Alcohol Consumption and the Diversity of the Oral Microbiome in Postmenopausal Women

BACKGROUND

Alcohol reduces neutrophil function and decreases salivary flow, which could affect the composition of the oral microbiome.

OBJECTIVE

We hypothesized that the α- and β-diversity of the oral microbiome and the relative abundance of bacterial taxa would differ by frequency and type of alcohol consumption.

METHODS

We used a food frequency questionnaire to assess the frequency of consumption of beer, wine, and liquor (drinks/week) in a sample of 1179 postmenopausal women in the Osteoporosis and Periodontal Disease Study. Women were categorized as nondrinkers, drinking <1 drink/wk, ≥1 to <7 drinks/wk, or ≥7 drinks/wk for total alcohol consumption and for beer, wine, and liquor consumption. The composition and diversity of the oral microbiome was assessed from subgingival plaque samples using 16S ribosomal RNA amplicon sequencing. Permutational multivariate analysis of variance (PERMANOVA) was used to examine β-diversity (between-sample diversity) in the microbiome between alcohol consumption categories. Analysis of covariance was used to examine the mean α-diversity (within-sample diversity), assessed by the Shannon index (species evenness), Chao1 index (species richness), and observed operational taxonomic unit (OTU) count and the mean relative abundance of 245 bacterial taxa across alcohol consumption categories.

RESULTS

Over half of the participants (67%) consumed alcohol, with 14% reporting ≥1 drink/d. The β-diversity across categories of total alcohol consumption, but not categories of alcohol type, was statistically significantly different (P for PERMANOVA = 0.016). Mean α-diversity measures were statistically significantly higher (P < 0.05) in the highest category of total alcohol and wine consumption compared to nondrinkers; no significant associations were found for beer or liquor consumption. The relative abundance of 1 OTU, Selenomonassp._oral_taxon_133, was significantly lower in the highest level of total alcohol consumption compared to nondrinkers after adjustment for multiple comparisons.

CONCLUSIONS

Alcohol consumption was associated with the diversity and composition of the subgingival microbiome.

Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development

While the accessibility of enhancers is dynamically regulated during development, promoters tend to be constitutively accessible and poised for activation by paused Pol II. By studying Lola-I, a Drosophila zinc finger transcription factor, we show here that the promoter state can also be subject to developmental regulation independently of gene activation. Lola-I is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers and reveal a mechanism for the de novo establishment of paused Pol II at promoters.

An integrated genomic approach identifies follistatin as a target of the p63-epidermal growth factor receptor oncogenic network in head and neck squamous cell carcinoma

Although numerous putative oncogenes have been associated with the etiology of head and neck squamous cell carcinoma (HNSCC), the mechanisms by which these oncogenes and their downstream targets mediate tumor progression have not been fully elucidated. We performed an integrative analysis to identify a crucial set of targets of the oncogenic transcription factor p63 that are common across multiple transcriptomic datasets obtained from HNSCC patients, and representative cell line models. Notably, our analysis revealed FST which encodes follistatin, a secreted glycoprotein that inhibits the transforming growth factor TGFβ/activin signaling pathways, to be a direct transcriptional target of p63. In addition, we found that FST expression is also driven by epidermal growth factor receptor EGFR signaling, thus mediating a functional link between the TGF-β and EGFR pathways. We show through loss- and gain-of-function studies that FST predominantly imparts a tumor-growth and migratory phenotype in HNSCC cells. Furthermore, analysis of single-cell RNA sequencing data from HNSCC patients unveiled cancer cells as the dominant source of FST within the tumor microenvironment and exposed a correlation between the expression of FST and its regulators with immune infiltrates. We propose FST as a prognostic biomarker for patient survival and a compelling candidate mediating the broad effects of p63 on the tumor and its associated microenvironment.

Alcohol Consumption and the Diversity of the Oral Microbiome in Postmenopausal Women

Objectives

Alcohol has been shown to reduce neutrophil function and decrease salivary flow, which could affect the composition of the oral microbiome. We hypothesized that the α- and β-diversity of the oral microbiome would differ by frequency of alcohol consumption.

Methods

A food frequency questionnaire was used to assess the frequency of consumption of beer, wine, and liquor in a sample of 1,179 postmenopausal women in an ancillary study of periodontal disease (OsteoPerio) of the Women's Health Initiative Observational Study. Frequency of alcohol consumption was converted to grams of alcohol consumed per day (g/d), and the following categories were created: non-drinkers and tertiles of alcohol consumption in g/d among drinkers. The oral microbiome was assessed from subgingival plaque samples using 16S rRNA amplicon sequencing. PERMANOVA was used to examine β-diversity (between-sample diversity) and ANOVA was used to examine α-diversity (within-sample diversity) across alcohol intake categories. The Shannon index (species evenness), Chao1 index (species richness), and observed operational taxonomic unit (OTU) count were used to assess α-diversity. Models were adjusted for age, race, education, neighborhood socioeconomic status, smoking, menopausal hormone use, non-alcohol total energy, body mass index, antibiotic use, and dental care habits. Sensitivity analyses were conducted by removing those who currently smoke (n = 32) and those that took antibiotics in the past 30 days (n = 123).

Results

Over half of the participants (66%) consumed alcohol, with 12% reporting ≥1 drinks/day. β-diversity across categories of alcohol consumption was statistically significantly different (PERMANOVA P = 0.016). α-diversity was significantly higher in the highest tertile of alcohol consumption compared to non-drinkers for all α-diversity measures. The adjusted means (SE) in the highest tertile of alcohol intake compared to non-drinkers were 5.17 (0.09) vs. 4.96 (0.09) for Shannon Index, 155.37 (4.24) vs. 146.00 (3.97) for Chao1 Index, and 124.94 (3.81) vs. 116.35 (3.57) for observed OTU count. Sensitivity analyses showed similar results.

Conclusions

Alcohol consumption was associated with subgingival bacterial diversity.

Funding Sources

National Heart, Lung, and Blood Institute, National Institute of Dental and Craniofacial Research, and Department of Defense.

Coffee and Tea Consumption and the Diversity of the Oral Microbiome in Postmenopausal Women

Objectives

The oral microbiome plays a central role in oral health. Coffee and tea are popular beverages, and their consumption may benefit health due to their polyphenol content. Impact of these beverages on the oral microbiome is not well understood; we examined associations of coffee and tea consumption with diversity of the oral microbiome among postmenopausal women.

Methods

This cross-sectional analysis used data from 1,124 postmenopausal women who participated in an ancillary study (1997–2001) of periodontal disease within the Women's Health Initiative Observational Study. Frequency of consumption for coffee was categorized as < 1 cup/week (w) (n = 171), ≥1 cup/w to < 1 cup/day (d) (n = 220), ≥1 to ≤ 2 cups/d (n = 178), >2 to ≤ 3 cups/d (n = 344), >3 cups/d (n = 211), and for tea as < 1 cup/w (n = 229), ≥1 cup/w to < 1 cup/d (n = 528), ≥1 to ≤ 2 cups/d (n = 152), >2 cups/d (n = 215). The oral microbiome was assessed in subgingival plaque samples by 16S rRNA gene sequencing. The microbiome operational taxonomic units (OTUs) data were transformed using the centered log-ratio transformation to account for the compositional data structure and reduce spurious associations with beverage intake. PERMANOVA was used to examine β-diversity (between-sample diversity) and ANOVA for α-diversity (within-sample diversity) of the microbiota across categories of coffee or tea. α-diversity was examined using OTU count, Chao1 Index, and Shannon Index. Models were adjusted for age, race, education, smoking status, body mass index, diabetes, antibiotic use, and dental hygiene behaviors.

Results

β-diversity did not differ across categories of beverage consumption (PERMANOVA p_coffee = 0.123, p_tea = 0.158). α-diversity measures were lower, but not significantly different, among those who consumed coffee or tea more vs. less frequently. For example, the adjusted means (SE) for the Shannon Index were 4.95 (0.10) vs. 5.00 (0.10), P = 0.871 in high (>3 cups/d) vs. low (<1 cup/w) coffee consumption and 4.90 (0.10) vs. 5.02 (0.10), P = 0.333 for high (>2 cups/d) vs. low (<1 cup/w) tea consumption.

Conclusions

In this study of postmenopausal women, we found no statistically significant associations between coffee or tea consumption and the diversity of oral microbiome.

Funding Sources

National Heart, Lung, and Blood Institute, National Institute of Dental and Craniofacial Research, and the Department of Defense.

Start-up, operation and thermal-hydraulic analysis of a self-propelling supercritical CO2 heat removal system coupled to a pressurized water reactor

The supercritical carbon dioxide (sCO2) heat removal system, which is based on a closed Brayton cycle with sCO2 as a working fluid, is an innovative, self-propelling and modular heat removal system for existing and future nuclear power plants. By changing the number of CO2 cycles, the heat removal capacity can be adapted. In this paper, up to four sCO2 cycles are analyzed in interaction with a pressurized water reactor, using the thermal-hydraulic system code ATHLET and considering a long-term station blackout and loss of ultimate heat sink scenario with conservatively high and low decay heat curves. The presented start-up procedure for the heat removal system might require further optimization due to the non-linear thermal gradients. Independent from the start-up, a heat removal system with three or four CO2 cycles keeps the primary loop temperatures sufficiently low. However, with only three cycles, the core is almost uncovered, and the danger of recriticality may occur due to cold leg deboration. Controlling the turbine inlet temperature via the turbomachinery speed and subsequent shutdown of single cycles successfully adapts the operation of the heat removal system to the declining decay heat. This enables reliable decay heat removal for more than 72 h.

Remediation of Mucorales-contaminated Healthcare Linens at a Laundry Facility Following an Investigation of a Case Cluster of Hospital-acquired Mucormycosis

BACKGROUND

In an investigation of hospital-acquired mucormycosis cases among transplant recipients, healthcare linens (HCLs) delivered to our center were found to be contaminated with Mucorales. We describe an investigation and remediation of Mucorales contamination at the laundry supplying our center.

METHODS

We performed monthly RODAC cultures of HCLs upon hospital arrival, and conducted site inspections and surveillance cultures at the laundry facility. Remediation was designed and implemented by infection prevention and facility leadership teams.

RESULTS

Prior to remediation, 20% of HCLs were culture-positive for Mucorales upon hospital arrival. Laundry facility layout and processes were consistent with industry standards. Significant step-ups in Mucorales and mould culture-positivity of HCLs were detected at the post-dryer step (0% to 12% (p=0.04) and 5% to 29% (p=0.01), respectively). Further increases to 17% and 40% culture-positivity, respectively, were noted during pre-transport holding. Site inspection revealed heavy Mucorales-positive lint accumulation in rooftop air intake and exhaust vents that cooled driers; intake and exhaust vents that were facing each other; rooftop and plant-wide lint accumulation, including in the pre-transport clean room; uncovered carts with freshly-laundered HCLs. Following environmental remediation, quality assurance measures and education directed toward these sources, Mucorales culture-positivity of newly-delivered HCLs was reduced to 0.3% (p=0.0001); area of lint-contaminated rooftop decreased from 918 m 2 to 0 m 2 on satellite images.

CONCLUSIONS

Targeted laundry facility interventions guided by site inspections and step-wise culturing significantly reduced Mucorales-contaminated HCLs delivered to our hospital. Collaboration between infection prevention and laundry facility teams was crucial to successful remediation.

High resolution measurements with miniature neutron scintillators in the SUR-100 zero power reactor

Three 1-mm3 miniature fiber-coupled scintillators have been used to perform cm-wise resolution measurements of the thermal neutron flux within experimental channels of the SUR-100 facility, a zero power thermal reactor operated by the Institute of Nuclear Technology and Energy Systems at the University of Stuttgart. The detection system is developed at the École Polytechnique Fédérale de Lausanne in collaboration with the Paul Scherrer Institut. Thermal neutrons count rates were measured along the experimental channels I and II, which cross the reactor at the center and tangentially to the core, respectively. The reactor was modelled with the Monte Carlo neutron transport code Serpent-2.1.31. The comparison of experimental and computed reaction rate distributions showed a good agreement within the core region, with discrepancies within 2σ. An unexpected discrepancy, probably caused by a geometric inconsistency in the computational model of the reactor, was observed in the reflector region of the experimental channel I, where a 20% difference (i.e. 8σ) was found between experimental and simulated results. Significant discrepancies, respectively worth 10σ and 15σ, were noticed at distance, in the lead shielding region, for both experimental channels I and II. In addition, reaction rate gradients across the 2.6 cm and 5.4 cm diameters of both channels were measured. A horizontal reaction rate gradient of (9.09 ± 0.20) % was measured within 2.4 cm across the diameter of the experimental channel II, with a difference from computed results of 2%. The absence of a vertical reaction rate gradient inside the experimental channel I was confirmed by measurements.

Criticality Characteristics and Sensitivity Analysis of Fukushima Debris Beds Containing MCCI Products

This study investigates the criticality characteristics of debris beds that may have been formed through the molten–core–concrete-interaction (MCCI) at the pedestal floor of the damaged reactors in Fukushima Daiichi Nuclear Power Station. These were modeled as UO2-concrete systems submerged in water. First, a conservative model was used to evaluate the impact that the presence of concrete has on the neutron multiplication factor (keff) of debris beds. The good moderation capacities of concrete were proved, and it was found that recriticality would be possible under the considered conservative assumptions. Second, a more realistic model was used to perform an uncertainty and sensitivity analysis of a wide range of debris parameters (debris porosity, core meltdown grade, debris size, debris composition, concrete erosion factor, etc.). In this case, the results indicate that the probability of a recriticality event is very remote. It was also found that the presence of boron (B4C) from the control rods within debris has by far the highest influence on keff.

P1060USING ARTIFICIAL INTELLIGENCE TO PREDICT HOME THERAPY CANDIDATES

Background and Aims

There are many benefits for performing dialysis at home including more flexibility and more frequent treatments. A possible barrier to election of home therapy (HT) by in-center patients is a lack of adequate HT education. To aid efficient education efforts, a predictive model was developed to help identify patients who are more likely to switch from in-center and succeed on HT.

Method

We developed a model using machine learning to predict which patients who are treated in-center without prior HT history are most likely to switch to HT in the next 90 days and stay on HT for at least 90 days. Training data was extracted from 2016–2019 for approximately 300,000 patients. We randomly sampled one in-center treatment date per patient and determined if the patient would switch and succeed on HT. The input features consisted of treatment vitals, laboratories, absence history, comprehensive assessments, facility information, county-level housing, and patient characteristics. Patients were excluded if they had less than 30 days on dialysis due to lack of data. A machine learning model (XGBoost classifier) was deployed monthly in a pilot with a team of HT educators to investigate the model’s utility for identifying HT candidates.

Results

There were approximately 1,200 patients starting a home therapy per month in a large dialysis provider, with approximately one-third being in-center patients. The prevalence of switching and succeeding to HT in this population was 2.54%. The predictive model achieved an area under the curve of 0.87, sensitivity of 0.77, and a specificity of 0.80 on a hold-out test dataset. The pilot was successfully executed for several months and two major lessons were learned: 1) some patients who reappeared on each month’s list should be removed from the list after expressing no interest in HT, and 2) a data collection mechanism should be put in place to capture the reasons why patients are not interested in HT.

Conclusion

This quality-improvement initiative demonstrates that predictive modeling can be used to identify patients likely to switch and succeed on home therapy. Integration of the model in existing workflows requires creating a feedback loop which can help improve future worklists.

ATHLET extensions for the simulation of supercritical carbon dioxide driven power cycles

The Fukushima accident reveals the need for additional safety systems for nuclear power plants. One promising option is the supercritical carbon-dioxide (sCO2) heat removal system, which consists of a simple Brayton cycle. This study provides an overview of the extensions and validation of the thermal-hydraulic system code ATHLET for the simulation of sCO2 power cycles, especially with regard to the sCO2 heat removal system. The properties of CO2, heat transfer and pressure drop correlations, as well as compact heat exchanger and turbomachinery modelling are considered.

A parallel computational framework for ultra-large-scale sequence clustering analysis

Motivation

The rapid development of sequencing technology has led to an explosive accumulation of genomic data. Clustering is often the first step to be performed in sequence analysis. However, existing methods scale poorly with respect to the unprecedented growth of input data size. As high-performance computing systems are becoming widely accessible, it is highly desired that a clustering method can easily scale to handle large-scale sequence datasets by leveraging the power of parallel computing.

Results

In this paper, we introduce SLAD (Separation via Landmark-based Active Divisive clustering), a generic computational framework that can be used to parallelize various de novo operational taxonomic unit (OTU) picking methods and comes with theoretical guarantees on both accuracy and efficiency. The proposed framework was implemented on Apache Spark, which allows for easy and efficient utilization of parallel computing resources. Experiments performed on various datasets demonstrated that SLAD can significantly speed up a number of popular de novo OTU picking methods and meanwhile maintains the same level of accuracy. In particular, the experiment on the Earth Microbiome Project dataset (∼2.2B reads, 437 GB) demonstrated the excellent scalability of the proposed method.

Availability and implementation

Open-source software for the proposed method is freely available at https://www.acsu.buffalo.edu/~yijunsun/lab/SLAD.html.

Supplementary information

Supplementary data are available at Bioinformatics online.

SENSE: Siamese neural network for sequence embedding and alignment-free comparison

MOTIVATION

Sequence analysis is arguably a foundation of modern biology. Classic approaches to sequence analysis are based on sequence alignment, which is limited when dealing with large-scale sequence data. A dozen of alignment-free approaches have been developed to provide computationally efficient alternatives to alignment-based approaches. However, existing methods define sequence similarity based on various heuristics and can only provide rough approximations to alignment distances.

RESULTS

In this article, we developed a new approach, referred to as SENSE (SiamEse Neural network for Sequence Embedding), for efficient and accurate alignment-free sequence comparison. The basic idea is to use a deep neural network to learn an explicit embedding function based on a small training dataset to project sequences into an embedding space so that the mean square error between alignment distances and pairwise distances defined in the embedding space is minimized. To the best of our knowledge, this is the first attempt to use deep learning for alignment-free sequence analysis. A large-scale experiment was performed that demonstrated that our method significantly outperformed the state-of-the-art alignment-free methods in terms of both efficiency and accuracy.

AVAILABILITY AND IMPLEMENTATION

Open-source software for the proposed method is developed and freely available at https://www.acsu.buffalo.edu/∼yijunsun/lab/SENSE.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Chronic kidney disease, uremic milieu, and its effects on gut bacterial microbiota dysbiosis

Several lines of evidence suggest that gut bacterial microbiota is altered in patients with chronic kidney disease (CKD), though the mechanism of which this dysbiosis takes place is not well understood. Recent studies delineated changes in gut microbiota in both CKD patients and experimental animal models using microarray chips. We present 16S ribosomal RNA gene sequencing of both stool pellets and small bowel contents of C57BL/6J mice that underwent a remnant kidney model and establish that changes in microbiota take place in the early gastrointestinal tract. Increased intestinal urea concentration has been hypothesized as a leading contributor to dysbiotic changes in CKD. We show that urea transporters (UT)-A and UT-B mRNA are both expressed throughout the whole gastrointestinal tract. The noted increase in intestinal urea concentration appears to be independent of UTs' expression. Urea supplementation in drinking water resulted in alteration in bacterial gut microbiota that is quite different than that seen in CKD. This indicates that increased intestinal urea concentration might not fully explain the CKD- associated dysbiosis.

Self-reactivity controls the basal metabolism and in vivo function of CD4 T cells

Relatively little is known with regard to CD4 T cell memory formation and metabolism, in part because CD4 T cell numbers remain low during a recall infection. Further, the contribution of self-peptide-MHC signaling (during both thymic T cell development and peripheral maintenance) to metabolic programming, if any, remains unknown. To address these questions, we have employed LLO-Hi5 and LLO-Lo5, two TCRtg CD4 T cells that recognize the same Listeria epitope with the same affinity. LLO-Hi5 CD4 T cells are highly self-reactive and respond poorly in a primary infection but robustly in a secondary infection. Less self-reactive LLO-Lo5 cells respond well during primary infection but poorly during secondary infection. We performed metabolic profiling to determine whether differences in response during infection were linked to metabolic differences between LLO-Lo5 and LLO-Hi5. We found that LLO-Lo5 had dramatically higher respiration and glycolytic rates relative to LLO-Hi5, and hypothesized that the decreased metabolism resulting from a strong interaction with self was mediated through TCR signaling. To test this hypothesis, we generated a knockin mouse expressing the Scn5a voltage gated sodium channel. This channel, when normally expressed in DP thymocytes, enhances TCR-mediated signaling. We found that overexpression of Scn5a in peripheral T cells increased TCR-proximal signaling. Further, Scn5a-expressing LLO-Lo5 cells displayed an impaired response during a primary infection. In this way, we demonstrate that tuning of TCR sensitivity to self can be used to alter in vivo immune responses. These studies highlight the critical relationship between TCR:self-pMHC interaction, metabolism, and the immune response to infection.

EZH2 Modifies Sunitinib Resistance in Renal Cell Carcinoma by Kinome Reprogramming

Acquired and intrinsic resistance to receptor tyrosine kinase inhibitors (RTKi) represents a major hurdle in improving the management of clear cell renal cell carcinoma (ccRCC). Recent reports suggest that drug resistance is driven by tumor adaptation via epigenetic mechanisms that activate alternative survival pathways. The histone methyl transferase EZH2 is frequently altered in many cancers, including ccRCC. To evaluate its role in ccRCC resistance to RTKi, we established and characterized a spontaneously metastatic, patient-derived xenograft model that is intrinsically resistant to the RTKi sunitinib, but not to the VEGF therapeutic antibody bevacizumab. Sunitinib maintained its antiangiogenic and antimetastatic activity but lost its direct antitumor effects due to kinome reprogramming, which resulted in suppression of proapoptotic and cell-cycle-regulatory target genes. Modulating EZH2 expression or activity suppressed phosphorylation of certain RTKs, restoring the antitumor effects of sunitinib in models of acquired or intrinsically resistant ccRCC. Overall, our results highlight EZH2 as a rational target for therapeutic intervention in sunitinib-resistant ccRCC as well as a predictive marker for RTKi response in this disease. Cancer Res; 77(23); 6651-66. ©2017 AACR.

Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial

The modern Western diet is rich in advanced glycation end products (AGEs). We have previously shown an association between dietary AGEs and markers of inflammation and oxidative stress in a population of end stage renal disease (ESRD) patients undergoing peritoneal dialysis (PD). In the current pilot study we explored the effects of dietary AGEs on the gut bacterial microbiota composition in similar patients. AGEs play an important role in the development and progression of cardiovascular (CVD) disease. Plasma concentrations of different bacterial products have been shown to predict the risk of incident major adverse CVD events independently of traditional CVD risk factors, and experimental animal models indicates a possible role AGEs might have on the gut microbiota population. In this pilot randomized open label controlled trial, twenty PD patients habitually consuming a high AGE diet were recruited and randomized into either continuing the same diet (HAGE, n = 10) or a one-month dietary AGE restriction (LAGE, n = 10). Blood and stool samples were collected at baseline and after intervention. Variable regions V3-V4 of 16s rDNA were sequenced and taxa was identified on the phyla, genus, and species levels. Dietary AGE restriction resulted in a significant decrease in serum N^ε-(carboxymethyl) lysine (CML) and methylglyoxal-derivatives (MG). At baseline, our total cohort exhibited a lower relative abundance of Bacteroides and Alistipes genus and a higher abundance of Prevotella genus when compared to the published data of healthy population. Dietary AGE restriction altered the bacterial gut microbiota with a significant reduction in Prevotella copri and Bifidobacterium animalis relative abundance and increased Alistipes indistinctus, Clostridium citroniae, Clostridium hathewayi, and Ruminococcus gauvreauii relative abundance. We show in this pilot study significant microbiota differences in peritoneal dialysis patients’ population, as well as the effects of dietary AGEs on gut microbiota, which might play a role in the increased cardiovascular events in this population and warrants further studies.

A time-series analysis of altered histone H3 acetylation and gene expression during the course of MMAIII-induced malignant transformation of urinary bladder cells

Our previous studies have shown that chronic exposure to low doses of monomethylarsonous acid (MMAIII) causes global histone acetylation dysregulation in urothelial cells (UROtsa cells) during the course of malignant transformation. To reveal the relationship between altered histone acetylation patterns and aberrant gene expression, more specifically, the carcinogenic relevance of these alterations, we performed a time-course analysis of the binding patterns of histone 3 lysine 18 acetylation (H3K18ac) across the genome and generated global gene-expression profiles from this UROtsa cell malignant transformation model. We showed that H3K18ac, one of the most significantly upregulated histone acetylation sites following MMAIII exposure, was enriched at gene promoter-specific regions across the genome and that MMAIII-induced upregulation of H3K18ac led to an altered binding pattern in a large number of genes that was most significant during the critical window for MMAIII-induced UROtsa cells' malignant transformation. Some genes identified as having a differential binding pattern with H3K18ac, acted as upstream regulators of critical gene networks with known functions in tumor development and progression. The altered H3K18ac binding patterns not only led to changes in expression of these directly affected upstream regulators but also resulted in gene-expression changes in their regulated networks. Collectively, our data suggest that MMAIII-induced alteration of histone acetylation patterns in UROtsa cells led to a time- and malignant stage-dependent aberrant gene-expression pattern, and that some gene regulatory networks were altered in accordance with their roles in carcinogenesis, probably contributing to MMAIII-induced urothelial cell malignant transformation and carcinogenesis.

Tolerogenic dendritic cells generated with dexamethasone and vitamin D3 regulate rheumatoid arthritis CD4+ T cells partly via transforming growth factor-β1

Tolerogenic dendritic cells (tolDC) are a new immunotherapeutic tool for the treatment of rheumatoid arthritis (RA) and other autoimmune disorders. We have established a method to generate stable tolDC by pharmacological modulation of human monocyte-derived DC. These tolDC exert potent pro-tolerogenic actions on CD4⁺ T cells. Lack of interleukin (IL)-12p70 production is a key immunoregulatory attribute of tolDC but does not explain their action fully. Here we show that tolDC express transforming growth factor (TGF)-β1 at both mRNA and protein levels, and that expression of this immunoregulatory cytokine is significantly higher in tolDC than in mature monocyte-derived DC. By inhibiting TGF-β1 signalling we demonstrate that tolDC regulate CD4⁺ T cell responses in a manner that is at least partly dependent upon this cytokine. Crucially, we also show that while there is no significant difference in expression of TGF-βRII on CD4⁺ T cells from RA patients and healthy controls, RA patient CD4⁺ T cells are measurably less responsive to TGF-β1 than healthy control CD4⁺ T cells [reduced TGF-β-induced mothers against decapentaplegic homologue (Smad)2/3 phosphorylation, forkhead box protein 3 (FoxP3) expression and suppression of (IFN)-γ secretion]. However, CD4⁺ T cells from RA patients can, nonetheless, be regulated efficiently by tolDC in a TGF-β1-dependent manner. This work is important for the design and development of future studies investigating the potential use of tolDC as a novel immunotherapy for the treatment of RA.

Lateralisation in agonistic encounters: do mirror tests reflect aggressive behaviour? A study on a West African cichlid

In this study, population level lateralisation and the suitability of mirror tests as a test of natural aggressive behaviour in male rainbow kribs Pelvicachromis pulcher was investigated. Aggressive behaviour in live agonistic trials correlated positively with behaviours towards a mirror image and no visual lateralisation was detected.

Abstract 3508: Inhibition of EZH2 overcomes resistance to sunitinib in clear cell renal cell carcinoma models

Background: Alterations in epigenetic mechanisms including histone modification and hyper-methylation at gene promoter regions have been implicated as mechanisms of drug resistance in cancer. Alternation of epigenetic regulators such histone methyltransferase, EZH2, has been reported in numerous cancer types including advanced renal cell carcinoma (RCC). Previous studies suggest that sunitinib may have a direct anti-tumor effect and that acquired sunitinib resistance may be induced in tumor cells rather than just in endothelial cells. In our study, we investigated the role of EZH2 in sunitinib resistance in clear cell renal cell carcinoma. Methods: Human RCC cell lines 786-0 were treated and exposed to increasing concentrations of sunitinib to develop a resistant cell line, 786-0R. Parental and resistant cell lines were treat with either sunitinib, GSK126 (EZH2 inhibitor) or both. In parallel, EZH2 was knocked down in 786-0 cells and exposed to increasing concentrations of sunitinib. Cell viability was quantitated by absorbance of crystal violet stained cells using a spectrometer at 570nm. In a second set of experiments, control and treated cells were collected for western analysis. Mice bearing human ccRCC patient derived xenograft (PDXs); RP-R-01, RP-R-02 and RP-R-02LM (a metastatic ccRCC model established from RP-R-02) were implanted into SCID mice either subcutaneously or orthotopic in the kidney (sub-renal). When tumors reached an average volume of 50mm3, mice were randomly grouped into 2 arms; control and sunitinib treatment (40mg/kg, 5days/week). Tumors volumes and body weight were assessed once per week. Tumor tissues and lungs were collected for immunohistochemistry analysis. All assessments and quantification were done blindly. Results: Our in vitro and in vivo data showed an increased expression of EZH2 with resistance to sunitinib. Furthermore, inhibition of EZH2 in our in vitro studies correlated with a significant decrease in the anti-tumor effect of sunitinib in both parental and resistant cell lines. Conclusion: Overall our data suggest the potential role of epigenetic alterations, specifically EZH2 overexpression and its association with resistance to sunitinib. We are currently assessing the effect of EZH2 inhibition with sunitinib resistance in our in vivo system using metastatic ccRCC PDX models.

Citation Format: Remi M. Adelaiye-Ogala, Sreenivasulu Chintala, Li Shen, Ashley Orillion, Eric Ciamporcero, May Elbanna, Kiersten Marie Miles, Bryan Gillard, Michael Buck, Roberto Pili. Inhibition of EZH2 overcomes resistance to sunitinib in clear cell renal cell carcinoma models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3508. doi:10.1158/1538-7445.AM2015-3508

Abstract 4132: Anti-tumor and anti-metastatic effect of sunitinib in a patient derived metastatic clear cell renal cell carcinoma xenograft model

Background: Sunitinib, a multi-tyrosine kinase inhibitor, is considered first-line therapy for patient with advanced renal cell carcinoma. The mechanism by which sunitinib harnesses angiogenesis is by targeting receptors of pro-angiogenic growth factors such as VEGF, PDGF and kit. Recently, it has been speculated that sunitinib may have a direct anti-tumor effect. Our previous studies have shown that tumors resistant to sunitinib still present decreased tumor vasculature compared to untreated tumors, suggesting that sunitinib anti-tumor effect may be in part independent from its anti-angiogenic effect. Hence, we wanted to further investigate the anti-tumor effect of sunitinib in human renal cell carcinoma (RCC) cell lines and a patient derived clear cell RCC xenograft model. In addition, we examined the effect of sunitinib on early and late stage metastasis in a spontaneous metastatic human ccRCC model. Methods: Human ccRCC PDX RP-R-02 was implanted into SCID mice subcutaneously. Spontaneous metastatic ccRCC model, RP-R-02LM was developed from RP-R-02. RP-R-02LM tumor bearing mice were treated with sunitinib (40mg/kg; 5days/week). Tumor tissues and lungs were collected for immunohistochemistry analysis. In parallel, human RCC cell lines were treated in vitro with varying concentrations of sunitinib and cell viability was assessed. Results: Human RCC cells lines treated in vitro with sunitinib at pharmacological achievable concentrations showed a decrease in cell proliferation, suggesting a direct anti-tumor effect of sunitinib in RCC. RP-R-02LM but not parental RP-R-02 implanted either subcutaneous or orthotopically in the kidney, spontaneously metastasize to the lungs and closely mimics what is seen in the clinic. PCR results indicated that both xenografts still maintain human origin. In our in vivo system, RP-R-02LM treated with sunitinib had no anti-tumor effect on tumor at the primary site; however, we observed an inhibition of dissemination to the metastatic lung site as indicated by significantly low numbers of metastasis compared to the controls. Immunohistochemical analysis showed decrease in tumor vasculature with sunitinib treatment compared to the control, with increased tumor cell proliferations. Conclusion: Our studies suggest that sunitinib has a direct anti-tumor in vitro and eventually tumor cells acquire drug resistance. Our in vivo studies show that tumors resistant to sunitinib have decreased vessel density as compared to the untreated tumors, suggesting that sunitinib is still a potent anti-angiogenic agent. In addition, we show the anti-metastatic effect of sunitinib in a spontaneous metastatic human clear cell renal cell carcinoma. Overall our data suggest that sunitinib maintains an anti-metastatic effect in sunitinib resistant tumor bearing animals that is independent from its anti-angiogenic effect.

Citation Format: Remi M. Adelaiye-Ogala, Li Shen, Sreenivasulu Chintala, Eric Ciamporcero, Ashley Orillion, May Elbanna, Shengyu Ku, Kiersten Marie Miles, Bryan Gillard, Michael Buck, Roberto Pili. Anti-tumor and anti-metastatic effect of sunitinib in a patient derived metastatic clear cell renal cell carcinoma xenograft model. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4132. doi:10.1158/1538-7445.AM2015-4132

Sunitinib dose escalation overcomes transient resistance in clear cell renal cell carcinoma and is associated with epigenetic modifications

Sunitinib is considered a first-line therapeutic option for patients with advanced clear cell renal cell carcinoma (ccRCC). Despite sunitinib's clinical efficacy, patients eventually develop drug resistance and disease progression. Herein, we tested the hypothesis whether initial sunitinib resistance may be transient and could be overcome by dose increase. In selected patients initially treated with 50 mg sunitinib and presenting with minimal toxicities, sunitinib dose was escalated to 62.5 mg and/or 75 mg at the time of tumor progression. Mice bearing two different patient-derived ccRCC xenografts (PDX) were treated 5 days per week with a dose-escalation schema (40-60-80 mg/kg sunitinib). Tumor tissues were collected before dose increments for immunohistochemistry analyses and drug levels. Selected intrapatient sunitinib dose escalation was safe and several patients had added progression-free survival. In parallel, our preclinical results showed that PDXs, although initially responsive to sunitinib at 40 mg/kg, eventually developed resistance. When the dose was incrementally increased, again we observed tumor response to sunitinib. A resistant phenotype was associated with transient increase of tumor vasculature despite intratumor sunitinib accumulation at higher dose. In addition, we observed associated changes in the expression of the methyltransferase EZH2 and histone marks at the time of resistance. Furthermore, specific EZH2 inhibition resulted in increased in vitro antitumor effect of sunitinib. Overall, our results suggest that initial sunitinib-induced resistance may be overcome, in part, by increasing the dose, and highlight the potential role of epigenetic changes associated with sunitinib resistance that can represent new targets for therapeutic intervention.

Organ Specific Storage of Dietary Pyrrolizidine Alkaloids in the Arctiid Moth Creatonotos transiens

Larvae of the arctiid moth Creatonotos transiens obtained each 5 mg of heliotrine, a pyrrolizidine alkaloid, via an artificial diet. 7 S-H eliotrine is converted into its enantiomer, 7 R1-heliotrine, and some minor metabolites, such as callimorphine. 7 S- and 7 R-heliotrine are present in the insect predominantly (more than 97%) as their N-oxides. The distribution of heliotrine in the organs and tissues of larvae, prepupae, pupae and imagines was analyzed by capillary gas-liquid chromatography. A large proportion of the alkaloid is stored in the integument of all developmental stages, where it probably serves as a chemical defence compound against predators. Female imagines had transferred substantial amounts of heliotrine to their ovaries and subsequently to their eggs; males partly directed it to their pheromone biosynthesis.

Electrochemical investigation of covalently post-synthetic modified SURGEL coatings

Thiol–yne click chemistry post synthesis modification (PSM) is used to further functionalize a fully organic porous polymer coating (SURGEL). By cyclic voltammetry the resulting electrochemical properties are addressed. The Nernstian diffusion limited process observed in the presence of ferrocene as electrolyte is explained in terms of a high permeability of the SURGELs for ferrocene after PSM.

Facilitates chromatin transcription complex is an "accelerator" of tumor transformation and potential marker and target of aggressive cancers

The facilitates chromatin transcription (FACT) complex is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT was previously considered to be ubiquitously expressed and not associated with any disease. However, we discovered that FACT is the target of a class of anticancer compounds and is not expressed in normal cells of adult mammalian tissues, except for undifferentiated and stem-like cells. Here, we show that FACT expression is strongly associated with poorly differentiated aggressive cancers with low overall survival. In addition, FACT was found to be upregulated during in vitro transformation and to be necessary, but not sufficient, for driving transformation. FACT also promoted survival and growth of established tumor cells. Genome-wide mapping of chromatin-bound FACT indicated that FACT's role in cancer most likely involves selective chromatin remodeling of genes that stimulate proliferation, inhibit cell death and differentiation, and regulate cellular stress responses.

The RecX protein interacts with the RecA protein and modulates its activity in Herbaspirillum seropedicae

DNA repair is crucial to the survival of all organisms. The bacterial RecA protein is a central component in the SOS response and in recombinational and SOS DNA repairs. The RecX protein has been characterized as a negative modulator of RecA activity in many bacteria. The recA and recX genes of Herbaspirillum seropedicae constitute a single operon, and evidence suggests that RecX participates in SOS repair. In the present study, we show that the H. seropedicae RecX protein (RecX Hs) can interact with the H. seropedicaeRecA protein (RecA Hs) and that RecA Hs possesses ATP binding, ATP hydrolyzing and DNA strand exchange activities. RecX Hs inhibited 90% of the RecA Hs DNA strand exchange activity even when present in a 50-fold lower molar concentration than RecA Hs. RecA Hs ATP binding was not affected by the addition of RecX, but the ATPase activity was reduced. When RecX Hs was present before the formation of RecA filaments (RecA-ssDNA), inhibition of ATPase activity was substantially reduced and excess ssDNA also partially suppressed this inhibition. The results suggest that the RecX Hs protein negatively modulates the RecA Hs activities by protein-protein interactions and also by DNA-protein interactions.

Study of electronic prescribing rates and barriers identified among providers using electronic health records in New York City

BACKGROUND

Increased electronic prescribing (eRx) rates have the potential to prevent errors, increase patient safety, and curtail fraud. US Federal meaningful use guidelines require at least a 40% electronic prescribing rate.

OBJECTIVE

We evaluated eRx rates among primary care providers in New York City in order to determine trends as well as identify any obstacles to increased eRx rates required by meaningful use guidelines.

METHODS

The data we analysed included automatic electronic data transmissions from providers enrolled in the Primary Care Information Project (PCIP) from 1 January 2009 to 1 July 2010 and follow-up telephone calls to a subset of these providers to identify potential barriers to increased eRx usage.

RESULTS

Over the course of the study, these providers increased the eRx rate from 12.9 to 27.5%, with an average rate of 24.1%. Conversations with providers identified their perceived barriers to increased eRx use as primarily patient preference for paper prescriptions and a belief that many pharmacies do not accept eRx.

CONCLUSIONS

The data gathered from our providers indicate that there is an increasing trend in the eRx rate to 27.5% by July 2010, but still short of the 40% meaningful use level. However, obstacles to increased rates remain primarily providers' belief that many patients prefer paper prescriptions and many pharmacies are not yet prepared to accept electronic prescriptions.

Physiologic and pharmacologic considerations for hypothermia therapy in neonates

With mounting evidence that hypothermia is neuroprotective in newborns with hypoxic-ischemic encephalopathy (HIE), an increasing number of centers are offering this therapy. Hypothermia is associated with a wide range of physiologic changes affecting every organ system, and awareness of these effects is essential for optimum patient management. Lowering the core temperature also alters pharmacokinetic and pharmacodynamic properties of medications commonly used in asphyxiated neonates, necessitating close attention to drug efficacy and side effects. Rewarming introduces additional risks and challenges as the hypothermia-associated physiologic and pharmacologic changes are reversed. In this review we provide an organ system-based assessment of physiologic changes associated with hypothermia. We also summarize evidence from randomized controlled trials showing lack of serious adverse effects of moderate hypothermia therapy in term and near-term newborns with moderate-to-severe HIE. Finally, we review the effects of hypothermia on drug metabolism and clearance based on studies in animal models and human adults, and limited data from neonates.

The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function

Sensing the environment and responding appropriately to it are key capabilities for the survival of an organism. All extant organisms must have evolved suitable sensors, signaling systems, and response mechanisms allowing them to survive under the conditions they are likely to encounter. Here, we investigate in detail the evolutionary history of one such system: The phage shock protein (Psp) stress response system is an important part of the stress response machinery in many bacteria, including Escherichia coli K12.

Here, we use a systematic analysis of the genes that make up and regulate the Psp system in E. coli in order to elucidate the evolutionary history of the system. We compare gene sharing, sequence evolution, and conservation of protein-coding as well as noncoding DNA sequences and link these to comparative analyses of genome/operon organization across 698 bacterial genomes. Finally, we evaluate experimentally the biological advantage/disadvantage of a simplified version of the Psp system under different oxygen-related environments.

Our results suggest that the Psp system evolved around a core response mechanism by gradually co-opting genes into the system to provide more nuanced sensory, signaling, and effector functionalities. We find that recruitment of new genes into the response machinery is closely linked to incorporation of these genes into a psp operon as is seen in E. coli, which contains the bulk of genes involved in the response. The organization of this operon allows for surprising levels of additional transcriptional control and flexibility. The results discussed here suggest that the components of such signaling systems will only be evolutionarily conserved if the overall functionality of the system can be maintained.

YB-1 Mediates a Crosstalk between ERα and TGFβ Signaling in Breast Cancer Cells

The multifunctional Y-box binding protein-1 (YB-1) belongs to the highly conserved family of cold shock proteins being involved in transcriptional/translational regulation, DNA repair as well as stress response. Additionally, it is highly expressed in many malignant tissues which seems to correlate with a high proliferation level, drug resistance and a poor prognosis in a variety of tumors including breast cancer.Using quantitative immunohistochemistry we now confirm the previously described negative prognostic impact of YB-1 on survival in a clinical study with tumor samples from 199 breast cancer patients (p=0.0146; median follow up 79 months).Treatment of the estrogen receptor α (ERα) positive human breast cancer cell line MCF-7 with antiestrogens (4-hydroxytamoxifen, faslodex) resulted in a time and dose dependent decrease of YB-1 expression on the RNA- as well as on the protein level. In contrast, antiestrogen treatment of the ERα negative cell line MDA-MB-231 does not have any effect indicating that the antiestrogen effect on YB-1 is mediated by ERα. We have already demonstrated that the action of all antiestrogens is at least partially mediated by transforming growth factor β (TGFβ) (e.g. Breast Cancer Res. Treat. 107: 15-24, 2008). Using TGFβ-responsive reporter gene assays we now show that overexpression of YB-1 in MCF-7 cells enhances the induction of p3TPlux activity by TGFβ suggesting a crosstalk between YB-1 and TGFβ signaling pathways. Moreover, YB-1 also increases the antiestrogen induction of the TGFβ2-mRNA level coming along with a YB-1 regulated enhancement of the antiestrogen effect on cell growth.Very recent findings of our group point towards a ligand-independent influence of ERα on TGFβ signaling (Breast Cancer Res. Treat., in press). Due to the antiestrogen regulation of YB-1 via ERα and its crosstalk with the TGFβ pathway, the potential role of YB-1 as a mediator of the interaction between ERα and TGFβ signaling was analyzed. Performing pull-down assays with recombinant GST-ERα and whole cell lysates of MCF-7 cells confirms a protein-protein interaction between YB-1 and ERα. The physiological relevance of this interaction could be demonstrated, as the TGFβ-induced p3TPlux activity is clearly modulated by both, YB-1 and ERα.In conclusion, we present evidence that YB-1 and TGFβ signaling are functionally linked in MCF-7 cells. Combined with the detection of a physical interaction between YB-1 and ERα, our findings shed new light on a potential role of YB-1 as a part of the mechanism responsible for switching TGFβ from its anti-proliferative role in early tumor stages to tumor promoting effects in late-stage disease, most likely via a YB-1 regulated shift of TGFβ-signaling to pro-invasive pathways. This would also explain why high levels of YB-1 correlate with a poor prognosis in breast cancer patients.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4172.