Regulation of GTPase function by autophosphorylation.

A unifying feature of the RAS superfamily is a conserved GTPase cycle by which these proteins transition between active and inactive states. We demonstrate that autophosphorylation of some GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, altering the on/off switch that forms the basis for their signaling functions. Using X-ray crystallography, nuclear magnetic resonance spectroscopy, binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II region and that autophosphorylation promotes nucleotide exchange by opening the active site and extracting the stabilizing Mg2+. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins in mammalian cells. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from their non-phosphorylated counterparts.

Targeting ROS production through inhibition of NADPH oxidases.

NADPH oxidases (NOXs) are transmembrane enzymes that are devoted to the production of reactive oxygen species (ROS). In cancers, dysregulation of NOX enzymes affects ROS production, leading to redox unbalance and tumor progression. Consequently, NOXs are a drug target for cancer therapeutics, although current therapies have off-target effects: there is a need for isoenzyme-selective inhibitors. Here, we describe fully validated human NOX inhibitors, obtained from an in silico screen, targeting the active site of Cylindrospermum stagnale NOX5 (csNOX5). The hits are validated by in vitro and in cellulo enzymatic and binding assays, and their binding modes to the dehydrogenase domain of csNOX5 studied via high-resolution crystal structures. A high-throughput screen in a panel of cancer cells shows activity in selected cancer cell lines and synergistic effects with KRAS modulators. Our work lays the foundation for the development of inhibitor-based methods for controlling the tightly regulated and highly localized ROS sources.

Notch3 signaling-mediated melanoma-endothelial crosstalk regulates melanoma stem-like cell homeostasis and niche morphogenesis.

Melanoma is among the most virulent cancers, owing to its propensity to metastasize and its resistance to current therapies. The treatment failure is largely attributed to tumor heterogeneity, particularly subpopulations possessing stem cell-like properties, ie, melanoma stem-like cells (MSLCs). Evidence indicates that the MSLC phenotype is malleable and may be acquired by non-MSLCs through phenotypic switching upon appropriate stimuli, the so-called 'dynamic stemness'. Since the phenotypic characteristics and functional integrity of MSLCs depend on their vascular niche, using a two-dimensional (2D) melanoma-endothelium co-culture model, where the MSLC niche is recapitulated in vitro, we identified Notch3 signaling pathway as a micro-environmental cue governing MSLC phenotypic plasticity via pathway-specific gene expression arrays. Accordingly, lentiviral shRNA-mediated Notch3 knockdown (KD) in melanoma cell lines exhibiting high levels of endogenous Notch3 led to retarded/abolished tumorigenicity in vivo through both depleting MSLC fractions, evinced by MSLC marker downregulation (eg, CD133 and CD271); and impeding the MSLC niche, corroborated by the attenuated tumor angiogenesis as well as vasculogenic mimicry. In contrast, Notch3 KD affected neither tumor growth nor MSLC subsets in a melanoma cell line with relatively low endogenous Notch3 expression. Thus, Notch3 signaling may facilitate MSLC plasticity and niche morphogenesis in a cell context-dependent manner. Our findings illustrate Notch3 as a molecular switch driving melanoma heterogeneity, and provide the biological rationale for Notch inhibition as a promising therapeutic option.

Association between markers of glucose metabolism and risk of colorectal adenoma.

BACKGROUND & AIMS: Diabetes is a risk factor for colorectal cancer. We studied the association between markers of glucose metabolism and metabolic syndrome and the presence of colorectal adenomas in a large number of asymptomatic men and women attending a health screening program in South Korea. We also investigated whether these associations depend on adenoma location. METHODS: In a cross-sectional study, we measured fasting levels of glucose, insulin, hemoglobin A1c, and C-peptide and calculated homeostatic model assessment (HOMA) values (used to quantify insulin resistance) for 19,361 asymptomatic South Korean subjects who underwent colonoscopy examinations from January 2006 to June 2009. Participants completed a standardized self-administered health questionnaire and a validated semiquantitative food frequency questionnaire. Blood samples were collected on the day of the colonoscopy; fasting blood samples were also collected. Robust Poisson regression was used to model the associations of glucose markers with the prevalence of any adenoma. RESULTS: Using detailed multivariable-adjusted dose-response models, the prevalence ratios (aPR, 95% confidence interval [CI]) for any adenoma, comparing the 90th with the 10th percentile, were 1.08 (1.00-1.16; P = .04) for fasting glucose, 1.07 (0.99-1.15; P = .10) for insulin, 1.09 (1.02-1.18, P = .02) for HOMA, 1.09 (1.01-1.17; P = .02) for hemoglobin A1c, and 1.14 (1.05-1.24; P = .002) for C-peptide. The corresponding ratios for nonadvanced adenomas were 1.11 (0.99-1.25; P = .08), 1.10 (0.98-1.24; P = .12), 1.15 (1.02-1.29; P = .02), 1.14 (1.01-1.28; P = .03), and 1.20 (1.05-1.37; P = .007), respectively. The corresponding ratios for advanced adenomas were 1.32 (0.94-1.84; P = .11), 1.23 (0.87-1.75; P = .24), 1.30 (0.92-1.85; P = .14), 1.13 (0.79-1.61; P = .50), and 1.67 (1.15-2.42; P = .007), respectively. Metabolic syndrome was associated with the prevalence of any adenoma (aPR, 1.18; 95% CI, 1.13-1.24; P < .001), nonadvanced adenoma (aPR, 1.30; 95% CI, 1.20-1.40; P < .001), and advanced adenoma (aPR, 1.42; 95% CI, 1.14-1.78; P = .002). Associations were similar for adenomas located in the distal versus proximal colon. CONCLUSIONS: Increasing levels of glucose, HOMA values, levels of hemoglobin A1c and C-peptide, and metabolic syndrome are significantly associated with the prevalence of adenomas. Adenomas should be added to the list of consequences of altered glucose metabolism.

CD133-targeted niche-dependent therapy in cancer: a multipronged approach.

Cancer treatment continues to be challenged by the development of therapeutic resistances and relapses in the clinical setting, which are largely attributed to tumor heterogeneity, particularly the existence of cancer stem cells (CSCs). Thus, targeting the CSC subpopulation may represent an effective therapeutic strategy. However, despite advances in identifying and characterizing CD133(+) CSCs in various human cancers, efforts to translate these experimental findings to clinical modalities have been slow in the making, especially in light of the growing awareness of CSC plasticity and the foreseeable pitfall of therapeutically targeting CSC base sorely on a surface marker. We, and others, have demonstrated that the CD133(+) CSCs reside in complex vascular niches, where reciprocal signaling between the CD133(+) CSCs and their microenvironment may govern niche morphogenesis and homeostasis. Herein, we discuss the multifaceted functional role of the CD133(+) cells in the context of their niche, and the potential of targeting CD133 as a niche-dependent approach in effective therapy.

Regulation of RAS oncogenicity by acetylation.

Members of the RAS small GTPase family regulate cellular responses to extracellular stimuli by mediating the flux through downstream signal transduction cascades. RAS activity is strongly dependent on its subcellular localization and its nucleotide-binding status, both of which are modulated by posttranslational modification. We have determined that RAS is posttranslationally acetylated on lysine 104. Molecular dynamics simulations suggested that this modification affects the conformational stability of the Switch II domain, which is critical for the ability of RAS to interact with guanine nucleotide exchange factors. Consistent with this model, an acetylation-mimetic mutation in K-RAS4B suppressed guanine nucleotide exchange factor-induced nucleotide exchange and inhibited in vitro transforming activity. These data suggest that lysine acetylation is a negative regulatory modification on RAS. Because mutations in RAS family members are extremely common in cancer, modulation of RAS acetylation may constitute a therapeutic approach.

The association of serum lipids with colorectal adenomas.

OBJECTIVES: There is suggestive but sparse evidence that dyslipidemia is associated with colorectal neoplasms. We investigated the association of serum lipid and apolipoprotein concentrations with the prevalence of colorectal adenomas. METHODS: Cross-sectional study of 19,281 consecutive participants aged 40-79 years undergoing screening colonoscopy at the Center for Health Promotion of the Samsung Medical Center in Korea from January 2006 to June 2009. RESULTS: We identified 5,958 participants with colorectal adenomas (30.9%), including 5,504 (28.5%) with non-advanced adenomas and 454 (2.4%) with advanced adenomas. The adjusted relative prevalence ratios (aRPRs) comparing the fourth with the first quartiles of serum triglycerides were 1.35 (95% confidence interval (CI) 1.20-1.52; P trend<0.001) for non-advanced adenomas and 1.45 (95% CI 1.02-2.06; P trend=0.005) for advanced adenomas. Higher levels of high-density lipoprotein (HDL) cholesterol and apolipoprotein A-1 (ApoA-1) were significantly associated with 12% (Q4 vs. Q1 aRPR 1.12; 95% CI 1.00-1.26; P trend=0.049) and 17% (Q4 vs. Q1 aRPR 1.17; 95% CI 1.04-1.31; P trend=0.004) higher prevalence of non-advanced adenoma. There was also a non-significant association between higher levels of low-density lipoprotein (LDL) cholesterol (Q4 vs. Q1 aRPR 1.22; 95% CI 0.91-1.66; P trend= 0.12) and apolipoprotein B (ApoB) (Q4 vs. Q1 aRPR 1.32; 95% CI 0.94-1.83; P trend=0.07) with higher prevalence of advanced adenoma. There was no association between total cholesterol levels with colorectal adenoma. CONCLUSIONS: In this large cross-sectional study, higher levels of serum triglycerides were significantly associated with an increasing prevalence of both non-advanced and advanced colorectal adenomas, while higher levels of ApoA-1 and HDL cholesterol were significantly associated with an increasing prevalence of non-advanced adenomas.

The association between cecal insertion time and colorectal neoplasm detection.

BACKGROUND: Information on the impact of cecal insertion time on colorectal neoplasm detection is limited. Our objective was to determine the association between cecal insertion time and colorectal neoplasm detection rate in colonoscopy screening. METHODS: We performed a cross-sectional study of 12,679 consecutive subjects aged 40-79 years undergoing screening colonoscopy in routine health check-ups at the Center for Health Promotion of the Samsung Medical Center from December 2007 to June 2009. Fixed effects logistic regression conditioning on colonoscopist was used to eliminate confounding due to differences in technical ability and other characteristics across colonoscopists. RESULTS: The mean cecal insertion time was 5.9 (SD, 4.4 minutes). We identified 4,249 (33.5%) participants with colorectal neoplasms, of whom 1,956 had small single adenomas (<5 mm), 595 had medium single adenomas (5-9 mm), and 1,699 had multiple adenomas or advanced colorectal neoplasms. The overall rates of colorectal neoplasm detection by quartiles of cecal insertion time were 36.8%, 33.4%, 32.7%, and 31.0%, respectively (p trend <0.001).The odds for small single colorectal adenoma detection was 16% lower (adjusted OR 0.84; 95% CI 0.71 to 0.99) in the fourth compared to the first quartile of insertion time (p trend 0.005). Insertion time was not associated with the detection rate of single adenomas ≥5 mm, multiple adenomas or advanced colorectal neoplasms. CONCLUSION: Shorter insertion times were associated with increased rates of detection of small colorectal adenomas <5 mm. Cecal insertion time may be clinically relevant as missed small colorectal adenomas may progress to more advanced lesions.

Allosteric Regulation of Switch-II Domain Controls KRAS Oncogenicity.

RAS proteins are GTPases that regulate a wide range of cellular processes. RAS activity is dependent on its nucleotide-binding status, which is modulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). KRAS can be acetylated at lysine 104 (K104), and an acetylation-mimetic mutation of K104 to glutamine (K104Q) attenuates the in vitro-transforming capacity of oncogenic KRAS by interrupting GEF-induced nucleotide exchange. To assess the effect of this mutation in vivo, we used CRISPR-Cas9 to generate mouse models carrying the K104Q point mutation in wild-type and conditional KrasLSL-G12D alleles. Homozygous animals for K104Q were viable, fertile, and arose at the expected Mendelian frequency, indicating that K104Q is not a complete loss-of-function mutation. Consistent with our previous findings from in vitro studies, however, the oncogenic activity of KRASG12D was significantly attenuated by mutation at K104. Biochemical and structural analysis indicated that the G12D and K104Q mutations cooperate to suppress GEF-mediated nucleotide exchange, explaining the preferential effect of K104Q on oncogenic KRAS. Furthermore, K104 functioned in an allosteric network with M72, R73, and G75 on the α2 helix of the switch-II region. Intriguingly, point mutation of glycine 75 to alanine (G75A) also showed a strong negative regulatory effect on KRASG12D. These data demonstrate that lysine at position 104 is critical for the full oncogenic activity of mutant KRAS and suggest that modulating the sites in its allosteric network may provide a unique therapeutic approach in cancers expressing mutant KRAS. SIGNIFICANCE: An allosteric network formed by interaction between lysine 104 and residues in the switch-II domain is required for KRAS oncogenicity, which could be exploited for developing inhibitors of the activated oncoprotein.

Is gynecological cancer a new indication for surveillance colonoscopy in Korea?

BACKGROUND/AIMS: Previous studies regarding the risk for colorectal neoplasms in women with a prior diagnosis of gynecological cancer have revealed conflicting results. Therefore, we conducted a cross-sectional study to quantify the risk for colorectal neoplasms in patients with gynecological cancers. METHODOLOGY: A total of 4613 women (including 27, 51 and 92 women with a prior diagnosis of endometrial, ovarian and cervical cancers, respectively) >20 years of age were recruited prospectively from 9 tertiary medical centers in Korea between January 2008 and February 2009. All participants underwent complete colonoscopies for vague abdominal signs or symptoms or for colorectal cancer screening. Several risk factors for colorectal neoplasms and a prior history of gynecological cancer were compared between women with and without colorectal neoplasms. RESULTS: The risk for colorectal neoplasms was only elevated among women with previous endometrial cancer, but with ovarian or cervical cancer, particularly when diagnosed at <50 years of age (adjusted OR=3.7; 95% CI=1.0-13.3, p=0.016). CONCLUSIONS: This study demonstrated a higher risk for colorectal neoplasms in women with previous endometrial cancer, particularly when diagnosed at <50 years of age. Greater emphasis on colorectal cancer screening in this population may be necessary.

Do we need colonoscopy in patients with gastric adenomas? The risk of colorectal adenoma in patients with gastric adenomas.

BACKGROUND: Gastric polyps are found frequently in various colonic polyposis syndromes. Genetic alterations of several genes occur in gastric adenomas and colorectal adenomas. However, it is unknown whether patients with gastric adenomas are at higher risk for colorectal adenomas. OBJECTIVE: To investigate the prevalence rate of colorectal adenoma in patients with gastric adenomas and to determine the association between the presence of gastric adenomas and synchronous colorectal adenomas. DESIGN: A retrospective, cross-sectional, case-control study. SETTING: Single center: Center for Health Promotion of Samsung Medical Center. PATIENTS: This study involved 87 patients with gastric adenomas and 174 sex-matched and age-matched controls among 19,019 participants who underwent EGD and colonoscopy simultaneously or within 6 months of each other from January 2001 to December 2008 at the Center for Health Promotion of Samsung Medical Center. INTERVENTION: EGD and colonoscopy. MAIN OUTCOME MEASUREMENTS: The prevalence rate of colorectal adenoma in patients with gastric adenomas. RESULTS: The 87 gastric adenoma patients included 72 men and 15 women. Colorectal adenomas were identified in 42 (48.3%) of 87 cases and in 58 (33.3%) of 174 controls (P = .022). The prevalence of colorectal adenoma was significantly higher in the gastric adenoma group than in the control group. The mean size and number of colorectal adenomas were not significantly different between the two groups. The majority of colorectal adenomas were located in distal colonic segments in the gastric adenoma group in contrast with proximal colonic segments in the control group. Multivariate logistic regression analysis revealed that independent risk factors for colorectal adenoma were the presence of gastric adenomas (odds ratio [OR], .915; 95% confidence interval [CI], 1.044-3.513) and increasing age over 55 years (OR, 2.943; 95% CI, 1.558-5.560). LIMITATIONS: Lack of data on previous colorectal adenomas and possible confounding factors such as hyperlipidemia or diabetes mellitus. CONCLUSION: The risk of colorectal adenoma increases significantly in patients with gastric adenomas and in patients over age 55. A screening colonoscopy may be necessary for patients with gastric adenomas to detect colorectal adenomas.

Gene expression profiling of the rewarding effect caused by methamphetamine in the mesolimbic dopamine system.

Methamphetamine, a commonly used addictive drug, is a powerful addictive stimulant that dramatically affects the CNS. Repeated METH administration leads to a rewarding effect in a state of addiction that includes sensitization, dependence, and other phenomena. It is well known that susceptibility to the development of addiction is influenced by sources of reinforcement, variable neuroadaptive mechanisms, and neurochemical changes that together lead to altered homeostasis of the brain reward system. These behavioral abnormalities reflect neuroadaptive changes in signal transduction function and cellular gene expression produced by repeated drug exposure. To provide a better understanding of addiction and the mechanism of the rewarding effect, it is important to identify related genes. In the present study, we performed gene expression profiling using microarray analysis in a reward effect animal model. We also investigated gene expression in four important regions of the brain, the nucleus accumbens, striatum, hippocampus, and cingulated cortex, and analyzed the data by two clustering methods. Genes related to signaling pathways including G-protein-coupled receptor-related pathways predominated among the identified genes. The genes identified in our study may contribute to the development of a gene modeling network for methamphetamine addiction.

Gene discovery analysis from mouse embryonic stem cells based on time course microarray data.

An embryonic stem cell is a powerful tool for investigation of early development in vitro. The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation. For the short time course microarray data, pattern analysis based on the quadratic regression method is an effective approach for identification and classification of a variety of expressed genes that have biological relevance. We studied the expression patterns, at each of 5 stages, after neuronal induction at the mRNA level of embryonic stem cells using the quadratic regression method for pattern analysis. As a result, a total of 316 genes (3.1%) including 166 (1.7%) informative genes in 8 possible expression patterns were identified by pattern analysis. Among the selected genes associated with neurological system, all three genes showing linearly increasing pattern over time, and one gene showing decreasing pattern over time, were verified by RT-PCR. Therefore, an increase in gene expression over time, in a linear pattern, may be associated with embryonic development. The genes: Tcfap2c, Ttr, Wnt3a, Btg2 and Foxk1 detected by pattern analysis, and verified by RT-PCR simultaneously, may be candidate markers associated with the development of the nervous system. Our study shows that pattern analysis, using the quadratic regression method, is very useful for investigation of time course cDNA microarray data. The pattern analysis used in this study has biological significance for the study of embryonic stem cells.

Proteomic analysis of methamphetamine-induced reinforcement processes within the mesolimbic dopamine system.

ABSTRACT Methamphetamine (MAP) is a commonly used, addictive drug, and a powerful stimulant that dramatically affects the central nervous system. In this study, we used the conditioned place preference (CPP) paradigm in order to study the reinforcing properties of MAP and the herewith associated changes in proteins within the mesolimbic dopamine system. A CPP was induced by MAP after three intermittent intraperitoneal injections (1 mg/kg) in rats and protein profiles in the nucleus accumbens, striatum, prefrontal cortex, cingulate cortex and hippocampus were compared with a saline-treated control group. In addition, a group of animals was run through extinction and protein profiles were compared with a non-extinguished group. Protein screening was conducted using two-dimensional electrophoresis analysis which identified 27 proteins in the group that showed MAP-induced CPP. Some of the proteins were confirmed by Western lot analysis. Identified proteins had functions related to the cytoskeleton, transport/endocytosis or exocytosis (e.g. profilin-2 and syntaxin-binding protein), and signal transduction, among others.

Gene expression profile related to prognosis of acute myeloid leukemia.

Acute myeloid leukemia (AML) is a heterogeneous group of diseases with respect to biology and clinical course. Through genome-wide scanning, we can have an improvement of the diagnosis and assay system of AML. Microarray was performed for the identification of acute myeloid leukemia prognosis. We divided patients into two groups (good prognosis group, GPG and poor prognosis group, PPG) based on differences in the individual reactions to treatment. Gene expression profiles were analyzed using microarray. Among genes up-regulated at least two-fold and down-regulated at least 0.5-fold in HL-60, we chose three up-regulated genes (PPP2CA, ME3, and CCDN2) and three down-regulated genes (GLO1, ANXA2, and BMI1) and confirmed the expression of these six genes by RT-PCR. We created a leukemia-specific subclass microarray, based on the gene expression profiles. Clinical samples from the bone marrow of four patients were hybridized on this microarray. Among the genes selected by the microarray technology, NB4, silenced TRIB3 and overexpressed XRN2 were not differentiated in spite of treatment with ATRA. This indicates that XRN2 and TRIB3 play an important role in cell differentiation. These data provided an expression profile for the diagnosis and prognosis of AML patients and identified candidate genes that might allow the prognosis of AML through the relative comparison of the expression level of genes between GPG and PPG.

Gene expression profiling of rewarding effect in methamphetamine treated Bax-deficient mouse.

Methamphetamine is an illicit drug that is often abused and can cause neuropsychiatric and neurotoxic damage. Repeated administration of psychostimulants such as methamphetamine induces a behavioral sensitization. According to a previous study, Bax was involved in neurotoxicity by methamphetamine, but the function of Bax in rewarding effect has not yet been elucidated. Therefore, we have studied the function of Bax in a rewarding effect model. In the present study, we treated chronic methamphetamine exposure in a Bax-deficient mouse model and examined behavioral change using a conditioned place preference (CPP) test. The CPP score in Bax knockout mice was decreased compared to that of wild-type mice. Therefore, we screened for Bax-related genes that are involved in rewarding effect using microarray technology. In order to confirm microarray data, we applied the RT-PCR method to observe relative changes of Bcl2, a pro-apoptotic family gene. As a result, using our experiment microarray, we selected genes that were associated with Bax in microarray data, and eventually selected the Tgfbr2 gene. Expression of the Tgfbr2 gene was decreased by methamphetamine in Bax knockout mice, and the gene was overexpressed in Bax wild-type mice. Additionally, we confirmed that Creb, FosB, and c-Fos were related to rewarding effect and Bax using immunohistochemistry.

The gene expression profiling in murine cortical cells undergoing programmed cell death (PCD) induced by serum deprivation.

PCD (programmed cell death) is important mechanism for development, homeostasis and disease. To analyze the gene expression pattern in brain cells undergoing PCD in response to serum deprivation, we analyzed the cDNA microarray consisting of 2,300 genes and 7 housekeeping genes of cortical cells derived from mouse embryonic brain. Cortical cells were induced apoptosis by serum deprivation for 8 hours. We identified 69 up-regulated genes and 21 down-regulated genes in apoptotic cells. Based on the cDNA microarray data four genes were selected and analyzed by RT-PCR and northern blotting. To characterize the role of UNC-51-like kinase (ULK2) gene in PCD, we investigated cell death effect by ULK2. And we examined expression of several genes that related with PCD. Especially GAPDH was increased by ULK2. Theses findings indicated that ULK2 is involved in apoptosis through p53 pathway.

Expression profiles and pathway analysis in HEK 293 T cells overexpressing HIV-1 Tat and nucleocapsid using cDNA microarray.

Human immunodeficiency virus type 1 (HIV-1) infections are responsible for a substantial number of deaths annually and represent a significant threat to public health. According to the latest study, the Tat (Transactivator of transcription) protein is essential in transcription and replication of viral genes, and is among the early expression genes involved in the life cycle of HIV. The virion NC (nucleocapsid) plays an important role in early mRNA expression and contributes to the rapid viral replication that occurs during HIV-1 infection. Therefore, we attempted to elucidate the relationship between the Tat protein and nucleocapsid protein. In a comparison of two independently prepared and hybridized samples, flag NC overexpressed HEK 293T cells and pTat overexpressed HEK 293T cells, and hybridization showed the differences in expression in each case. Among the microarray results confirmed with real-time reverse transcriptase assay, twelve genes were identified to be involved according to their gene expression profiles. Of approximately 8,208 human genes that were analyzed, we monitored candidate genes that might have been related to NC and Tat genes from gene expression profiles. Additionally, the pathways could be viewed and analyzed through the use of PathwayStudio software. The pathways from the gene list were built and paths were found among the molecules/cell objects/processes by the curation method.

GEDA: new knowledge base of gene expression in drug addiction.

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and nonredundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

The associations between apolipoprotein B, A1, and the B/A1 ratio and nonalcoholic fatty liver disease in both normal-weight and overweight Korean population.

BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is associated with a higher risk of cardiovascular disease, but the relationship has not been established in nonobese populations. Higher apolipoprotein B (apo B) levels and the apo B/A1 ratio and lower apo A1 levels are associated with an elevated risk of cardiovascular disease. We investigated the associations between apo B, apo A1, and the apo B/A1 ratio and the presence of metabolic syndrome and NAFLD in both normal-weight and overweight Koreans. METHODS: This cross-sectional study consisted of 8327 consecutive both normal-weight and overweight Koreans with NAFLD diagnosed by ultrasonography at the Samsung Medical Center in Korea from January 2008 to December 2010. RESULTS: The prevalence of NAFLD was 27.1% among the 8327 participants. Higher serum triglyceride levels and the apo B/A1 ratio and lower high-density lipoprotein cholesterol and apo A1 levels were significantly associated with higher prevalence of metabolic syndrome in both normal-weight group and overweight group. The multivariate-adjusted odds ratios (ORs) for NAFLD in normal-weight group after comparing the fourth vs the first quartiles of the triglyceride, HDL cholesterol, low-density lipoprotein (LDL) cholesterol, apo B, apo A1, and the apo B/A1 ratio data were 2.89 (95% confidence interval [CI], 2.19-3.83; P trend < .001), 0.60 (95% CI, 0.46-0.78; P trend < .001), 1.67 (95% CI, 1.33-2.11; P trend < .001), 1.88 (95% CI, 1.48-2.39; P trend < .001), 0.73 (95% CI, 0.58-0.93; P trend < .001), and 1.86 (95% CI, 1.45-2.38; P trend < .001), respectively. The corresponding adjusted ORs in the overweight group were 3.43 (95% CI, 2.60-4.54; P trend < .001), 0.89 (95% CI, 0.68-1.16; P trend = .221), 1.41 (95% CI, 1.11-1.78; P trend = .001), 1.58 (95% CI, 1.21-2.06; P trend < .001), 0.99 (95% CI, 0.77-1.27; P trend = .958), and 1.53 (1.16-2.01; P trend = .002), respectively. CONCLUSIONS: Higher serum triglyceride, LDL cholesterol, apo B1 levels, and the apo B/A1 ratio were significantly associated with NAFLD independent of metabolic syndrome in both normal-weight and overweight Koreans. Lower serum HDL cholesterol and apo A1 levels were related to NAFLD in normal-weight participants. Our results suggest that the presence of NAFLD may be associated with increased risk for coronary artery disease in both normal-weight and overweight Koreans.