A double-blind randomized phase I clinical trial targeting ALVAC-HIV vaccine to human dendritic cells

Background

We conducted a novel pilot study comparing different delivery routes of ALVAC-HIV (vCP205), a canarypox vaccine containing HIV gene inserts: env, gag and pol. We explored the concept that direct ex vivo targeting of human dendritic cells (DC) would enhance the immune response compared to either conventional intramuscular or intradermal injections of the vaccine alone.

Methodology/Principal Findings

Healthy HIV-1 uninfected volunteers were administered ALVAC-HIV or placebo by intramuscular injection (IM), intradermal injection (ID) or subcutaneous injection (SQ) of autologous ex vivo transfected DC at months 0, 1, 3 and 6. All vaccine delivery routes were well tolerated. Binding antibodies were observed to both the ALVAC vector and HIV-1 gp160 proteins. Modest cellular responses were observed in 2/7 individuals in the DC arm and 1/8 in the IM arm as determined by IFN-γ ELISPOT. Proliferative responses were most frequent in the DC arm where 4/7 individuals had measurable responses to multiple HIV-1 antigens. Loading DC after maturation resulted in lower gene expression, but overall better responses to both HIV-1 and control antigens, and were associated with better IL-2, TNF-α and IFN-γ production.

Conclusions/Significance

ALVAC-HIV delivered IM, ID or SQ with autologous ex vivo transfected DC proved to be safe. The DC arm was most immunogenic. Proliferative immune responses were readily detected with only modest cytotoxic CD8 T cell responses. Loading mature DC with the live viral vaccine induced stronger immune responses than loading immature DC, despite increased transgene expression with the latter approach. Volunteers who received the autologous vaccine loaded mature DC developed a broader and durable immune response compared to those vaccinated by conventional routes.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00013572","term_id":"NCT00013572"}}NCT00013572     

Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map

To pursue a systematic approach to discovery of mechanisms of action of traditional Chinese medicine (TCM), we used microarrays, bioinformatics and the "Connectivity Map" (CMAP) to examine TCM-induced changes in gene expression. We demonstrated that this approach can be used to elucidate new molecular targets using a model TCM herbal formula Si-Wu-Tang (SWT) which is widely used for women's health. The human breast cancer MCF-7 cells treated with 0.1 μM estradiol or 2.56 mg/ml of SWT showed dramatic gene expression changes, while no significant change was detected for ferulic acid, a known bioactive compound of SWT. Pathway analysis using differentially expressed genes related to the treatment effect identified that expression of genes in the nuclear factor erythroid 2-related factor 2 (Nrf2) cytoprotective pathway was most significantly affected by SWT, but not by estradiol or ferulic acid. The Nrf2-regulated genes HMOX1, GCLC, GCLM, SLC7A11 and NQO1 were upregulated by SWT in a dose-dependent manner, which was validated by real-time RT-PCR. Consistently, treatment with SWT and its four herbal ingredients resulted in an increased antioxidant response element (ARE)-luciferase reporter activity in MCF-7 and HEK293 cells. Furthermore, the gene expression profile of differentially expressed genes related to SWT treatment was used to compare with those of 1,309 compounds in the CMAP database. The CMAP profiles of estradiol-treated MCF-7 cells showed an excellent match with SWT treatment, consistent with SWT's widely claimed use for women's diseases and indicating a phytoestrogenic effect. The CMAP profiles of chemopreventive agents withaferin A and resveratrol also showed high similarity to the profiles of SWT. This study identified SWT as an Nrf2 activator and phytoestrogen, suggesting its use as a nontoxic chemopreventive agent, and demonstrated the feasibility of combining microarray gene expression profiling with CMAP mining to discover mechanisms of actions and to identify new health benefits of TCMs.     

Novel feature for catalytic protein residues reflecting interactions with other residues

Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship.     

Promoter hypermethylation of tumor suppressor genes in serum as potential biomarker for the diagnosis of nasopharyngeal carcinoma

Purpose: Promoter hypermethylation of tumor suppressor genes may serve as a promising biomarker for the diagnosis of cancer. Cell-free circulating DNA (cf-DNA) shares hypermethylation status with primary tumors. This study investigated promoter hypermethylation of five tumor suppressor genes as markers in the detection of nasopharyngeal carcinoma (NPC) in serum samples. Methods: cf-DNA was extracted from serum collected from 40 NPC patients and 41 age- and sex-matched healthy subjects. The promoter hypermethylation status of the five genes (RASSF1, CDKN2A, DLEC1, DAPK1 and UCHL1) was assessed by methylation-specific PCR after sodium bisulfite conversion. Differences in the methylation status of these five genes between NPC patients and healthy subjects were compared. Results: The concentration of cf-DNA in the serum of NPC patients was significantly higher than that in normal controls. The five tumor suppressor genes – RASSF1, CDKN2A, DLEC1, DAPK1 and UCHL1 – were found to be methylated in 17.5%, 22.5%, 25.0%, 51.4% and 64.9% of patients, respectively. The combination of four-gene marker – CDKN2A, DLEC1, DAPK1 and UCHL1 – had the highest sensitivity and specificity in predicting NPC. Conclusion: Screening DNA hypermethylation of tumor suppressor genes in serum was a promising approach for the diagnosis of NPC.     

Nutsedge Counts Predict Meloidogyne incognita Juvenile Counts in an Integrated Management System

The southern root-knot nematode (Meloidogyne incognita), yellow nutsedge (Cyperus esculentus) and purple nutsedge (Cyperus rotundus) are important pests in crops grown in the southern US. Management of the individual pests rather than the pest complex is often unsuccessful due to mutually beneficial pest interactions. In an integrated pest management scheme using alfalfa to suppress nutsedges and M. incognita, we evaluated quadratic polynomial regression models for prediction of the number of M. incognita J2 in soil samples as a function of yellow and purple nutsedge plant counts, squares of nutsedge counts and the cross-product between nutsedge counts . In May 2005, purple nutsedge plant count was a significant predictor of M. incognita count. In July and September 2005, counts of both nutsedges and the cross-product were significant predictors. In 2006, the second year of the alfalfa rotation, counts of all three species were reduced. As a likely consequence, the predictive relationship between nutsedges and M. incognita was not significant for May and July. In September 2006, purple nutsedge was a significant predictor of M. incognita. These results lead us to conclude that nutsedge plant counts in a field infested with the M. incognita-nutsedge pest complex can be used as a visual predictor of M. incognita J2 populations, unless the numbers of nutsedge plants and M. incognita are all very low.     

In silico method for systematic analysis of feature importance in microRNA-mRNA interactions

Background  

MicroRNA (miRNA), which is short non-coding RNA, plays a pivotal role in the regulation of many biological processes and affects the stability and/or translation of mRNA. Recently, machine learning algorithms were developed to predict potential miRNA targets. Most of these methods are robust but are not sensitive to redundant or irrelevant features. Despite their good performance, the relative importance of each feature is still unclear. With increasing experimental data becoming available, research interest has shifted from higher prediction performance to uncovering the mechanism of microRNA-mRNA interactions.     

Association between XRCC1 and XRCC3 polymorphisms and colorectal cancer risk: a meta-analysis of 23 case–control studies

Several potential functional polymorphisms in the DNA repair gene X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln (rs25487), Arg194Trp (rs1799782), Arg280His (rs25489) and X-ray repair cross-complementing group 3 (XRCC3) T241M (rs861539) have been implicated in colorectal cancer (CRC) risk, but the results are conflicting. Here, we performed a meta-analysis of 23 published case control datasets and assessed genetic heterogeneity between those datasets. All the case–control studies published from January 2000 to June 2012 on the association between those polymorphisms and CRC risk were identified by searching the electronic literature Medline. Statistical analysis was performed with the software programs Review Manager (version 4.2). For overall CRC, no significant association was observed, the pooled odds ratios for XRCC1 Arg399Gln, Arg194Trp, Arg280His, and XRCC3 T241M were 1.02 (95 % CI: 0.93, 1.12), 1.03 (95 % CI: 0.94, 1.14), 0.98 (95 % CI: 0.85, 1.13) and 1.03 (95 % CI: 0.85, 1.26), respectively. Furthermore, no significant association was observed in subgroup analyses based on ethnicity. The results suggested that these four SNPs evaluated are not associated with risk of CRC.     

Dissipative particle dynamics simulation on the properties of the oil/water/surfactant system in the absence and presence of polymer

Dissipative particle dynamics is used to simulate the oil/water/surfactant system in the absence and presence of polymer. Structural properties, interfacial properties, and their dependence on the surfactant concentration, polymer concentration and oil/water ratio were investigated. The snapshots illustrate the variation of the structure of oil/water/surfactant system. In the presence of polymer, the interface is supersaturated at a lower surfactant concentration. The end-to-end distance increases with surfactant concentration and polymer chains but shows weak dependence on the oil/water ratio. The peak of density grows higher with surfactant concentration, but it is not affected by oil/water ratio. The density profiles of polymer grow higher with polymer chains, indicating that most of the polymer chains stay at the interface for stability. Interfacial thickness shows an adsorption of polymer/surfactant complexes at the interface, where the polymer is in an extended conformation at the interface. The formation of polymer/surfactant complexes is favourable for the decrease of oil/water interfacial tension.     

Differential roles of breakfast and supper in rats of a daily three-meal schedule upon circadian regulation and physiology

The timing of meals has been suggested to play an important role in circadian regulation and metabolic health. Three meals a day is a well-established human feeding habit, which in today's lifestyle may or may not be followed. The aim of this study was to test whether the absence of breakfast or supper significantly affects the circadian system and physiological function. The authors developed a rat model for their daily three meals study, whereby animals were divided into three groups (three meals, TM; no first meal, NF; no last meal, NL) all fed with the same amount of food every day. Rats in the NF group displayed significantly decreased levels of plasma triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and glucose in the activity phase, accompanied by delayed circadian phases of hepatic peripheral clock and downstream metabolic genes. Rats in the NL group showed lower concentration of plasma TC, HDL-C, and glucose in the rest phase, plus reduced adipose tissue accumulation and body weight gain. Real-time polymerase chain reaction (PCR) analysis indicated an attenuated rhythm in the food-entraining pathway, including down-regulated expression of the clock genes Per2, Bmal1, and Rev-erbα, which may further contribute to the delayed and decreased expression of FAS in lipogenesis in this group. Our findings are consistent with the conclusion that the daily first meal determines the circadian phasing of peripheral clocks, such as in the liver, whereas the daily last meal tightly couples to lipid metabolism and adipose tissue accumulation, which suggests differential physiological effects and function of the respective meal timings.     

Effects of the position and manner of hydration on the stability of solvated N-methylacetamides and the strength of binding between N-methylacetamide and water clusters: a computational study

This work mainly studies the effects of the position (there are two possible hydrated sites) and the manner (i.e., whether water acts as a proton donor or acceptor) of hydration by various numbers of water molecules on the stability of 14 solvated N-methylacetamide structures, NMA-(H₂O) _n (n = 1–3), as well as the binding strength between the NMA and the water cluster, using molecular dynamics (MD) and B3LYP methods. Natural bond orbital (NBO) analysis is used to explore the origin of these effects. Some novel observations are obtained from the work. Our results show that monohydration at the carbonyl site favors stability and binding strength compared to monohydration at the amino site. Similarly, the preferred hydration at the carbonyl site is observed for dihydrated NMAs when the second water is added as a proton donor to the C=O group or the first water is H-bonded to the C=O group. However, unfavorable hydration at the C=O site occurs if the second water acts as a proton acceptor. Trihydration by a ring cluster of three water molecules at either the carbonyl site or the amino one yields relatively stable complexes, but significantly disfavors binding strength. The other trihydrated NMAs show similar behavior to dihydrated NMAs. In addition, our results show that the C=O and N–H frequencies can still be utilized to examine the H-bond effects of the water cluster.