TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers.

Mammalian cells stably maintain high levels of DNA methylation despite expressing both positive (DNMT3A/B) and negative (TET1-3) regulators. Here, we analyzed the independent and combined effects of these regulators on the DNA methylation landscape using a panel of knockout human embryonic stem cell (ESC) lines. The greatest impact on global methylation levels was observed in DNMT3-deficient cells, including reproducible focal demethylation at thousands of normally methylated loci. Demethylation depends on TET expression and occurs only when both DNMT3s are absent. Dynamic loci are enriched for hydroxymethylcytosine and overlap with subsets of putative somatic enhancers that are methylated in ESCs and can be activated upon differentiation. We observe similar dynamics in mouse ESCs that were less frequent in epiblast stem cells (EpiSCs) and scarce in somatic tissues, suggesting a conserved pluripotency-linked mechanism. Taken together, our data reveal tightly regulated competition between DNMT3s and TETs at thousands of somatic regulatory sequences within pluripotent cells.

Discovery and optimization of ATX inhibitors via modeling, synthesis and biological evaluation.

Autotaxin (ATX) is a potential target for the treatment of various cancers. A new series of ATX inhibitors was rationally designed and synthesized based on our previous study. Biological evaluation and structure-activity relationship (SAR) of this series are discussed. Among fourteen synthesized derivatives, six compounds (2, 3, 4, 12, 13 and 14) exhibited enhanced ATX inhibitory activities with IC50 values in the low nanomolar range. Molecular interactions of all the synthesized compounds within the active site of ATX were studied through molecular docking studies. Herein, we describe our lead optimization efforts that resulted in the identification of a potent ATX inhibitor (compound 4 with IC50 = 1.23 nM, FS-3 and 2.18 nM, bis-pNPP). Furthermore, pharmacokinetic properties of this most promising compound are profiled.

Design, synthesis, docking and biological evaluation of 4-phenyl-thiazole derivatives as autotaxin (ATX) inhibitors.

The autotaxin-lysophophatidic acid (ATX-LPA) signaling pathway is involved in several human diseases such as cancer, autoimmune diseases, inflammatory diseases neurodegenerative diseases and fibrotic diseases. Herein, a series of 4-phenyl-thiazole based compounds was designed and synthesized. Compounds were evaluated for their ATX inhibitory activity using FS-3 and human plasma assays. In the FS-3 assay, compounds 20 and 21 significantly inhibited the ATX at low nanomolar level (IC50=2.99 and 2.19nM, respectively). Inhibitory activity of 21 was found to be slightly better than PF-8380 (IC50=2.80nM), which is one of the most potent ATX inhibitors reported till date. Furthermore, 21 displayed higher potency (IC50=14.99nM) than the first clinical ATX inhibitor, GLPG1690 (IC50=242.00nM) in the human plasma assay. Molecular docking studies were carried out to explore the binding pattern of newly synthesized compounds within active site of ATX. Docking studies suggested the putative binding mode of the novel compounds. Good ATX inhibitory activity of 21 was attributed to the hydrogen bonding interactions with Asn230, Trp275 and active site water molecules; electrostatic interaction with catalytic zinc ion and hydrophobic interactions with amino acids of the hydrophobic pocket.

NFIB is a potential target for estrogen receptor-negative breast cancers.

BACKGROUND: The association between nuclear factor I/B (NFIB) gene and triple negative breast cancer has been previously suggested. METHODS: We investigated the relationship between NFIB mRNA and protein expression and molecular subtypes of breast cancer as well as the effect of NFIB silencing on the proliferation and apoptosis of breast cancer cells. Also, the clinical importance of NFIB expression was investigated in 163 breast cancer patients. RESULTS: By using 20 frozen human breast cancer tissues and various breast cancer cell lines, we observed a significant high level of NFIB mRNA level in triple negative breast cancer. NFIB protein was upregulated in ER negative breast cancer tissues but the expression level was similar between HER2 subtype and triple negative subtype. The clinical significance of NFIB was further examined in a tissue microarray from 163 invasive breast cancer patients, and the immunohistochemistry results showed a significant association between NFIB expression and nuclear grade, ER, and HER2 expression status. NFIB positive tumors were more likely to have high nuclear grade, ER negativity and HER2 over-expression. HCC1954 cells transfected with siRNA against NFIB showed a significant reduction in cell proliferation and increase in apoptotic signaling pathway. CONCLUSIONS: Our results show a potential role of NFIB as a novel target in ER negative breast cancers.

Coded cause of death and timing of COPD diagnosis.

The aims of this study were to characterize causes of death among veterans with COPD using multiple cause of death coding, and to examine whether causes of death differed according to timing of COPD diagnosis. Veterans with COPD who died during a five-year follow-up period were identified from national VA databases linked to National Death Index files. Primary, secondary, underlying, and all-coded causes of death were compared between recent and preexistent COPD cohorts using proportional mortality ratios (PMRs), which compares proportion dying from specific causes as opposed to absolute risk of death. Of 26,357 decedents, 7,729 were categorized preexistent and 18,628 were recent COPD cases. Unspecified COPD was listed as underlying cause of death in a significantly greater proportion of preexistent COPD cases compared to recent cases, 20% vs 10%, PMR = 2.0 (95% CI: 1.9-2.1). A relatively higher proportion of recently diagnosed cases died from lung/bronchus, prostate, and site-unspecified cancers. Respiratory failure (J969) was rarely coded as an underlying or primary cause (< 1%), but was a second-code cause of death in 9% of recent and 12% of preexistent cases. Differences in coded causes of death between patients with a recent diagnosis of COPD compared to a preexistent diagnosis of COPD suggests that there is either coded cause-related bias or true differences in cause of death related to length of time with diagnosis. Thus, methods used to identify cohorts of COPD patients, i.e., incidence versus prevalence-based approaches, and coded cause of death can affect estimates of cause-specific mortality.

Medication adherence and persistence in the last year of life in COPD patients.

OBJECTIVE: To examine medication adherence and persistence among COPD patients during their last year of life. DATA SOURCE: National VA databases were used to identify patients who had COPD and died between 1999 and 2003. STUDY DESIGN: We examined use of inhaled corticosteroids (ICS), long acting beta(2) agonists (LABA), methylxanthines (MTX), and anticholinergics (AC), alone and in combination. Medication possession ratios (MPR) were compared between regimens by quarterly periods using General Estimating Equations (GEE). Medication persistence was examined in monotherapy users with Kaplan-Meier survival analysis and extended Cox proportional hazard models. PRINCIPAL FINDINGS: Only half of the identified patients in the COPD cohort (5913 of 11,376) used any medications. Among 5913 patients, overall mean (SD) MPR was 0.44 (0.32) during the last year of life. A positive linear trend in MPR was observed across quarterly periods in AC users (beta=0.014, p<0.0001), and was highest for MTX users (beta=0.11, p<0.0001). Of 3436 on monotherapy only, 40% discontinued medication within 30 days, and 70% discontinued within 90 days. MTX users were less likely to discontinue (HR=0.714, p=0.012) than reference (AC) group. CONCLUSION: COPD patients in their last year of life tended to use respiratory medications sporadically. Further research is needed to qualify whether minor differences in MPR between regimens reflect behavioral differences related to regimen or reflect refill policy and MPR calculation technique.

DNA copy number alterations and expression of relevant genes in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is defined by a lack of expression of estrogen, progesterone, and HER2 receptors, and genetically most of them fall into the basal subgroup of breast cancer. The important issue of TNBC is poorer clinical outcome and absence of effective targeted therapy. In this study, we sought to identify DNA copy number alterations and expression of relevant genes characteristic of TNBC to discover potential therapeutic targets. Frozen tissues from 114 breast cancers were analyzed using high-resolution array comparative genomic hybridization. The classification into subtype was determined by estrogen and progesterone receptor expression, and by the presence or absence of gain on the ERBB2 containing clone. The ACE algorithm was used for calling gain and loss of clones. Twenty-eight cases (25%) were classified as TNBC. Recurrent gains (> or =25%) unique to TNBC were 9p24-p21, 10p15-p13, 12p13, 13q31-q34, 18q12, 18q21-q23, and 21q22. Two published gene expression array data sets comparing basal subtype versus other subtype breast cancers were used for searching candidate genes. Of the genes upregulated in the basal subtype, 45 of 686 genes in one data set and 59 of 1,428 in the second data set were found to be located in the gained regions. Of these candidate genes, gain of NFIB (9p24.1) was specific for TNBC in a validation set by real-time PCR. In conclusion, we have identified recurrently gained regions characteristic of TNBC, and found that NFIB copy number and expression is increased in TNBC across the data sets. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

Nonalcoholic fatty liver disease predicts chronic kidney disease in nonhypertensive and nondiabetic Korean men.

In the absence of significant research, we performed a prospective study to examine the association between nonalcoholic fatty liver disease (NAFLD) and chronic kidney disease (CKD). The study cohort comprised a total of 8329 healthy men, with normal baseline kidney functions and no proteinuria, working in a semiconductor manufacturing company and its 13 affiliates. Alcohol intake was assessed with a self-reported questionnaire. Biochemical tests for liver and metabolic function and abdominal ultrasonography were done. Chronic kidney disease was defined as either the presence of proteinuria or a glomerular filtration rate (GFR) of <60 mL/min per 1.73 m(2). Cox proportional hazards model was used to estimate hazard ratios in the model for CKD. During 26717.1 person-years of follow-up, 324 men developed CKD. Nonalcoholic fatty liver disease was associated with the development of CKD (crude relative risk, 2.18; 95% confidence interval [CI], 1.75-2.71); and this relationship remained significant even after adjustment for age, GFR, triglyceride, and high-density lipoprotein cholesterol (adjusted relative risk [aRR], 1.55; 95% CI, 1.23-1.95). The association between NAFLD and incident CKD was evident in the NAFLD group with elevated serum gamma-glutamyltransferase (GGT) (aRR, 2.31; 95% CI, 1.53-3.50), even after adjustment for age, GFR, triglyceride, and high-density lipoprotein cholesterol, but not in the NAFLD group without elevated GGT (aRR, 1.09; 95% CI, 0.79-1.50) (P = .008 for interaction). To summarize, NAFLD with elevated GGT concentration was associated with an increased CKD risk among nondiabetic, nonhypertensive Korean men, irrespective of metabolic syndrome.

Use of a preference-based measure of health (EQ-5D) in COPD and asthma.

BACKGROUND: EQ-5D is a generic preference-based measure of health that can help to understand the impact of asthma and chronic obstructive pulmonary disease (COPD). The purpose of this paper was to synthesize literature on the validity and reliability of EQ-5D use in studies of asthma and COPD, and estimate EQ-5D utility scores associated with stage of disease. METHODS: A structured search was conducted in EMBASE and MEDLINE (1988-2007) using keywords relevant to respiratory disease and EQ-5D. Original research studies in asthma or COPD that reported EQ-5D results and/or psychometric properties were included. RESULTS: Studies that reported psychometric properties supported the construct validity, test-retest reliability, and responsiveness of EQ-5D in asthma (seven studies) and COPD (nine studies), although some evidence of ceiling effects were observed in asthma studies. In asthma studies that reported summary scores (n=11), EQ-5D index-based scores ranged from 0.42 (SD 0.30) to 0.93 (SD not reported). In COPD studies (n=8), scores ranged from 0.52 (SD 0.16) to 0.84 (SD 0.15). While few asthma studies reported scores by severity level, sufficient studies in COPD were available to calculate pooled mean utility scores according to GOLD stage: stage I=0.74 (0.62-0.87), stage II=0.74 (0.66-0.83), stage III=0.69 (0.60-0.78) and stage IV=0.61 (0.44-0.77) (most severe). CONCLUSIONS: Evidence generally supported the validity and reliability of EQ-5D in asthma and COPD. Utility scores associated with COPD stage may be useful for modeling health outcomes in economic evaluations of treatments for COPD.

Pro-oxidative DEP chemicals induce heat shock proteins and an unfolding protein response in a bronchial epithelial cell line as determined by DIGE analysis.

Ambient particulate matter (PM) induces adverse health effects through the ability of pro-oxidative chemicals to induce the production of oxygen radicals and oxidant injury. Utilizing a proteomics strategy involving 2-D DIGE, immunoblotting, and real-time PCR, we demonstrate that organic diesel exhaust particle (DEP) chemicals induce an unfolding protein response (UPR) and proinflammatory effects in the human bronchial epithelial cell line, BEAS-2B. DIGE and MS showed the induction of at least 14 proteins, among which heat shock protein 70 (HSP70), HSP40, TPR2, and T-complex protein 1 (zeta-subunit) are known to play a role in the UPR. Demonstrating increased HSP70 mRNA expression and nuclear translocation of HSF1, the key transcription factor responsible for HSP expression, further strengthened this notion. Immunoblotting demonstrated increased expression of ATF4, an ER stress-associated transcriptional enhancer responsible for differential protein translation under conditions of ER stress. Finally, the DEP extract induced the expression of IL-6 and IL-8 in the culture supernatant. The role of oxidative stress was demonstrated further by response subtraction in the presence of the thiol antioxidant, N-acetyl cysteine. Our data suggest that pro-oxidative DEP chemicals induce protein unfolding/misfolding that lead to UPR and proinflammatory effects in a cell type that is targeted by PM in the lung.

Putative conventional protein kinase C inhibitor Gödecke 6976 [12-(2-cyanoethyl)-6,7,12,13-tetrahydro-13-methyl-5-oxo-5H-indolo(2,3-a)pyrrolo(3,4-c)-carbazole] stimulates transglutaminase activity in primary mouse epidermal keratinocytes.

Much data in the literature suggest a role for protein kinase C (PKC) in regulating keratinocyte proliferation and differentiation. Nevertheless, the exact role of this family of isoenzymes is unclear, since PKC agonists (e.g., phorbol esters) are known to stimulate expression of both proliferative and differentiative markers in keratinocytes. Similarly, PKC inhibitors have been demonstrated both to inhibit [2-[1-3(aminopropyl)indol-3-yl]-3(1-methyl-1H-indol-3-yl)maleimide, acetate (Ro 31-7549) and 3-[1-[3-(amidinothio)propyl-1H-indol-3-(1-methyl-1H-indol-3yl) maleimide (Ro 31-8220)] and to induce (staurosporine) keratinocyte differentiation. In this study, we examined the role of the PKC inhibitor, Gödecke 6976 (Gö6976) [12-(2-cyanoethyl)-6,7,12,13-tetrahydro-13-methyl-5-oxo-5H-indolo(2,3-a)pyrrolo (3,4-c)-carbazole], on keratinocyte proliferation, as measured by DNA synthesis, and differentiation, as monitored by transglutaminase activity. This compound is reported to be selective for the conventional PKC isoforms, of which keratinocytes express only PKCalpha, and for protein kinase D (PKD; also known as PKCmu). We report that Gö6976 stimulated transglutaminase activity. Consistent with this effect, Gö6976 also potently inhibited [(3)H]thymidine incorporation (a half-maximal inhibitory concentration of approximately 0.1 microM). In addition, Gö6976 (1 microM) was able to enhance the stimulation of transglutaminase activity by 1,25-dihydroxyvitamin D(3) but had no effect on D(3)-induced expression of keratin-1. Conversely, Gö6983 [2-[1-(3-dimethylaminopropy)-5-methoxyindol-3-yl]-3-(1H-indol-3-yl)maleimide], a similar compound that also selectively inhibits conventional PKCalpha, but not PKD, had little or no effect on DNA synthesis or transglutaminase activity (up to 1 microM). The effect of Gö6976 was not due to cytotoxicity as its effect on thymidine incorporation was largely reversible, and its stimulation of transglutaminase activity could be inhibited by another general PKC inhibitor, bisindolylmaleimide I. Therefore, our results suggest a proproliferative, antidifferentiative role for PKD in epidermal maturation.

Mechanism of angiotensin II-induced phospholipase D activation in bovine adrenal glomerulosa cells.

Based on previous data demonstrating activation of phospholipase D (PLD) in response to angiotensin II (AngII), we have hypothesized a role for PLD in mediating aldosterone secretion from bovine adrenal glomerulosa cells. In this study we demonstrate that a PLD-generated signal(s) is required for the AngII-elicited secretory response, since interfering with lipid second messenger formation using a primary alcohol inhibited AngII-induced aldosterone secretion, but not that elicited by incubation with a hydrophilic cholesterol analog, 22(R)-hydroxycholesterol, which bypasses signaling pathways. Three mechanisms for hormonal activation of PLD have been described in other systems: direct receptor coupling, activation through protein kinase C (PKC) and a combination of these two mechanisms. Our results indicate that the PKC activator, phorbol 12-myristic 13-acetate (PMA), is able to activate PLD, and that receptor engagement is apparently not necessary for PLD activation in response to this agent. Maximal doses of AngII and PMA produced no additive effect on PLD activation, suggesting that these two agents function through a common PKC pathway. This interpretation was confirmed by the ability of a PKC inhibitor, Gö 6976, to inhibit partially AngII-induced PLD activation. Finally, treatment with the calcium ionophores A23187 or ionomycin or the calcium channel agonist BAY K8644 had no effect on PLD activity. Likewise, inhibiting calcium influx with high-dose nitrendipine affected neither basal PLD activity nor that stimulated by AngII. Thus, our results suggest a role for PKC, independent of calcium influx, in mediating AngII-induced PLD activation in glomerulosa cells.