite comparable falls in total cholesterol (2, 3), suggest the existence of low density lipoprotein-cholesterol-independent effects (4, 5). Judging from in vitro studies, these may include immunomodulatory, anti-inflammatory, anti-adhesive, anti-thrombotic, and cytoprotective actions (6). However, the experimental work demonstrating these pleiotropic effects has predominantly used statin concentrations exceeding those achieved by therapeutic dosing, raising questions concerning clinical relevance (4).Heme oxygenase-1 (HO-1)² acts as the rate-limiting factor in the catabolism of heme into biliverdin, releasing free iron and carbon monoxide (CO). Biliverdin is subsequently converted to bilirubin by biliverdin reductase, whereas intracellular iron induces expression of heavy chain-ferritin and the opening of Fe²⁺ export channels (7). The biologic activity of HO-1 represents an important adaptive response in cellular homeostasis, as revealed by widespread inflammation and persistent endothelial injury in human HO-1 deficiency (8).Expression of HO-1 in atherosclerotic lesions, and its ability to inhibit vascular smooth muscle cell proliferation, exert anti-inflammatory, antioxidant, and antithrombotic effects, suggests a protective role during atherogenesis (9, 10). HMOX1 promoter polymorphisms affecting HO-1 expression may influence susceptibility to intimal hyperplasia and coronary artery disease, whereas a low serum bilirubin constitutes a cardiovascular risk factor (11). Moreover, overexpression of HO-1 inhibited atherogenesis, whereas Hmox1^−/− mice bred onto an ApoE^−/− background developed more extensive and complex atherosclerotic plaques (12, 13).Recent interest has focused on the therapeutic potential of HO-1 and its products, with probucol, statins, rapamycin, nitric oxide donors, and aspirin being shown to induce HO-1 (reviewed in Ref. 10). Indeed, induction of HO-1 may represent an important component of the vasculoprotective profile of statins, with simvastatin, atorvastatin, and rosuvastatin variously shown to increase HMOX1 promoter activity and mRNA levels, to induce enzyme activity and increase antioxidant capacity in human endothelial cells (EC) (14–18). However, induction of HO-1 in vascular EC in vivo has not yet been demonstrated.Vascular endothelium exposed to unidirectional, pulsatile laminar shear stress (LSS) >10 dynes/cm² is relatively protected against atherogenesis. LSS increases nitric oxide (NO) biosynthesis, prolongs EC survival, and generates an anticoagulant, anti-adhesive cell surface. In contrast, endothelium exposed to disturbed blood flow, with low shear reversing or oscillatory flow patterns, such as that located at arterial branch points and curvatures, is atheroprone. Thus endothelial cells exposed to disturbed blood flow exhibit reduced levels of endothelial nitric-oxide synthase (eNOS), increased apoptosis, oxidative stress, permeability to low density lipoprotein, and leukocyte adhesion (19).The atheroprotective influence of unidirectional LSS and the overlap between these actions and those of statins led us to hypothesize that LSS increases endothelial responsiveness to statins. We demonstrate for the first time that treatment of mice with atorvastatin induces HO-1 expression in the aortic endothelium and that this occurs preferentially at sites exposed to LSS. In vitro, pre-conditioning human EC with an atheroprotective, but not an atheroprone waveform, significantly reduces the concentration of atorvastatin required to enhance HO-1-mediated cytoprotection against oxidant-induced injury. A synergistic relationship between LSS and statins is revealed, resulting in maximal Akt phosphorylation and dependence upon eNOS, Kruppel-like factor 2 (KLF2), and NF-E2-related factor-2 (Nrf2) activation.     

Scavenger Receptor BI Protects against Septic Death through Its Role in Modulating Inflammatory Response

Sepsis is a leading cause of death that is characterized by uncontrolled inflammatory response. In this study, we report that scavenger receptor BI (SR-BI), a high density lipoprotein receptor, is a critical survival factor of sepsis. We induced sepsis using an established septic animal model, cecal ligation and puncture (CLP). CLP induced 100% fatality in SR-BI-null mice but only 21% fatality in wild type littermates. SR-BI-null mice exhibited aberrant inflammatory responses with delayed inflammatory cytokine generation at the early stage of sepsis and highly elevated inflammatory cytokine production 20 h after CLP treatment. To understand the mechanisms underlying SR-BI protection, we elucidated the effect of mac ro phage SR-BI on inflammatory cytokine generation. Macrophages from SR-BI-null mice produced significantly higher levels of inflammatory cytokines than those of wild type controls in response to LPS. Importantly, transgenic mice overexpressing SR-BI were more resistant to CLP-induced septic death. Using an HEK-Blue^TM cell system, we demonstrated that expression of SR-BI suppressed TLR4-mediated NF-κB activation. To understand why SR-BI-null mice had a delayed inflammatory response, we elucidated the effect of SR-BI on LPS clearance during sepsis. Compared with wild type controls, SR-BI-null mice had lower plasma LPS levels in the early stage of sepsis and elevated plasma LPS levels 20 h following CLP treatment. In conclusion, our findings demonstrate that SR-BI is a critical protective modulator of sepsis in mice. SR-BI exerts its protective function through its role in modulating inflammatory response in mac ro phages and facilitating LPS recruitment and clearance.Sepsis is one of the major causes of death that claims over 215,000 lives and costs $16.7 billion per year in America alone (1–4). The death rate from sepsis is high, exceeding 50%, due to poor understanding of the disease (5). Identifying molecules involved in sepsis, especially endogenous protective modulators, is of great importance not only in understanding the mechanisms but also in providing new insights for efficient therapies.Scavenger receptor BI (SR-BI² or Scarb1) is a 75-kDa membrane protein expressed in the liver, endothelial cells, macrophages, and steroidogenic tissues (6, 7). It is a well established high density lipoprotein (HDL) receptor. It mediates intracellular uptake of cholesterol ester from HDL, which plays a key role in regulating plasma cholesterol levels and steroidogenesis (8–11). Mice deficient in SR-BI have a 2-fold increase in plasma cholesterol levels and develop cardiovascular diseases (10, 12–16). Recent studies reveal that SR-BI is a multifunctional protein. It activates endothelial nitric-oxide synthase in endothelial cells in the presence of HDL (17–20), induces apoptosis in the absence of HDL/endothelial nitric-oxide synthase (21), and protects against nitric oxide (NO)-induced oxidative damage (22). Emerging evidence indicates that specific expression of SR-BI in macrophages provides protection against the development of atherosclerosis, and importantly, it seems that SR-BI exerts this protection independently of its role in regulating lipoprotein metabolism or cholesterol efflux (23–25). The mechanisms underlying the protection of macrophage SR-BI against atherosclerosis are unclear.We recently reported that SR-BI protects against endotoxin-induced animal death through suppression of NO-induced cytotoxicity (22). A recent study by Cai et al. (26) confirmed the protective role of SR-BI in LPS-induced animal death, and the authors demonstrated that SR-BI-mediated glucocorticoid synthesis contributes to its protective function. These studies suggest that SR-BI might play a role in sepsis. Interestingly, using in vitro cell culture, Vishnyakova et al. (27) reported recently that SR-BI enhances the uptake of Gram-negative bacteria, which raises a possibility that this SR-BI-mediated bacterial uptake may facilitate bacterial infection and therefore play a deleterious role in sepsis. Given the limitations of endotoxemia animal model (28), it is of importance to determine whether and how SR-BI plays a protective role in sepsis. In this study, we assessed the role of SR-BI in sepsis using an established septic animal model, cecal ligation and puncture (CLP). We demonstrated that SR-BI is a critical survival factor of sepsis in mice. In contrast to significant protection against LPS-induced animal death by SR-BI-mediated corticosterone generation, corticosterone did not provide protection against CLP-induced septic animal death, indicating that SR-BI has other functions than regulating corticosterone production in sepsis. Using a transgenic animal model, primary macrophages, and HEK-Blue cell system, we demonstrated that SR-BI modulates inflammatory response in macrophages via TLR4 signaling, which contributes to protection against septic death.     

Dissection of the Endogenous Cellular Pathways of PCSK9-induced Low Density Lipoprotein Receptor Degradation: EVIDENCE FOR AN INTRACELLULAR ROUTE*

Elevated levels of plasma low density lipoprotein (LDL)-cholesterol, leading to familial hypercholesterolemia, are enhanced by mutations in at least three major genes, the LDL receptor (LDLR), its ligand apolipoprotein B, and the proprotein convertase PCSK9. Single point mutations in PCSK9 are associated with either hyper- or hypocholesterolemia. Accordingly, PCSK9 is an attractive target for treatment of dyslipidemia. PCSK9 binds the epidermal growth factor domain A (EGF-A) of the LDLR and directs it to endosomes/lysosomes for destruction. Although the mechanism by which PCSK9 regulates LDLR degradation is not fully resolved, it seems to involve both intracellular and extracellular pathways. Here, we show that clathrin light chain small interfering RNAs that block intracellular trafficking from the trans-Golgi network to lysosomes rapidly increased LDLR levels within HepG2 cells in a PCSK9-dependent fashion without affecting the ability of exogenous PCSK9 to enhance LDLR degradation. In contrast, blocking the extracellular LDLR endocytosis/degradation pathway by a 4-, 6-, or 24-h incubation of cells with Dynasore or an EGF-AB peptide or by knockdown of endogenous autosomal recessive hypercholesterolemia did not significantly affect LDLR levels. The present data from HepG2 cells and mouse primary hepatocytes favor a model whereby depending on the dose and/or incubation period, endogenous PCSK9 enhances the degradation of the LDLR both extra- and intracellularly. Therefore, targeting either pathway, or both, would be an effective method to reduce PCSK9 activity in the treatment of hypercholesterolemia and coronary heart disease.High levels of circulating low-density lipoprotein (LDL)³-cholesterol represent a major risk factor that leads to coronary heart disease, the main cause of death and morbidity worldwide (1). LDL particles are cleared mainly from the bloodstream by the hepatic cell surface LDL receptor (LDLR) (2). Genetics studies demonstrated that loss-of-function mutations in either LDLR or apolipoprotein B, the protein component of LDL that binds LDLR, result in familial hypercholesterolemia and premature coronary heart disease (3). More recently, the proprotein convertases subtilisin kexin 9 (PCSK9) gene (4), which is highly expressed in liver and small intestine (5), was identified as the third locus associated with familial hypercholesterolemia (6). It is now clear that PCSK9 binds the LDLR and triggers its intracellular degradation in acidic compartments, resulting in increased circulating plasma cholesterol (7–10).After its autocatalytic cleavage, PCSK9 is secreted as a stable noncovalent complex with its prosegment (pro·PCSK9) (5, 7). This cleavage results in a conformational change (11) that favors the binding of PCSK9 to the epidermal growth factor A domain (EGF-A) of the LDLR (12), with increased affinity at acidic pH values (11). Although the C-terminal Cys-His-rich domain of PCSK9 is a spatially separate domain (11) that does not participate directly in the PCSK9-EGF-A interaction (12), it is a critical determinant for the PCSK9-enhanced cellular degradation of the LDLR (13). In agreement, we recently demonstrated that annexin A2, which binds the Cys-His-rich domain of PCSK9, blocks its effect on LDLR degradation (14).Overexpression studies in liver suggested that both intra- and extracellular PCSK9 target the LDLR (9, 15, 16) toward degradation in late endosomes/lysosomes (LE/L) (7–10). It was shown that the adaptor protein ARH, which interacts with the cytosolic tail of the LDLR, is essential for the endocytosis and degradation of the cell surface PCSK9·LDLR complex in vivo (16). However, hepatic LDLR protein levels were also reduced upon overexpression of PCSK9 in Arh ^−/− mice (9), suggesting the presence of an ARH-independent intracellular pathway. Intriguingly, at endogenous levels of PCSK9, the absence of ARH did not affect hepatic LDLR subcellular localization in LE/L or protein levels (17). This is not the expected result if PCSK9 mostly targets LDLR by the extracellular pathway (18), as one would have expected that in Arh^−/− mice total LDLR levels should have been more elevated.In this study, we focused on the relative contribution of the intra- versus extracellular pathways of endogenous PCSK9-induced LDLR degradation. This information should guide the choice of therapeutic approaches that will best target the site of PCSK9-LDLR interaction to control hypercholesterolemia and coronary heart disease.     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Paradoxical Condensation of Copper with Elevated ��-Amyloid in Lipid Rafts under Cellular Copper Deficiency Conditions: IMPLICATIONS FOR ALZHEIMER DISEASE*

Redox-active copper is implicated in the pathogenesis of Alzheimer disease (AD), β-amyloid peptide (Aβ) aggregation, and amyloid formation. Aβ·copper complexes have been identified in AD and catalytically oxidize cholesterol and lipid to generate H₂O₂ and lipid peroxides. The site and mechanism of this abnormality is not known. Growing evidence suggests that amyloidogenic processing of the β-amyloid precursor protein (APP) occurs in lipid rafts, membrane microdomains enriched in cholesterol. β- and γ-secretases, and Aβ have been identified in lipid rafts in cultured cells, human and rodent brains, but the role of copper in lipid raft amyloidogenic processing is presently unknown. In this study, we found that copper modulates flotillin-2 association with cholesterol-rich lipid raft domains, and consequently Aβ synthesis is attenuated via copper-mediated inhibition of APP endocytosis. We also found that total cellular copper is associated inversely with lipid raft copper levels, so that under intracellular copper deficiency conditions, Aβ·copper complexes are more likely to form. This explains the paradoxical hypermetallation of Aβ with copper under tissue copper deficiency conditions in AD.Imbalance of metal ions has been recognized as one of the key factors in the pathogenesis of Alzheimer disease (AD).² Aberrant interactions between copper or zinc with the β-amyloid peptide (Aβ) released into the glutamatergic synaptic cleft vicinity could result in the formation of toxic Aβ oligomers and aggregation into plaques characteristic of AD brains (reviewed in Ref. 1). Copper, iron, and zinc are highly concentrated in extracellular plaques (2, 3), and yet brain tissues from AD (4–6) and human β-amyloid precursor protein (APP) transgenic mice (7–10) are paradoxically copper deficient compared with age-matched controls. Elevation of intracellular copper levels by genetic, dietary, and pharmacological manipulations in both AD transgenic animal and cell culture models is able to attenuate Aβ production (7, 9, 11–15). However, the underlying mechanism is at present unclear.Abnormal cholesterol metabolism is also a contributing factor in the pathogenesis of AD. Hypercholesterolemia increases the risk of developing AD-like pathology in a transgenic mouse model (16). Epidemiological and animal model studies show that a hypercholesterolemic diet is associated with Aβ accumulation and accelerated cognitive decline, both of which are further aggravated by high dietary copper (17, 18). In contrast, biochemical depletion of cholesterol using statins, inhibitors of 3-hydroxy-3-methyglutaryl coenzyme A reductase, and methyl-β-cyclodextrin, a cholesterol sequestering agent, inhibit Aβ production in animal and cell culture models (19–25).Cholesterol is enriched in lipid rafts, membrane microdomains implicated in Aβ generation from APP cleavage by β- and γ-secretases. Recruitment of BACE1 (β-secretase) into lipid rafts increases the production of sAPP_β and Aβ (23, 26). The β-secretase-cleaved APP C-terminal fragment (β-CTF), and γ-secretase, a multiprotein complex composed of presenilin (PS1 or PS2), nicastrin (Nct), PEN-2 and APH-1, colocalize to lipid rafts (27). The accumulation of Aβ in lipid rafts isolated from AD and APP transgenic mice brains (28) provided further evidence that cholesterol plays a role in APP processing and Aβ generation.Currently, copper and cholesterol have been reported to modulate APP processing independently. However, evidence indicates that, despite tissue copper deficiency, Aβ·Cu²⁺ complexes form in AD that catalytically oxidize cholesterol and lipid to generate H₂O₂ and lipid peroxides (e.g. hydroxynonenal and malondialdehyde), which contribute to oxidative damage observed in AD (29–35). The underlying mechanism leading to the formation of pathological Aβ·Cu²⁺ complexes is unknown. In this study, we show that copper alters the structure of lipid rafts, and attenuates Aβ synthesis in lipid rafts by inhibition of APP endocytosis. We also identify a paradoxical inverse relationship between total cellular copper levels and copper distribution to lipid rafts, which appear to possess a privileged pool of copper where Aβ is more likely to interact with Cu²⁺ under copper-deficiency conditions to form Aβ·Cu²⁺ complexes. These data provide a novel mechanism by which cellular copper deficiency in AD could foster an environment for potentially adverse interactions between Aβ, copper, and cholesterol in lipid rafts.     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.     

Hemoglobin and Its Scavenger Protein Haptoglobin Associate with ApoA-1-containing Particles and Influence the Inflammatory Properties and Function of High Density Lipoprotein

Hemoglobin (Hb) uniquely associates with proinflammatory HDL in atherogenic mice and coronary heart disease (CHD) patients. In this paper, we report that Hb and its scavenger proteins, haptoglobin (Hp) and hemopexin (Hx) are significantly increased in apoA-1-containing particles of HDL both in mouse models of hyperlipidemia and in CHD patients, when compared with wild type mice and healthy donors, respectively. We further demonstrate that the association of Hb, Hp, and Hx proteins with HDL positively correlates with inflammatory properties of HDL and systemic inflammation in CHD patients. Interestingly, HDL from Hp^−/− mice under atherogenic conditions does not accumulate Hb and is anti-inflammatory, suggesting that (i) Hp is required for the association of Hb with HDL and (ii) Hb·Hp complexes regulate the inflammatory properties of HDL. Moreover, treatment of apoE^−/− mice with an apoA-1 mimetic peptide resulted in significant dissociation of Hb·Hp complexes from HDL and improvement of HDL inflammatory properties. Our data strongly suggest that HDL can become proinflammatory via the Hb·Hp pathway in mice and humans, and dissociation of Hb·Hp·Hx complexes from apoA-1-containing particles of HDL may be a novel target for the treatment of CHD.Atherosclerosis is the leading cause of morbidity and mortality in Western society. The inverse relationship between HDL² cholesterol and the risk of atherosclerosis is well established. Although HDL cholesterol is an epidemiological predictor of risk for coronary heart disease (CHD) (1), a significant number of CHD events occur in patients with normal LDL and HDL cholesterol levels (1, 2). Based on a number of recent studies in both animal models and human samples, it appears that the anti- or proinflammatory nature of HDL may be a more sensitive indicator of the presence or absence of atherosclerosis than HDL cholesterol levels. HDL exerts anti-inflammatory functions by promoting reverse cholesterol transport and preventing the oxidation of LDL (3, 4). We have previously shown that the anti-inflammatory functions of HDL can be impaired in humans (5) rabbits (6), and mice (7) during inflammatory processes. This impaired HDL is proinflammatory in nature, as characterized by (i) decreased levels and activity of anti-inflammatory, antioxidant factors, including apolipoprotein A1 (apoA-1) and PON1 (paraoxonase 1) (8); (ii) gain of proinflammatory proteins, such as serum amyloid A and ceruloplasmin (6); (iii) increased lipid hydroperoxide (LOOH) content (9); (iv) reduced potential to efflux cholesterol (10); and (v) diminished ability to prevent LDL oxidation (11). The molecular changes and mechanisms that promote anti-inflammatory HDL conversion to proinflammatory HDL are currently not well understood.We recently reported the identification and characterization of Hb associated with proinflammatory HDL in atherogenic/hyperlipidemic mice and in human CHD patients (12). We demonstrated that under normal circumstances, a small amount of Hb is always found outside of red blood cells (RBC) in the non-lipoprotein fractions of serum (on the order of 10 μm compared with the >1 m concentration of Hb in RBC). We further demonstrated that under conditions of hyperlipidemia in mice and in CHD patients, the non-RBC Hb moves out of the non-lipoprotein fractions and associates with HDL. This HDL-associated Hb was shown to play an important role in the modulation of HDL function, suggesting that Hb is not only a novel biomarker but may also serve as a therapeutic target for atherosclerosis (12). We therefore sought to determine the molecular mechanisms that play a role in the association of Hb with HDL.Hp and Hx are plasma proteins with the highest binding affinity for Hb (K_d ≈ 1 pm) and heme (K_d < 1 pm), respectively. They are expressed mainly in the liver and belong to the family of acute phase proteins, whose synthesis is induced during inflammatory processes (13, 14). Under conditions of increased hemolysis, Hb becomes highly toxic because of the oxidative properties of heme, which participates in the Fenton reaction to produce reactive oxygen species causing cell injury (15). Under these conditions, Hb is known to be scavenged by Hp·Hx complexes that utilize specific receptor pathways, thus protecting the body against the harmful effects of excess free Hb. We set out to determine whether the Hb·Hp·Hx system (i) also participates in the association of Hb with proinflammatory HDL and (ii) plays a role in the inflammatory properties of HDL.In this paper, we demonstrate that (i) Hb·Hp·Hx complexes associate with HDL in CHD patients and mouse models of hyperlipidemia but not in healthy human donors and wild type mice, and (ii) Hb·Hp·Hx association with HDL positively correlates with proinflammatory properties of HDL. We further show that HDL from Hp^−/− mice on an atherogenic diet is anti-inflammatory and did not contain any Hb, suggesting that (i) Hp is required for the association of Hb with HDL, and (ii) Hp regulates the inflammatory properties of HDL. In contrast to HDL from Hp^−/− mice, HDL from Hx^−/− mice on normal chow was proinflammatory and associated with Hb and Hp, suggesting a novel protective role for Hx in HDL function. When apoE^−/− mice were treated in vivo with an apoA-1 mimetic peptide, 4F, Hb·Hp·Hx dissociated from HDL. Our data strongly suggest that the association of Hb·Hp·Hx with HDL plays an important role in the functional status and inflammatory properties of HDL.     

Dual 12/15- and 5-Lipoxygenase Deficiency in Macrophages Alters Arachidonic Acid Metabolism and Attenuates Peritonitis and Atherosclerosis in ApoE Knock-out Mice

Lipoxygenase (LO) enzymes catalyze the conversion of arachidonic acid (AA) into biologically active lipid mediators. Two members, 12/15-LO and 5-LO, regulate inflammatory responses and have been studied for their roles in atherogenesis. Both 12/15-LO and 5-LO inhibitors have been suggested as potential therapy to limit the development of atherosclerotic lesions. Here we used a genetic strategy to disrupt both 12/15-LO and 5-LO on an apolipoprotein E (apoE) atherosclerosis-susceptible background to study the impact of dual LO blockade in atherosclerosis and inflammation. Resident peritoneal macrophages are the major cell type that expresses both LO enzymes, and we verified their absence in dual LO-deficient mice. Examination of AA conversion by phorbol myristate acetate-primed and A23187-challenged macrophages from dual LO-deficient mice revealed extensive accumulation of AA with virtually no diversion into the most common cyclooxygenase (COX) products measured (prostaglandin E₂ and thromboxane B₂). Instead the COX-1 by-products 11-hydroxy-eicosatetraenoic acid (HETE) and 15-HETE were elevated. The interrelationship between the two LO pathways in combination with COX-1 inhibition (SC-560) also revealed striking patterns of unique substrate utilization. 5-LO- and dual LO-deficient mice exhibited an attenuated response to zymosan-induced peritoneal inflammation, emphasizing roles for 5-LO in regulating vascular permeability. We observed gender-specific attenuation of atheroma formation at 6 months of age at both the aortic root and throughout the entire aorta in chow-fed female dual LO-deficient mice. We propose that some of the inconsistent data obtained with single LO-deficient mice could be attributable to macrophage-specific patterns of altered AA metabolism.Lipoxygenase (LO)² enzymes are an important source of lipid mediators throughout the plant and animal kingdoms (1, 2). In mammals, these mediators are predominantly formed from arachidonic acid (AA) and act in various physiological and pathological contexts (1–3). Accordingly 5-LO and 12/15-LO are two members of the LO family involved in cardiovascular and inflammatory diseases expressed to variable degrees in several cell types of the myeloid lineage, and their expression is strictly regulated and incompletely understood (2, 4, 5). Despite considerable structural homology between 5-LO and 12/15-LO, both enzymes generate distinct products. The 5-LO metabolite leukotriene (LT) A₄ is precursor to the proinflammatory LTB₄ and cysteinyl LTs, which regulate leukocyte subset-specific chemotaxis (LTB₄) and vascular permeability (cysteinyl LTs), both crucial events during acute peritonitis (1, 6, 7). 12- and 15-HETE, end products synthesized by 12/15-LO, play potential roles in cellular chemotaxis, cancer growth, and inflammation (2, 8). Transcellular interaction products derived from both 12/15-LO and 5-LO, such as lipoxins and maresins, indicate that these enzymes can possess anti-inflammatory activities in innate immunity and the resolution of inflammation (9, 10).In mice, only one cell type is known to express substantial quantities of both 5-LO and 12/15-LO, the peritoneal macrophage (PMΦ) (2, 11, 12). However, differences in subcellular localization, trafficking, and activation (8, 12–16) of these two LOs indicate that they are independently regulated and not functionally coupled. Tissue-resident MΦ (such as PMΦ) represent the first line of defense against invading pathogens and activate the immunological and inflammatory response (17). These phagocytes are capable of elaborating a wide spectrum of bioactive lipid mediators from the LO and cyclooxygenase (COX) pathways. Little is known about the regulation and putative interdependence of these pathways. Some insight was gained using mice lacking 12/15-LO where substrate shunting from the 12/15-LO into the 5-LO pathway was observed (12).The generation of knock-out mice for 12/15-LO (12) and 5-LO (18) has enabled the study of these lipid mediator pathways in models of health and disease. Because 12/15-LO and 5-LO are primarily expressed in distinct hematopoietic cells, their implication in various inflammatory disorders and models of host defense mechanisms have been investigated (2, 3). Atherosclerosis, an inflammatory disease prevalent in societies with high dietary fat intake, is initiated by low density lipoprotein (LDL) retention in the vascular wall (19) and subsequent oxidative modification. This process greatly enhances the LDL atherogenic potential, and intriguingly 12/15-LO can contribute to lipoprotein oxidation (11, 20). Initial studies using 12/15-LO- and 5-LO-deficient mice indicated proatherogenic roles for these enzymes (20, 21). Additionally mice lacking the LTB₄ receptor BLT-1 exhibit protection in early atherogenesis (22), but subsequent data from our laboratory using 5-LO-deficient mouse models have not supported an involvement of 5-LO in atherogenesis (3, 23, 24). Here we studied the consequences of simultaneous 12/15-LO and 5-LO knock-out on peritoneal inflammation and atherosclerosis in apoE-deficient mice and surmised whether some of the capricious results in atherosclerotic lesion studies could be attributable to variable eicosanoid profiles.     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]