Inhibition of Nicotinamide Phosphoribosyltransferase (NAMPT), an Enzyme Essential for NAD+ Biosynthesis,Leads to Altered Carbohydrate Metabolism in Cancer Cells

Nicotinamide phosphoribosyltransferase (NAMPT) has been extensively studied due to its essential role in NAD⁺ biosynthesis in cancer cells and the prospect of developing novel therapeutics. To understand how NAMPT regulates cellular metabolism, we have shown that the treatment with FK866, a specific NAMPT inhibitor, leads to attenuation of glycolysis by blocking the glyceraldehyde 3-phosphate dehydrogenase step (Tan, B., Young, D. A., Lu, Z. H., Wang, T., Meier, T. I., Shepard, R. L., Roth, K., Zhai, Y., Huss, K., Kuo, M. S., Gillig, J., Parthasarathy, S., Burkholder, T. P., Smith, M. C., Geeganage, S., and Zhao, G. (2013) Pharmacological inhibition of nicotinamide phosphoribosyltransferase (NAMPT), an enzyme essential for NAD⁺ biosynthesis, in human cancer cells: metabolic basis and potential clinical implications. J. Biol. Chem. 288, 3500–3511). Due to technical limitations, we failed to separate isotopomers of phosphorylated sugars. In this study, we developed an enabling LC-MS methodology. Using this, we confirmed the previous findings and also showed that NAMPT inhibition led to accumulation of fructose 1-phosphate and sedoheptulose 1-phosphate but not glucose 6-phosphate, fructose 6-phosphate, and sedoheptulose 7-phosphate as previously thought. To investigate the metabolic basis of the metabolite formation, we carried out biochemical and cellular studies and established the following. First, glucose-labeling studies indicated that fructose 1-phosphate was derived from dihydroxyacetone phosphate and glyceraldehyde, and sedoheptulose 1-phosphate was derived from dihydroxyacetone phosphate and erythrose via an aldolase reaction. Second, biochemical studies showed that aldolase indeed catalyzed these reactions. Third, glyceraldehyde- and erythrose-labeling studies showed increased incorporation of corresponding labels into fructose 1-phosphate and sedoheptulose 1-phosphate in FK866-treated cells. Fourth, NAMPT inhibition led to increased glyceraldehyde and erythrose levels in the cell. Finally, glucose-labeling studies showed accumulated fructose 1,6-bisphosphate in FK866-treated cells mainly derived from dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Taken together, this study shows that NAMPT inhibition leads to attenuation of glycolysis, resulting in further perturbation of carbohydrate metabolism in cancer cells. The potential clinical implications of these findings are also discussed.     

Targeted purification development enabled by computational biophysical modeling

Chromatographic and non‐chromatographic purification of biopharmaceuticals depend on the interactions between protein molecules and a solid–liquid interface. These interactions are dominated by the protein–surface properties, which are a function of protein sequence, structure, and dynamics. In addition, protein–surface properties are critical for in vivo recognition and activation, thus, purification strategies should strive to preserve structural integrity and retain desired pharmacological efficacy. Other factors such as surface diffusion, pore diffusion, and film mass transfer can impact chromatographic separation and resin design. The key factors that impact non‐chromatographic separations (e.g., solubility, ligand affinity, charges and hydrophobic clusters, and molecular dynamics) are readily amenable to computational modeling and can enhance the understanding of protein chromatographic. Previously published studies have used computational methods such as quantitative structure–activity relationship (QSAR) or quantitative structure–property relationship (QSPR) to identify and rank order affinity ligands based on their potential to effectively bind and separate a desired biopharmaceutical from host cell protein (HCP) and other impurities. The challenge in the application of such an approach is to discern key yet subtle differences in ligands and proteins that influence biologics purification. Using a relatively small molecular weight protein (insulin), this research overcame limitations of previous modeling efforts by utilizing atomic level detail for the modeling of protein–ligand interactions, effectively leveraging and extending previous research on drug target discovery. These principles were applied to the purification of different commercially available insulin variants. The ability of these computational models to correlate directionally with empirical observation is demonstrated for several insulin systems over a range of purification challenges including resolution of subtle product variants (amino acid misincorporations). Broader application of this methodology in bioprocess development may enhance and speed the development of a robust purification platform. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:154–164, 2015     

Deficiency of Niemann-Pick Type C-1 Protein Impairs Release of Human Immunodeficiency Virus Type 1 and Results in Gag Accumulation in Late Endosomal/Lysosomal Compartments

Human immunodeficiency virus type 1 (HIV-1) relies on cholesterol-laden lipid raft membrane microdomains for entry into and egress out of susceptible cells. In the present study, we examine the need for intracellular cholesterol trafficking pathways with respect to HIV-1 biogenesis using Niemann-Pick type C-1 (NPC1)-deficient (NPCD) cells, wherein these pathways are severely compromised, causing massive accumulation of cholesterol in late endosomal/lysosomal (LE/L) compartments. We have found that induction of an NPC disease-like phenotype through treatment of various cell types with the commonly used hydrophobic amine drug U18666A resulted in profound suppression of HIV-1 release. Further, NPCD Epstein-Barr virus-transformed B lymphocytes and fibroblasts from patients with NPC disease infected with a CD4-independent strain of HIV-1 or transfected with an HIV-1 proviral clone, respectively, replicated HIV-1 poorly compared to normal cells. Infection of the NPCD fibroblasts with a vesicular stomatitis virus G-pseudotyped strain of HIV-1 produced similar results, suggesting a postentry block to HIV-1 replication in these cells. Examination of these cells using confocal microscopy showed an accumulation and stabilization of Gag in LE/L compartments. Additionally, normal HIV-1 production could be restored in NPCD cells upon expression of a functional NPC1 protein, and overexpression of NPC1 increased HIV-1 release. Taken together, our findings demonstrate that intact intracellular cholesterol trafficking pathways mediated by NPC1 are needed for efficient HIV-1 production.Human immunodeficiency virus type 1 (HIV-1) is a complex retrovirus highly dependent upon a myriad of cellular mechanisms for successful virus replication. Cholesterol plays a pivotal role throughout the HIV-1 life cycle (23, 40, 41, 64). HIV-1 entry, assembly, and budding processes occur at cholesterol-enriched membrane microdomains known as lipid rafts, and depletion of cellular cholesterol markedly and specifically reduces HIV-1 particle production. Virion-associated cholesterol is required for fusion and subsequent infection of susceptible cells (41), and cholesterol-sequestering drugs, such as β-cyclodextrin, render the virus incompetent for cell entry (4, 25, 57). Therefore, intracellular cholesterol trafficking pathways that allow nascent HIV-1 particles to acquire lipids appear critical for virus replication.Recent evidence supports a critical role for cholesterol trafficking and homeostasis in viral replication, showing that the HIV-1 accessory protein Nef increases synthesis and transport of cholesterol to both lipid rafts and progeny virions and induces multiple genes involved in cholesterol synthesis (80, 88). More recent studies have revealed that binding of Nef to the ATP-binding cassette transporter A1 (ABCA1) leads to impairment of ABCA1-dependent cholesterol efflux and an accumulation of lipids within the cell (51).Mammalian cells acquire cholesterol primarily from endocytosed low-density lipoproteins (LDL). The Niemann-Pick type C-1 (NPC1) protein is well known for its role in intracellular trafficking of LDL-derived free unesterified cholesterol. Dysfunctional NPC1 activity leads to development of NPC disease, a rare, autosomal recessive, neurodegenerative disorder characterized by the massive accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal (LE/L) compartments (61). In normal cells, endocytosed LDLs are delivered to the LE/Ls, where they are hydrolyzed and free cholesterol is released. Homeostasis is achieved when cholesterol is then rapidly transported out of the LE/Ls to the plasma membrane and endoplasmic reticulum (ER) (17, 19, 42, 73, 85), or first to the trans-Golgi (TG) network (TGN) and then to the ER (76). In NPC1-deficient (NPCD) cells, the cholesterol does not exit the endocytic pathway, resulting in its accumulation within LE/L structures.In 95% of NPC patients, the disease is caused by mutations in the NPC1 gene, while the remaining 5% harbor mutations in the NPC2 gene (50, 72, 79). One of the most frequently found and extensively characterized NPC1 mutations is the I1061T mutation (37, 38, 86). This mutation results in misfolding of the NPC1 protein, leading to its degradation and causing an 85% decrease in cellular NPC1 expression (20). Cells with such low levels of functional NPC1 maintain only 38% of normal sphingomyelinase activity and have impaired cholesterol esterification and trafficking.NPC1 is a large, multispanning protein that resides in the limiting membrane of the LE and binds cholesterol via its N-terminal domain (31). While the complete physiological function of NPC1 is still unclear, NPC1 does share homology with the resistance-nodulation-division family of prokaryotic permeases and may function as a transmembrane efflux pump to transport cargos in LEs (9, 75). Other studies suggest that NPC1 might also function in vesicle-mediated pathways for cargo transportation from LEs to other intracellular sites (21, 33). Recent studies by Infante et al. have propelled forward our understanding of how NPC1 works together with NPC2, also known to bind cholesterol, to support cholesterol efflux from the LE (32). Their findings provide a basis for either of two possible models, with respect to cholesterol trafficking: (i) NPC1 binds cholesterol found within the LE and mediates either direct export or transfer to NPC2 for delivery to a cholesterol efflux transporter, such as ABCA1; or (ii) NPC2 is the first to bind cholesterol and then mediate its delivery to NPC1 for direct export or transfer to ABCA1. These recent findings underscore the highly critical role of these proteins in maintaining intracellular cholesterol homeostasis.In addition to its role in sterol trafficking, some studies suggest that the NPC pathway may be directly involved in trafficking multiple proteins from LE/L compartments. LEs act as sorting stations to deliver endocytosed molecules to L''s for degradation, while at the same time retrieving other classes of proteins and lipids for transport back to nondegradative compartments (3, 14, 15, 28, 63, 69, 78). LE compartments also serve as sorting stations for HIV-1 viral proteins and represent a major site for HIV-1 assembly and budding (7, 12, 16, 22, 24, 57, 59).The endosomal trafficking defects observed in NPCD cells extend to proteins such as IGF2/MPR, NPC1, and annexin II, all of which utilize the endosomal recycling pathway (42, 74). Electron microscopy studies have shown that within the LEs of NPCD cells these proteins are trapped in the cholesterol-enriched membrane-bound vesicular structures (47). Cholesterol and glycosphingolipid accumulation within NPCD cells appears to disrupt Rab9 GTPase function in LE-to-TGN transport, trapping Rab9-associated proteins, such as vimentin, Tip47, and the mannose-6-phosphate receptor in LEs (18, 83). Overexpression of Rab7 and Rab9 GTPases can reverse the cholesterol accumulation phenotype caused by NPCD (8, 84). These observations suggest that NPC1, directly or indirectly, plays a role in protein export from LEs. It is unknown whether NPC1 is involved in the export of HIV-1 proteins from LEs; however, the Rab9 GTPase-mediated pathway is known to be required for HIV-1 replication (53). This strongly suggests that HIV assembly will be hindered when the NPC pathway is disrupted.Given the function of NPC1 in mediating intracellular cholesterol trafficking within the LE and given the need of HIV-1 for cholesterol, NPC1 involvement in HIV-1 biogenesis is highly likely. In the present study, using cells treated with U18666A or NPCD cells, we show that impaired NPC1 function results in profound suppression of HIV-1 replication. Further, our findings demonstrate that the NPC1 protein is essential for proper trafficking of the HIV-1 Gag protein during the late stages of assembly and budding. It appears that in NPCD cells, in which cholesterol and cellular proteins accumulate in LE/L compartments, the viral Gag protein fails to traffic properly and accumulates within these compartments, resulting in decreased particle production. Our findings not only reinforce the dependence of HIV-1 on cholesterol homeostasis but also support a role for NPC1 in HIV-1 viral protein trafficking and particle release from infected cells.     

Evaluation of an in vitro coculture model for the blood-brain barrier: Comparison of human umbilical vein endothelial cells (ECV304) and rat glioma cells (C6) from two commercial sources

Summary Cocultures of human umbilical vein endothelial cells (ECV304) and rat glioma cells (C6) from two commercial sources, American Type Culture Collection and European Collection of Animal Cell Cultures, were evaluated as an in vitro model for the blood-brain barrier. Monolayers of endothelial cells grown in the presence or absence of glial cells were examined for transendothelial electrical resistance, sucrose permeability, morphology, multidrug resistance-associated protein expression, and P-glycoprotein expression and function. Coculture of glial cells with endothelial cells increased electrical resistance and decreased sucrose permeability across European endothelial cell monolayers, but had no effect on American endothelial cells. Coculture of European glial cells with endothelial cells caused cell flattening and decreased cell stacking with both European and American endothelial cells. No P-glycoprotein or multidrug resistance-associated protein was immunodetected in endothelial cells grown in glial cell-conditioned medium. Functional P-glycoprotein was demonstrated in American endothelial cells selected in vinblastine-containing medium over eight passages, but these cells did not form a tight endothelium. In conclusion, while European glial cells confer blood-brain barrier-like morphology and barrier integrity to European endothelial cells in coculture, the European endothelial-glial cell coculture model does not express P-glycoprotein, normally found at the blood-brain barrier. Further, the response of endothelial cells to glial factors was dependent on cell source, implying heterogeneity among cell populations. On the basis of these observations, the umbilical vein endothelial cell-glial cell coculture model does not appear to be a viable model for predicting blood-brain barrier penetration of drug molecules.     

Seasonal and spatial patterns of S,Ca, and N dynamics of a Northern Hardwood forest ecosystem

Seasonal dynamics of S, Ca and N were examined at the Huntington Forest, a northern hardwood ecosystem in the central Adirondacks of New York for a period of 34 months (1985–1988). Solute concentrations and fluxes in bulk precipitation, throughfall (TF) and leachates from the forest floor, E horizon and B horizon were quantified. Both above and below-ground elemental fluxes mediated by vegetation (e.g. uptake, litter inputs, and fine roots production) were also determined. The roles of abiotic and biotic processes were ascertained based on both changes in solute concentrations through the strata of the ecosystem as well as differences between dormant and growing seasons. Concentrations of SO₄ ²⁻, NO₃ ⁻, NH₄ ⁺ and Ca²⁺ were greater in TF than precipitation. Forest floor leachates had greater concentrations of SO₄ ²⁻, NO₃ ⁻ + NH₄ ⁺ and Ca²⁺ (9, 6 and 77 μeq L⁻¹, respectively) than TF. There were differences in concentrations of ions in leachates from the forest floor between the dormant and growing seasons presumably due to vegetation uptake and microbial immobilization. Concentrations and fluxes of NO₃ ⁻ and NH; were greatest in early spring followed by a rapid decline which coincided with a demand for N by vegetation in late spring. Vegetation uptake (44.7 kg N ha⁻¹ yr⁻¹ ) could account for the low leaching rates of N0₃ ⁻. Within the mineral soil, changes with soil depth and the absence of seasonal patterns suggest that cation exchange (Ca⁺) or anion sorption (SO₄ ²⁻) are primarily responsible for regulating solute concentrations. The increase in SO₄ ²⁻ concentration after leachates passed through the mineral soil may be attributed to desorption of sulfate that was adsorbed during an earlier period when SO₄ ²⁻ concentrations would have been greater due to elevated S inputs.     

Whole-blood immunoassay for γH2AX as a radiation biodosimetry assay with minimal sample preparation

The current state of the art in high-throughput minimally invasive radiation biodosimetry involves the collection of samples in the field and analysis at a centralized facility. We have developed a simple biological immunoassay for radiation exposure that could extend this analysis out of the laboratory into the field. Such a forward placed assay would facilitate triage of a potentially exposed population. The phosphorylation and localization of the histone H2AX at double-stranded DNA breaks has already been proven to be an adequate surrogate assay for reporting DNA damage proportional to radiation dose. Here, we develop an assay for phosphorylated H2AX directed against minimally processed sample lysates. We conduct preliminary verification of H2AX phosphorylation using irradiated mouse embryo fibroblast cultures. Additional dosimetry is performed using human blood samples irradiated ex vivo. The assay reports H2AX phosphorylation in human blood samples in response to ionizing radiation over a range of 0–5 Gy in a linear fashion, without requiring filtering, enrichment, or purification of the blood sample.     

Identification of Aerobically and Anaerobically Induced Genes in Enterococcus faecalis by Random Arbitrarily Primed PCR

Enterococci have emerged among the leading causes of nosocomial infection. With the goal of analyzing enterococcal genes differentially expressed in environments related to commensal or environmental colonization and infection sites, we adapted and optimized a method more commonly used in the study of eukaryotic gene expression, random arbitrarily primed PCR (RAP-PCR). The RAP-PCR method was systematically optimized, allowing the technique to be used in a highly reproducible manner with gram-positive bacterial RNA. In the present study, aerobiosis was chosen as a variable for the induction of changes in gene expression by Enterococcus faecalis. Aerobically and anaerobically induced genes were detected and identified to the sequence level, and differential gene expression was confirmed by quantitative, specifically primed RT-PCR. Differentially expressed genes included several sharing identity with those of other organisms related to oxygen metabolism, as well as hypothetical genes lacking identity to known genes.     

Local-scale environmental variation generates highly divergent lineages associated with stream drainages in a terrestrial salamander, Plethodon caddoensis

Spatial and temporal heterogeneity in environmental factors can have profound effects on diversification in species that are tightly linked to their environments. The Caddo Mountain Salamander (Plethodon caddoensis) inhabits a unique physiographic section of the Ouachita Mountains in central North America, a region in which Pleistocene climatic fluctuations have been implicated in driving lineage diversification in two other closely related salamanders. We examined P. caddoensis to determine whether it was similarly impacted by historic climatic changes and test whether physiographic features unique to the area also contributed to its diversification. We found that P. caddoensis is composed of four highly divergent, geographically distinct lineages that abut one another along an east-west axis. Phylogeographic structure was significantly related to both geographic distance and stream drainages, indicating that connectivity of streams and stream-associated habitats (e.g., talus) influence patterns of interpopulation gene flow. Lineages originated during the Middle Miocene and population size decreased in all lineages during the Pleistocene. Surface Geology and precipitation were the most important variables predicting the species distribution. Our results show that the unique physiographic features of the area coupled with species response to climatic factors have driven lineage diversification and phylogeographic structure in P. caddoensis. Variation in responses to historic climatic fluctuations among salamander species in this region underscore the importance of integrating species ecology with other factors such as geology and hydrology in order to better understand the effects of climate change on species with close associations to their environments.     

Heterokaryon identification through simultaneous fluorescence of tetramethylrhodamine isothiocyanate and fluorescein isothiocyanate labelled protoplasts

Protoplasts were separately stained with the fluorescent dyes fluorescein isothiocyanate (FITC) and tetramethylrhodamine isothiocyanate (TRITC). Following fusion, doubly stained heterokaryons were identified under fluorescence microscopy by using the Zeiss filter set 48 77 05 (excitation filter 450-490 nm, dichroic reflector 510 nm, and barrier filter 520 nm) which allowed simultaneous fluorochrome emissions. Previously, either emission spectrum, but not both, was possible for any single filter set.